Starting phenix.real_space_refine on Mon Aug 25 22:46:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wp2_37708/08_2025/8wp2_37708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wp2_37708/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wp2_37708/08_2025/8wp2_37708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wp2_37708/08_2025/8wp2_37708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wp2_37708/08_2025/8wp2_37708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wp2_37708/08_2025/8wp2_37708.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1} 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, 'HIS:plan': 1, 'ASP: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: {'ASP:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1} 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: 6.98, per 1000 atoms: 0.22 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: 2.46 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 3.70 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: 5.39 Time building geometry restraints manager: 3.32 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: 5.000 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: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.670 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.310 ------------------------------------------------------------------------------- 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 : 17.35 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.000 ARG B 19 TYR 0.022 0.001 TYR C 397 PHE 0.030 0.002 PHE I 304 TRP 0.057 0.002 TRP B 124 HIS 0.006 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00897 (32614) covalent geometry : angle 0.78341 (44698) hydrogen bonds : bond 0.30142 ( 875) hydrogen bonds : angle 10.41487 ( 2415) *********************** 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 : 0.812 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: 0.1707 time to fit residues: 74.6203 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 : 0.896 ------------------------------------------------------------------------------- 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 197 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- 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 66 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** C 98 ASN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 ASN I 59 HIS I 131 ASN ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 48 ASN L 174 ASN ** L 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.115543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.098987 restraints weight = 96736.646| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 2.62 r_work: 0.4048 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4045 r_free = 0.4045 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2762 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2839 | |-----------------------------------------------------------------------------| r_final: 0.4034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.167 32614 Z= 0.370 Angle : 0.901 12.249 44698 Z= 0.466 Chirality : 0.054 0.546 4858 Planarity : 0.007 0.076 5130 Dihedral : 18.296 179.908 5587 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.90 % Favored : 89.82 % Rotamer: Outliers : 6.23 % Allowed : 27.33 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.91 (0.13), residues: 3466 helix: -1.86 (0.14), residues: 1085 sheet: -2.30 (0.24), residues: 434 loop : -1.88 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 213 TYR 0.037 0.003 TYR K 467 PHE 0.037 0.003 PHE I 419 TRP 0.027 0.003 TRP I 269 HIS 0.014 0.002 HIS K 16 Details of bonding type rmsd covalent geometry : bond 0.00825 (32614) covalent geometry : angle 0.90119 (44698) hydrogen bonds : bond 0.07426 ( 875) hydrogen bonds : angle 7.07266 ( 2415) *********************** 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 489 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 297 time to evaluate : 0.935 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: A 16 HIS cc_start: 0.6908 (OUTLIER) cc_final: 0.5010 (p90) REVERT: B 122 MET cc_start: 0.7792 (ppp) cc_final: 0.7284 (ppp) REVERT: B 410 PHE cc_start: 0.6668 (OUTLIER) cc_final: 0.5961 (m-80) REVERT: C 59 HIS cc_start: 0.7480 (t-90) cc_final: 0.7084 (t-170) REVERT: C 505 TYR cc_start: 0.3582 (OUTLIER) cc_final: 0.1426 (m-80) REVERT: D 260 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6514 (mm-30) REVERT: D 277 MET cc_start: 0.7520 (tpt) cc_final: 0.7041 (tpt) REVERT: I 91 ILE cc_start: 0.5951 (OUTLIER) cc_final: 0.5560 (mm) REVERT: I 142 ILE cc_start: 0.7593 (mp) cc_final: 0.7341 (mt) REVERT: I 224 PHE cc_start: 0.6796 (m-80) cc_final: 0.6145 (m-80) REVERT: I 231 TRP cc_start: 0.7366 (p-90) cc_final: 0.6899 (p-90) REVERT: I 430 GLN cc_start: 0.6178 (OUTLIER) cc_final: 0.5972 (mt0) REVERT: I 437 VAL cc_start: 0.5923 (OUTLIER) cc_final: 0.5713 (t) REVERT: I 459 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7950 (mp) REVERT: K 57 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7450 (tp) REVERT: K 141 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8275 (m) REVERT: K 148 TYR cc_start: 0.5152 (p90) cc_final: 0.4938 (p90) REVERT: L 102 GLN cc_start: 0.7860 (mm-40) cc_final: 0.6816 (tp40) REVERT: L 176 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7128 (mp) REVERT: L 251 TYR cc_start: 0.3132 (t80) cc_final: 0.2502 (t80) outliers start: 192 outliers final: 93 residues processed: 460 average time/residue: 0.1641 time to fit residues: 122.1424 Evaluate side-chains 374 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 270 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 119 SER 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 278 VAL 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 A residue 489 ILE Chi-restraints excluded: chain B residue 20 TRP 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 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 114 ARG 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 332 PHE Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain I residue 5 ILE 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 33 LEU Chi-restraints excluded: chain I residue 91 ILE 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 203 ASP 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 403 TYR 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 437 VAL Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 459 ILE 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 57 LEU Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 141 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 312 VAL Chi-restraints excluded: chain K residue 387 THR Chi-restraints excluded: chain K residue 397 TYR Chi-restraints excluded: chain K residue 398 LYS Chi-restraints excluded: chain K residue 406 LEU Chi-restraints excluded: chain K residue 413 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 K residue 465 LEU Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 34 CYS 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 334 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 