Starting phenix.real_space_refine on Sat Mar 7 02:22:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p6u_13232/03_2026/7p6u_13232_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p6u_13232/03_2026/7p6u_13232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p6u_13232/03_2026/7p6u_13232_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p6u_13232/03_2026/7p6u_13232_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p6u_13232/03_2026/7p6u_13232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p6u_13232/03_2026/7p6u_13232.map" } resolution = 3.9 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= 0.000 sd= 0.003 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 15 5.49 5 S 78 5.16 5 C 23394 2.51 5 N 6552 2.21 5 O 6901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36940 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6123 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 47, 'TRANS': 723} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 6127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6127 Classifications: {'peptide': 772} Link IDs: {'CIS': 1, 'PTRANS': 47, 'TRANS': 723} Chain: "C" Number of atoms: 6122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6122 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 48, 'TRANS': 722} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 6127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6127 Classifications: {'peptide': 772} Link IDs: {'CIS': 1, 'PTRANS': 47, 'TRANS': 723} Chain: "E" Number of atoms: 6123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6123 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 47, 'TRANS': 723} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 6127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6127 Classifications: {'peptide': 772} Link IDs: {'CIS': 1, 'PTRANS': 47, 'TRANS': 723} Chain: "S" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 36 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1446 residue: pdb=" N ARG A 6 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG A 6 " occ=0.00 residue: pdb=" N LEU A 7 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 7 " occ=0.00 residue: pdb=" N GLU A 8 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU A 8 " occ=0.00 residue: pdb=" N LEU A 9 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 9 " occ=0.00 residue: pdb=" N PRO A 10 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 10 " occ=0.00 residue: pdb=" N VAL A 11 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL A 11 " occ=0.00 residue: pdb=" N LEU A 12 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 12 " occ=0.00 residue: pdb=" N PRO A 13 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 13 " occ=0.00 residue: pdb=" N LEU A 14 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 14 " occ=0.00 residue: pdb=" N ARG A 15 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG A 15 " occ=0.00 residue: pdb=" N ASN A 16 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN A 16 " occ=0.00 residue: pdb=" N THR A 17 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR A 17 " occ=0.00 ... (remaining 1434 not shown) Time building chain proxies: 9.59, per 1000 atoms: 0.26 Number of scatterers: 36940 At special positions: 0 Unit cell: (213.4, 161.7