247 optimal weight: 0.0070 chunk 267 optimal weight: 1.9990 chunk 343 optimal weight: 20.0000 chunk 224 optimal weight: 0.0770 chunk 210 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 304 optimal weight: 0.0070 chunk 320 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 285 optimal weight: 0.9980 overall best weight: 0.3974 ------------------------------------------------------------------------------- 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** B 267 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN C 98 ASN C 207 HIS C 209 GLN C 360 HIS ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 ASN I 466 ASN ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 ASN ** K 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.120040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.102889 restraints weight = 97489.737| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 2.64 r_work: 0.4169 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4165 r_free = 0.4165 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2839 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4155 r_free = 0.4155 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2902 | |-----------------------------------------------------------------------------| r_final: 0.4155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32614 Z= 0.143 Angle : 0.658 10.935 44698 Z= 0.339 Chirality : 0.046 0.332 4858 Planarity : 0.005 0.060 5130 Dihedral : 17.858 179.162 5581 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.10 % Favored : 92.64 % Rotamer: Outliers : 4.02 % Allowed : 29.05 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.55 (0.14), residues: 3466 helix: -1.54 (0.14), residues: 1092 sheet: -1.95 (0.23), residues: 481 loop : -1.68 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 186 TYR 0.023 0.001 TYR K 346 PHE 0.022 0.002 PHE D 17 TRP 0.032 0.002 TRP L 319 HIS 0.005 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00314 (32614) covalent geometry : angle 0.65754 (44698) hydrogen bonds : bond 0.05110 ( 875) hydrogen bonds : angle 6.00759 ( 2415) *********************** 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 421 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 297 time to evaluate : 0.824 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 101 ILE cc_start: 0.7340 (OUTLIER) cc_final: 0.6896 (mt) REVERT: A 231 TRP cc_start: 0.8013 (p-90) cc_final: 0.7786 (p-90) REVERT: B 1 MET cc_start: 0.7916 (tpp) cc_final: 0.7119 (ppp) REVERT: B 122 MET cc_start: 0.7657 (ppp) cc_final: 0.7136 (ppp) REVERT: C 59 HIS cc_start: 0.7446 (t-90) cc_final: 0.7159 (t-170) REVERT: C 78 PHE cc_start: 0.4654 (t80) cc_final: 0.4426 (t80) REVERT: D 33 TRP cc_start: 0.8534 (OUTLIER) cc_final: 0.7848 (m100) REVERT: D 124 TRP cc_start: 0.4397 (p-90) cc_final: 0.1650 (t-100) REVERT: D 137 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7378 (tmtt) REVERT: D 251 TYR cc_start: 0.6353 (t80) cc_final: 0.6005 (t80) REVERT: D 260 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6594 (mm-30) REVERT: D 277 MET cc_start: 0.7335 (tpt) cc_final: 0.6812 (tpt) REVERT: D 309 MET cc_start: 0.6029 (tpt) cc_final: 0.4832 (tpt) REVERT: D 392 TYR cc_start: 0.7955 (p90) cc_final: 0.7588 (p90) REVERT: I 161 MET cc_start: 0.4872 (ptm) cc_final: 0.4458 (ptp) REVERT: I 223 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7523 (tt) REVERT: I 248 ILE cc_start: 0.6851 (tt) cc_final: 0.6606 (mp) REVERT: I 304 PHE cc_start: 0.6380 (t80) cc_final: 0.6116 (t80) REVERT: I 374 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6928 (mm) REVERT: I 400 GLU cc_start: 0.5675 (pm20) cc_final: 0.5203 (pm20) REVERT: I 471 ILE cc_start: 0.4925 (OUTLIER) cc_final: 0.4588 (pt) REVERT: J 128 LEU cc_start: 0.8146 (tp) cc_final: 0.7905 (tt) REVERT: J 154 TYR cc_start: 0.4625 (t80) cc_final: 0.4326 (t80) REVERT: J 278 LYS cc_start: 0.7748 (tppt) cc_final: 0.7302 (mmtt) REVERT: K 66 ASN cc_start: 0.3161 (OUTLIER) cc_final: 0.1651 (m110) REVERT: K 141 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8032 (m) REVERT: K 479 THR cc_start: 0.5259 (OUTLIER) cc_final: 0.4398 (p) REVERT: L 102 GLN cc_start: 0.7806 (mm-40) cc_final: 0.6775 (tp40) outliers start: 124 outliers final: 52 residues processed: 403 average time/residue: 0.1654 time to fit residues: 107.6727 Evaluate side-chains 322 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 260 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 217 HIS Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 239 ILE 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 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 122 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 430 GLN Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 33 TRP Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 137 LYS 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 I residue 5 ILE Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 151 CYS Chi-restraints excluded: chain I residue 164 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 374 LEU Chi-restraints excluded: chain I residue 412 VAL Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 471 ILE 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 66 ASN Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 229 LEU Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 398 LYS Chi-restraints excluded: chain K residue 405 ILE 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 K residue 496 ILE Chi-restraints excluded: chain L residue 110 ILE 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 144 optimal weight: 7.9990 chunk 60 optimal weight: 30.0000 chunk 320 optimal weight: 20.0000 chunk 106 optimal weight: 0.0870 chunk 68 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 282 optimal weight: 6.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- 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 322 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** 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 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.116119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.098773 restraints weight = 95457.573| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 2.36 r_work: 0.4067 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4067 r_free = 0.4067 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2902 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4060 r_free = 0.4060 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2951 | |-----------------------------------------------------------------------------| r_final: 0.4060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 32614 Z= 0.270 Angle : 0.765 12.363 44698 Z= 0.393 Chirality : 0.050 0.505 4858 Planarity : 0.006 0.067 5130 Dihedral : 18.132 176.408 5581 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.32 % Favored : 90.36 % Rotamer: Outliers : 6.06 % Allowed : 28.05 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.77 (0.14), residues: 3466 helix: -1.65 (0.14), residues: 1106 sheet: -2.26 (0.23), residues: 459 loop : -1.82 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 126 TYR 0.032 0.002 TYR C 467 PHE 0.034 0.003 PHE A 210 TRP 0.027 0.003 TRP L 319 HIS 0.013 0.001 HIS K 16 Details of bonding type rmsd covalent geometry : bond 0.00615 (32614) covalent geometry : angle 0.76493 (44698) hydrogen bonds : bond 0.05592 ( 875) hydrogen bonds : angle 6.19754 ( 2415) *********************** 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 488 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 301 time to evaluate : 1.004 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: A 16 HIS cc_start: 0.6865 (OUTLIER) cc_final: 0.5164 (p90) REVERT: A 54 ARG cc_start: 0.6229 (OUTLIER) cc_final: 0.5444 (mmp-170) REVERT: A 101 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.6977 (mt) REVERT: B 1 MET cc_start: 0.8054 (tpp) cc_final: 0.7281 (ppp) REVERT: B 71 ARG cc_start: 0.6320 (mmt90) cc_final: 0.6031 (mmt90) REVERT: B 122 MET cc_start: 0.7701 (ppp) cc_final: 0.7367 (ppp) REVERT: B 169 GLU cc_start: 0.6369 (mm-30) cc_final: 0.5875 (mm-30) REVERT: B 277 MET cc_start: 0.3262 (mpp) cc_final: 0.2282 (mpp) REVERT: B 410 PHE cc_start: 0.6634 (OUTLIER) cc_final: 0.5955 (m-80) REVERT: C 13 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7327 (mp) REVERT: C 59 HIS cc_start: 0.7562 (t-90) cc_final: 0.7115 (t-170) REVERT: C 74 MET cc_start: 0.3213 (OUTLIER) cc_final: 0.2916 (ttt) REVERT: C 505 TYR cc_start: 0.3107 (OUTLIER) cc_final: 0.1198 (m-80) REVERT: D 137 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7420 (tmtt) REVERT: D 260 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6544 (mm-30) REVERT: I 85 LYS cc_start: 0.5902 (OUTLIER) cc_final: 0.5339 (mtmm) REVERT: I 91 ILE cc_start: 0.5747 (OUTLIER) cc_final: 0.5361 (mm) REVERT: I 115 TYR cc_start: 0.6351 (t80) cc_final: 0.5985 (t80) REVERT: I 146 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7505 (mm-30) REVERT: I 161 MET cc_start: 0.4887 (ptm) cc_final: 0.4478 (ptp) REVERT: I 231 TRP cc_start: 0.7335 (p-90) cc_final: 0.6840 (p-90) REVERT: I 248 ILE cc_start: 0.7095 (tt) cc_final: 0.6781 (mp) REVERT: I 400 GLU cc_start: 0.5645 (pm20) cc_final: 0.5276 (pm20) REVERT: I 471 ILE cc_start: 0.6390 (OUTLIER) cc_final: 0.5756 (pt) REVERT: J 154 TYR cc_start: 0.5003 (t80) cc_final: 0.4691 (t80) REVERT: J 391 PHE cc_start: 0.5764 (OUTLIER) cc_final: 0.5340 (t80) REVERT: K 57 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7292 (tp) REVERT: K 141 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8240 (m) REVERT: K 150 TYR cc_start: 0.4389 (OUTLIER) cc_final: 0.4139 (m-10) REVERT: L 20 TRP cc_start: 0.1942 (OUTLIER) cc_final: -0.0434 (t60) REVERT: L 102 GLN cc_start: 0.7797 (mm-40) cc_final: 0.6746 (tp40) REVERT: L 108 ILE cc_start: 0.5635 (OUTLIER) cc_final: 0.5399 (mp) outliers start: 187 outliers final: 115 residues processed: 454 average time/residue: 0.1645 time to fit residues: 120.1306 Evaluate side-chains 403 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 270 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 54 ARG 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 249 GLU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 278 VAL 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 486 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 184 GLU 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 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 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 122 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 283 LEU Chi-restraints excluded: chain C residue 307 ASN Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 399 THR 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 137 LYS 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 D residue 395 MET Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 91 ILE 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 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 309 ASP Chi-restraints excluded: chain I residue 359 ILE Chi-restraints excluded: chain I residue 367 HIS 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 471 ILE Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 370 ASN Chi-restraints excluded: chain J residue 386 ASP 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 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 57 LEU 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 251 HIS Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 303 MET Chi-restraints excluded: chain K residue 330 LEU 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 398 LYS Chi-restraints excluded: chain K residue 405 ILE 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 496 ILE Chi-restraints excluded: chain K residue 501 LEU 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 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 262 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 231 optimal weight: 8.9990 chunk 281 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 219 optimal weight: 0.7980 chunk 254 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN B 370 ASN C 98 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN C 439 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 ASN I 98 ASN I 329 HIS ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 ASN K 66 ASN K 135 ASN K 207 HIS ** K 251 HIS ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.116531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.099145 restraints weight = 95876.370| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 2.37 r_work: 0.4074 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4077 r_free = 0.4077 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2951 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4071 r_free = 0.4071 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3005 | |-----------------------------------------------------------------------------| r_final: 0.4071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 32614 Z= 0.212 Angle : 0.709 13.808 44698 Z= 0.365 Chirality : 0.048 0.393 4858 Planarity : 0.005 0.062 5130 Dihedral : 18.112 176.453 5581 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.80 % Favored : 90.91 % Rotamer: Outliers : 6.16 % Allowed : 28.50 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.69 (0.14), residues: 3466 helix: -1.51 (0.14), residues: 1093 sheet: -2.21 (0.22), residues: 487 loop : -1.81 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 126 TYR 0.025 0.002 TYR C 467 PHE 0.027 0.002 PHE A 210 TRP 0.034 0.002 TRP L 319 HIS 0.009 0.001 HIS K 16 Details of bonding type rmsd covalent geometry : bond 0.00483 (32614) covalent geometry : angle 0.70927 (44698) hydrogen bonds : bond 0.05067 ( 875) hydrogen bonds : angle 5.99165 ( 2415) *********************** 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 468 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 278 time to evaluate : 1.051 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: 0.6727 (OUTLIER) cc_final: 0.5051 (p90) REVERT: A 101 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.6917 (mt) REVERT: B 1 MET cc_start: 0.8259 (tpp) cc_final: 0.7549 (ppp) REVERT: B 122 MET cc_start: 0.7750 (ppp) cc_final: 0.7491 (ppp) REVERT: B 169 GLU cc_start: 0.6329 (mm-30) cc_final: 0.5846 (mm-30) REVERT: B 410 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.5910 (m-80) REVERT: C 59 HIS cc_start: 0.7576 (t-90) cc_final: 0.7190 (t-170) REVERT: C 505 TYR cc_start: 0.2715 (OUTLIER) cc_final: 0.0967 (m-80) REVERT: D 260 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6544 (mm-30) REVERT: D 392 TYR cc_start: 0.7846 (p90) cc_final: 0.7611 (p90) REVERT: I 91 ILE cc_start: 0.5568 (OUTLIER) cc_final: 0.5162 (mt) REVERT: I 146 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7636 (mm-30) REVERT: I 161 MET cc_start: 0.4984 (ptm) cc_final: 0.4516 (ptp) REVERT: I 248 ILE cc_start: 0.7093 (tt) cc_final: 0.6822 (mp) REVERT: I 374 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6980 (mm) REVERT: I 400 GLU cc_start: 0.6005 (pm20) cc_final: 0.5652 (pm20) REVERT: I 430 GLN cc_start: 0.5942 (OUTLIER) cc_final: 0.5686 (mt0) REVERT: J 109 ASN cc_start: 0.8055 (p0) cc_final: 0.7855 (p0) REVERT: J 121 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6154 (mmtt) REVERT: K 57 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7215 (tp) REVERT: K 141 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8200 (m) REVERT: L 20 TRP cc_start: 0.1739 (OUTLIER) cc_final: -0.0500 (t60) REVERT: L 102 GLN cc_start: 0.7947 (mm-40) cc_final: 0.6767 (tp40) REVERT: L 231 GLU cc_start: 0.6672 (pm20) cc_final: 0.5131 (pm20) outliers start: 190 outliers final: 128 residues processed: 436 average time/residue: 0.1801 time to fit residues: 127.6381 Evaluate side-chains 407 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 267 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 136 VAL Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 245 PHE 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 359 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 395 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 B residue 20 TRP Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 196 LYS 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 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 52 ILE 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 122 ILE Chi-restraints excluded: chain C residue 242 ILE 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 283 LEU Chi-restraints excluded: chain C residue 307 ASN Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 367 HIS 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 459 ILE Chi-restraints excluded: chain C residue 465 LEU 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 290 LYS Chi-restraints excluded: chain D residue 306 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 D residue 371 ASN Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain I residue 5 ILE 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 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 309 ASP 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 430 GLN Chi-restraints excluded: chain I residue 446 ASN Chi-restraints excluded: chain I residue 454 GLN 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 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 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 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 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 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 398 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 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 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 334 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 321 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 314 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 211 optimal weight: 0.6980 chunk 285 optimal weight: 0.6980 chunk 273 optimal weight: 2.9990 chunk 304 optimal weight: 10.0000 chunk 319 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 ASN ** I 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 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 K 207 HIS ** K 251 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.116735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.099186 restraints weight = 96854.467| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 2.61 r_work: 0.4074 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4073 r_free = 0.4073 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3005 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4068 r_free = 0.4068 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3070 | |-----------------------------------------------------------------------------| r_final: 0.4068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 32614 Z= 0.181 Angle : 0.686 15.225 44698 Z= 0.350 Chirality : 0.047 0.357 4858 Planarity : 0.005 0.066 5130 Dihedral : 18.041 176.108 5581 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.89 % Favored : 90.83 % Rotamer: Outliers : 5.87 % Allowed : 28.83 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.14), residues: 3466 helix: -1.36 (0.15), residues: 1098 sheet: -2.25 (0.23), residues: 473 loop : -1.74 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 276 TYR 0.025 0.002 TYR C 467 PHE 0.026 0.002 PHE K 442 TRP 0.034 0.002 TRP D 192 HIS 0.008 0.001 HIS K 16 Details of bonding type rmsd covalent geometry : bond 0.00413 (32614) covalent geometry : angle 0.68592 (44698) hydrogen bonds : bond 0.04698 ( 875) hydrogen bonds : angle 5.77175 ( 2415) *********************** 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 462 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 281 time to evaluate : 0.816 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: 0.6635 (OUTLIER) cc_final: 0.5007 (p90) REVERT: A 54 ARG cc_start: 0.6006 (OUTLIER) cc_final: 0.5776 (mmt-90) REVERT: A 101 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6819 (mt) REVERT: A 225 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6725 (mpp-170) REVERT: B 1 MET cc_start: 0.8208 (tpp) cc_final: 0.7538 (ppp) REVERT: B 71 ARG cc_start: 0.6707 (mmt90) cc_final: 0.6495 (mmt90) REVERT: B 122 MET cc_start: 0.7723 (ppp) cc_final: 0.7337 (mmp) REVERT: B 169 GLU cc_start: 0.6450 (mm-30) cc_final: 0.6076 (mm-30) REVERT: B 277 MET cc_start: 0.3352 (mpp) cc_final: 0.2965 (mpp) REVERT: B 410 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.5851 (m-80) REVERT: C 13 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7291 (mp) REVERT: C 59 HIS cc_start: 0.7616 (t-90) cc_final: 0.7264 (m170) REVERT: C 206 PHE cc_start: 0.5184 (t80) cc_final: 0.4969 (t80) REVERT: C 358 PHE cc_start: 0.7155 (t80) cc_final: 0.6761 (t80) REVERT: C 505 TYR cc_start: 0.2298 (OUTLIER) cc_final: 0.0710 (m-80) REVERT: D 124 TRP cc_start: 0.4381 (p-90) cc_final: 0.2058 (t-100) REVERT: D 137 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7485 (tmtt) REVERT: D 251 TYR cc_start: 0.6396 (t80) cc_final: 0.6167 (t80) REVERT: D 260 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6705 (mm-30) REVERT: I 91 ILE cc_start: 0.5521 (OUTLIER) cc_final: 0.5183 (mt) REVERT: I 161 MET cc_start: 0.4806 (ptm) cc_final: 0.4415 (ptp) REVERT: I 248 ILE cc_start: 0.6852 (tt) cc_final: 0.6649 (mp) REVERT: I 283 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7875 (pp) REVERT: I 374 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7122 (mm) REVERT: I 400 GLU cc_start: 0.6167 (pm20) cc_final: 0.5909 (pm20) REVERT: I 471 ILE cc_start: 0.6195 (OUTLIER) cc_final: 0.5510 (pt) REVERT: J 121 LYS cc_start: 0.6624 (OUTLIER) cc_final: 0.6035 (mmtt) REVERT: J 309 MET cc_start: 0.5440 (ttt) cc_final: 0.5168 (tpp) REVERT: K 57 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7241 (tp) REVERT: K 141 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8203 (m) REVERT: K 150 TYR cc_start: 0.5075 (OUTLIER) cc_final: 0.4215 (m-10) REVERT: K 251 HIS cc_start: 0.5004 (OUTLIER) cc_final: 0.4394 (p90) REVERT: K 358 PHE cc_start: 0.6138 (m-80) cc_final: 0.5747 (m-80) REVERT: L 20 TRP cc_start: 0.1727 (OUTLIER) cc_final: -0.0500 (t60) REVERT: L 45 PHE cc_start: 0.4121 (OUTLIER) cc_final: 0.3668 (p90) REVERT: L 102 GLN cc_start: 0.7952 (mm-40) cc_final: 0.6783 (tp40) REVERT: L 231 GLU cc_start: 0.6842 (pm20) cc_final: 0.5334 (pm20) outliers start: 181 outliers final: 133 residues processed: 429 average time/residue: 0.1688 time to fit residues: 118.0101 Evaluate side-chains 419 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 266 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 54 ARG 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 225 ARG 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 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 484 ASP Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 185 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 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 B residue 416 TYR 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 36 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 43 VAL 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 122 ILE Chi-restraints excluded: chain C residue 242 ILE 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 283 LEU Chi-restraints excluded: chain C residue 307 ASN Chi-restraints excluded: chain C residue 360 HIS 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 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 486 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 180 SER 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 335 LEU Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 368 TRP Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 12 ILE 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 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 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 406 LEU 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 471 ILE Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 227 LEU Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 370 ASN 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 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 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 398 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 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 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 334 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 170 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 chunk 99 optimal weight: 0.4980 chunk 295 optimal weight: 0.5980 chunk 182 optimal weight: 0.9990 chunk 287 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 chunk 348 optimal weight: 10.0000 chunk 87 optimal weight: 0.0570 chunk 67 optimal weight: 0.0470 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN C 98 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 ASN I 129 ASN I 135 ASN I 209 GLN ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 466 ASN ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 ASN K 207 HIS ** K 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 446 ASN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.118996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.101376 restraints weight = 97416.534| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 2.51 r_work: 0.4144 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4144 r_free = 0.4144 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3070 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3150 | |-----------------------------------------------------------------------------| r_final: 0.4139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32614 Z= 0.130 Angle : 0.641 13.109 44698 Z= 0.325 Chirality : 0.045 0.281 4858 Planarity : 0.005 0.068 5130 Dihedral : 17.883 176.046 5581 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.13 % Favored : 92.59 % Rotamer: Outliers : 4.25 % Allowed : 30.25 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.14), residues: 3466 helix: -1.22 (0.15), residues: 1109 sheet: -2.08 (0.23), residues: 492 loop : -1.65 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 126 TYR 0.023 0.001 TYR K 148 PHE 0.025 0.002 PHE K 442 TRP 0.040 0.002 TRP D 192 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00292 (32614) covalent geometry : angle 0.64058 (44698) hydrogen bonds : bond 0.04162 ( 875) hydrogen bonds : angle 5.38451 ( 2415) *********************** 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 416 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 285 time to evaluate : 1.157 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 50 LEU cc_start: 0.5922 (mt) cc_final: 0.5630 (mt) REVERT: A 101 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6933 (mt) REVERT: A 225 ARG cc_start: 0.6841 (mpp-170) cc_final: 0.6280 (mpp-170) REVERT: B 1 MET cc_start: 0.8094 (tpp) cc_final: 0.7534 (ppp) REVERT: B 71 ARG cc_start: 0.6719 (mmt90) cc_final: 0.6483 (mmt90) REVERT: B 122 MET cc_start: 0.7703 (ppp) cc_final: 0.7360 (mmp) REVERT: B 169 GLU cc_start: 0.6275 (mm-30) cc_final: 0.5851 (mm-30) REVERT: B 277 MET cc_start: 0.3421 (mpp) cc_final: 0.3061 (mpp) REVERT: B 308 THR cc_start: 0.3709 (OUTLIER) cc_final: 0.3271 (p) REVERT: C 59 HIS cc_start: 0.7532 (t-90) cc_final: 0.7269 (m170) REVERT: C 358 PHE cc_start: 0.6925 (t80) cc_final: 0.6554 (t80) REVERT: C 367 HIS cc_start: 0.7095 (OUTLIER) cc_final: 0.6788 (m90) REVERT: D 124 TRP cc_start: 0.4472 (p-90) cc_final: 0.1973 (p-90) REVERT: I 161 MET cc_start: 0.5004 (ptm) cc_final: 0.4583 (ptp) REVERT: I 283 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7818 (pp) REVERT: I 374 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6894 (mm) REVERT: I 446 ASN cc_start: 0.6400 (OUTLIER) cc_final: 0.6076 (m-40) REVERT: J 121 LYS cc_start: 0.6648 (OUTLIER) cc_final: 0.6178 (mmtt) REVERT: K 96 VAL cc_start: 0.6746 (OUTLIER) cc_final: 0.6461 (m) REVERT: K 141 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.8044 (m) REVERT: K 248 ILE cc_start: 0.6914 (mt) cc_final: 0.6665 (mp) REVERT: K 251 HIS cc_start: 0.4792 (OUTLIER) cc_final: 0.4140 (p90) REVERT: K 358 PHE cc_start: 0.6088 (m-80) cc_final: 0.5717 (m-80) REVERT: L 102 GLN cc_start: 0.7938 (mm-40) cc_final: 0.6796 (tp40) REVERT: L 231 GLU cc_start: 0.6707 (pm20) cc_final: 0.6021 (mp0) outliers start: 131 outliers final: 84 residues processed: 397 average time/residue: 0.1502 time to fit residues: 97.2832 Evaluate side-chains 357 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 263 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 101 ILE Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 405 ILE 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 20 TRP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 185 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 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 308 THR 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 C residue 39 ILE Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 122 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 283 LEU Chi-restraints excluded: chain C residue 360 HIS 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 430 GLN 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 D residue 112 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 290 LYS 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 37 TYR Chi-restraints excluded: chain I residue 44 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 147 ILE Chi-restraints excluded: chain I residue 151 CYS Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 251 HIS Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 309 ASP 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 446 ASN Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 370 ASN Chi-restraints excluded: chain J residue 386 ASP 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 96 VAL 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 376 VAL Chi-restraints excluded: chain K residue 398 LYS 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 496 ILE Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain L residue 198 PHE Chi-restraints excluded: chain L residue 224 THR Chi-restraints excluded: chain L residue 234 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 235 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 334 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 343 optimal weight: 0.0470 chunk 270 optimal weight: 0.0370 chunk 230 optimal weight: 9.9990 chunk 285 optimal weight: 1.9990 chunk 306 optimal weight: 5.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- 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 ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 HIS ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 466 ASN ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 ASN K 207 HIS ** K 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.117019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.099515 restraints weight = 97015.037| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 2.82 r_work: 0.4071 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4069 r_free = 0.4069 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3150 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4065 r_free = 0.4065 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3191 | |-----------------------------------------------------------------------------| r_final: 0.4065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 32614 Z= 0.178 Angle : 0.677 12.290 44698 Z= 0.345 Chirality : 0.047 0.351 4858 Planarity : 0.005 0.067 5130 Dihedral : 17.888 176.414 5581 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.63 % Favored : 91.08 % Rotamer: Outliers : 4.77 % Allowed : 29.77 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.14), residues: 3466 helix: -1.20 (0.15), residues: 1097 sheet: -2.08 (0.22), residues: 499 loop : -1.66 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 126 TYR 0.022 0.002 TYR C 467 PHE 0.024 0.002 PHE A 210 TRP 0.040 0.002 TRP L 319 HIS 0.008 0.001 HIS K 16 Details of bonding type rmsd covalent geometry : bond 0.00407 (32614) covalent geometry : angle 0.67670 (44698) hydrogen bonds : bond 0.04425 ( 875) hydrogen bonds : angle 5.47573 ( 2415) *********************** 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 418 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 271 time to evaluate : 0.948 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: 0.6621 (OUTLIER) cc_final: 0.5061 (p90) REVERT: A 101 ILE cc_start: 0.7214 (OUTLIER) cc_final: 0.6905 (mt) REVERT: B 1 MET cc_start: 0.8176 (tpp) cc_final: 0.7574 (ppp) REVERT: B 122 MET cc_start: 0.7683 (ppp) cc_final: 0.7280 (mmp) REVERT: B 169 GLU cc_start: 0.6305 (mm-30) cc_final: 0.5952 (mm-30) REVERT: B 277 MET cc_start: 0.3568 (mpp) cc_final: 0.3181 (mpp) REVERT: B 323 ILE cc_start: 0.7933 (pt) cc_final: 0.7590 (mt) REVERT: B 410 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.5579 (m-10) REVERT: C 59 HIS cc_start: 0.7673 (t-90) cc_final: 0.7301 (m170) REVERT: C 358 PHE cc_start: 0.7151 (t80) cc_final: 0.6788 (t80) REVERT: D 124 TRP cc_start: 0.4622 (p-90) cc_final: 0.1562 (t-100) REVERT: D 260 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6664 (mm-30) REVERT: I 146 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7570 (mm-30) REVERT: I 161 MET cc_start: 0.4872 (ptm) cc_final: 0.4452 (ptp) REVERT: I 283 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7990 (pp) REVERT: I 374 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7042 (mm) REVERT: J 121 LYS cc_start: 0.6537 (OUTLIER) cc_final: 0.6002 (mmtt) REVERT: K 141 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8162 (m) REVERT: K 248 ILE cc_start: 0.7013 (mt) cc_final: 0.6705 (mp) REVERT: K 251 HIS cc_start: 0.4837 (OUTLIER) cc_final: 0.4137 (p90) REVERT: K 358 PHE cc_start: 0.6212 (m-80) cc_final: 0.5826 (m-80) REVERT: L 102 GLN cc_start: 0.7907 (mm-40) cc_final: 0.6821 (tp40) REVERT: L 213 TYR cc_start: 0.6647 (m-80) cc_final: 0.6385 (m-80) REVERT: L 231 GLU cc_start: 0.6926 (pm20) cc_final: 0.6285 (mp0) outliers start: 147 outliers final: 113 residues processed: 394 average time/residue: 0.1601 time to fit residues: 103.7020 Evaluate side-chains 384 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 262 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 101 ILE 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 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 482 PHE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 308 THR 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 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 43 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 91 ILE 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 367 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 430 GLN 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 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 290 LYS Chi-restraints excluded: chain D residue 318 ASN 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 44 ILE Chi-restraints excluded: chain I residue 59 HIS 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 251 HIS Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 309 ASP 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 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 164 VAL Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 370 ASN 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 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 330 LEU Chi-restraints excluded: chain K residue 353 TYR Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain K residue 398 LYS 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 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 266 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 210 optimal weight: 5.9990 chunk 260 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 155 optimal weight: 0.6980 chunk 172 optimal weight: 5.9990 chunk 339 optimal weight: 2.9990 chunk 333 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 161 optimal weight: 20.0000 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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 ** 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 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 HIS ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 ASN ** K 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 468 ASN ** 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 = 0.4534 r_free = 0.4534 target = 0.115858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.098126 restraints weight = 96715.377| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.64 r_work: 0.4046 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3191 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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: 3244 | |-----------------------------------------------------------------------------| r_final: 0.4043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 32614 Z= 0.218 Angle : 0.727 13.476 44698 Z= 0.371 Chirality : 0.048 0.388 4858 Planarity : 0.005 0.068 5130 Dihedral : 17.997 176.492 5581 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.17 % Favored : 90.54 % Rotamer: Outliers : 4.90 % Allowed : 29.93 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.14), residues: 3466 helix: -1.24 (0.15), residues: 1094 sheet: -2.16 (0.23), residues: 481 loop : -1.72 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 126 TYR 0.038 0.002 TYR C 346 PHE 0.028 0.002 PHE A 210 TRP 0.044 0.002 TRP D 192 HIS 0.013 0.001 HIS I 59 Details of bonding type rmsd covalent geometry : bond 0.00498 (32614) covalent geometry : angle 0.72717 (44698) hydrogen bonds : bond 0.04772 ( 875) hydrogen bonds : angle 5.63465 ( 2415) *********************** 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 419 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 268 time to evaluate : 0.806 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: 0.6588 (OUTLIER) cc_final: 0.5084 (p90) REVERT: A 101 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.7027 (mt) REVERT: A 225 ARG cc_start: 0.7066 (mpp-170) cc_final: 0.6766 (mpp-170) REVERT: B 122 MET cc_start: 0.7733 (ppp) cc_final: 0.7325 (mmp) REVERT: B 169 GLU cc_start: 0.6407 (mm-30) cc_final: 0.6063 (mm-30) REVERT: B 277 MET cc_start: 0.3209 (mpp) cc_final: 0.2712 (mpp) REVERT: B 410 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.5574 (m-10) REVERT: C 13 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7312 (mp) REVERT: C 59 HIS cc_start: 0.7730 (t-90) cc_final: 0.7303 (m170) REVERT: C 358 PHE cc_start: 0.7126 (t80) cc_final: 0.6851 (t80) REVERT: C 431 THR cc_start: 0.4319 (p) cc_final: 0.4029 (p) REVERT: D 124 TRP cc_start: 0.4794 (p-90) cc_final: 0.1650 (t-100) REVERT: D 260 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6679 (mm-30) REVERT: I 8 GLU cc_start: 0.6517 (mp0) cc_final: 0.6191 (mp0) REVERT: I 91 ILE cc_start: 0.5518 (OUTLIER) cc_final: 0.5170 (mt) REVERT: I 146 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7569 (mm-30) REVERT: I 161 MET cc_start: 0.4724 (ptm) cc_final: 0.4288 (ptp) REVERT: I 283 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8035 (pp) REVERT: I 304 PHE cc_start: 0.6392 (t80) cc_final: 0.6126 (t80) REVERT: I 374 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7013 (mm) REVERT: J 121 LYS cc_start: 0.6615 (OUTLIER) cc_final: 0.6043 (mmtt) REVERT: K 57 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7216 (tp) REVERT: K 141 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8168 (m) REVERT: K 251 HIS cc_start: 0.4768 (OUTLIER) cc_final: 0.4061 (p90) REVERT: K 506 TYR cc_start: 0.5555 (OUTLIER) cc_final: 0.1999 (m-80) REVERT: L 20 TRP cc_start: 0.1575 (OUTLIER) cc_final: -0.0601 (t60) REVERT: L 102 GLN cc_start: 0.7964 (mm-40) cc_final: 0.6853 (tp40) REVERT: L 144 VAL cc_start: 0.5990 (m) cc_final: 0.5740 (p) REVERT: L 213 TYR cc_start: 0.6632 (m-80) cc_final: 0.6377 (m-80) outliers start: 151 outliers final: 118 residues processed: 394 average time/residue: 0.1598 time to fit residues: 102.7915 Evaluate side-chains 393 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 261 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 101 ILE 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 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 486 ILE Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 110 ILE 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 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 308 THR 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 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 43 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 85 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 430 GLN 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 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 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 368 TRP 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 59 HIS 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 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 251 HIS Chi-restraints excluded: chain I residue 283 LEU 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 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 227 LEU Chi-restraints excluded: chain J residue 341 ILE Chi-restraints excluded: chain J residue 370 ASN 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 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 330 LEU Chi-restraints excluded: chain K residue 353 TYR Chi-restraints excluded: chain K residue 357 VAL Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain K residue 398 LYS 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 496 ILE 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 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 266 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 347 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 155 optimal weight: 0.3980 chunk 220 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 274 optimal weight: 0.8980 chunk 348 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 9 HIS ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 GLN I 135 ASN ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 466 ASN ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 ASN ** 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** L 370 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.117971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.099921 restraints weight = 96593.921| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 2.65 r_work: 0.4099 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4096 r_free = 0.4096 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3244 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4093 r_free = 0.4093 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3276 | |-----------------------------------------------------------------------------| r_final: 0.4093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32614 Z= 0.139 Angle : 0.667 14.467 44698 Z= 0.336 Chirality : 0.046 0.279 4858 Planarity : 0.005 0.066 5130 Dihedral : 17.849 176.200 5581 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.88 % Favored : 91.83 % Rotamer: Outliers : 3.89 % Allowed : 30.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.14), residues: 3466 helix: -1.12 (0.15), residues: 1104 sheet: -2.05 (0.22), residues: 511 loop : -1.64 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 126 TYR 0.033 0.001 TYR C 346 PHE 0.026 0.002 PHE C 78 TRP 0.045 0.002 TRP D 192 HIS 0.008 0.001 HIS I 59 Details of bonding type rmsd covalent geometry : bond 0.00318 (32614) covalent geometry : angle 0.66660 (44698) hydrogen bonds : bond 0.04172 ( 875) hydrogen bonds : angle 5.34063 ( 2415) ********************** 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 398 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 278 time to evaluate : 1.057 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: 0.6532 (OUTLIER) cc_final: 0.4873 (p90) REVERT: A 101 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6993 (mt) REVERT: B 122 MET cc_start: 0.7684 (ppp) cc_final: 0.7298 (mmp) REVERT: B 169 GLU cc_start: 0.6207 (mm-30) cc_final: 0.5853 (mm-30) REVERT: C 59 HIS cc_start: 0.7620 (t-90) cc_final: 0.7300 (m170) REVERT: C 211 LYS cc_start: 0.6737 (OUTLIER) cc_final: 0.5873 (mmtt) REVERT: C 358 PHE cc_start: 0.7049 (t80) cc_final: 0.6846 (t80) REVERT: C 465 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6984 (mt) REVERT: D 124 TRP cc_start: 0.4896 (p-90) cc_final: 0.2322 (p-90) REVERT: D 260 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6670 (mm-30) REVERT: I 8 GLU cc_start: 0.6367 (mp0) cc_final: 0.5974 (mp0) REVERT: I 146 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7622 (mm-30) REVERT: I 161 MET cc_start: 0.4765 (ptm) cc_final: 0.4309 (ptp) REVERT: I 238 PHE cc_start: 0.6382 (p90) cc_final: 0.6031 (p90) REVERT: I 283 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7993 (pp) REVERT: I 374 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6901 (mm) REVERT: I 446 ASN cc_start: 0.6472 (OUTLIER) cc_final: 0.6105 (m-40) REVERT: J 121 LYS cc_start: 0.6511 (OUTLIER) cc_final: 0.5998 (mmtt) REVERT: K 96 VAL cc_start: 0.6751 (OUTLIER) cc_final: 0.6466 (m) REVERT: K 141 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.8066 (m) REVERT: K 251 HIS cc_start: 0.4605 (OUTLIER) cc_final: 0.3899 (p90) REVERT: K 358 PHE cc_start: 0.6091 (m-80) cc_final: 0.5698 (m-80) REVERT: K 435 MET cc_start: 0.6152 (ppp) cc_final: 0.5788 (tpt) REVERT: K 506 TYR cc_start: 0.5284 (OUTLIER) cc_final: 0.1934 (m-80) REVERT: L 102 GLN cc_start: 0.7943 (mm-40) cc_final: 0.6809 (tp40) REVERT: L 144 VAL cc_start: 0.5782 (m) cc_final: 0.5564 (p) REVERT: L 213 TYR cc_start: 0.6520 (m-80) cc_final: 0.6281 (m-80) outliers start: 120 outliers final: 98 residues processed: 380 average time/residue: 0.1733 time to fit residues: 107.0872 Evaluate side-chains 375 residues out of total 3129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 264 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 101 ILE Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 305 LEU 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 486 ILE Chi-restraints excluded: chain B residue 20 TRP Chi-restraints excluded: chain B residue 110 ILE 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 308 THR 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 414 VAL Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 39 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 98 ASN 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 278 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 307 ASN Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 389 SER 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 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 290 LYS 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 44 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 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 251 HIS Chi-restraints excluded: chain I residue 283 LEU 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 426 VAL Chi-restraints excluded: chain I residue 446 ASN 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 386 ASP 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 96 VAL 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 252 LEU 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 376 VAL Chi-restraints excluded: chain K residue 398 LYS 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 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 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 266 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 83 optimal weight: 2.9990 chunk 246 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 190 optimal weight: 0.0470 chunk 131 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 342 optimal weight: 5.9990 chunk 279 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 148 optimal weight: 0.0970 overall best weight: 0.7678 ------------------------------------------------------------------------------- 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 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 GLN ** I 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 370 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.117882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.099724 restraints weight = 97030.921| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.66 r_work: 0.4094 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3276 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4089 r_free = 0.4089 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3329 | |-----------------------------------------------------------------------------| r_final: 0.4089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 32614 Z= 0.166 Angle : 0.752 59.197 44698 Z= 0.404 Chirality : 0.049 1.136 4858 Planarity : 0.005 0.065 5130 Dihedral : 17.850 176.204 5581 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.08 % Favored : 91.69 % Rotamer: Outliers : 3.99 % Allowed : 30.71 % Favored : 65.30 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.14), residues: 3466 helix: -1.11 (0.15), residues: 1105 sheet: -2.04 (0.22), residues: 511 loop : -1.65 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 19 TYR 0.029 0.001 TYR C 346 PHE 0.025 0.002 PHE C 78 TRP 0.040 0.002 TRP D 192 HIS 0.008 0.001 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00356 (32614) covalent geometry : angle 0.75212 (44698) hydrogen bonds : bond 0.04171 ( 875) hydrogen bonds : angle 5.34588 ( 2415) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7314.55 seconds wall clock time: 126 minutes 11.47 seconds (7571.47 seconds total)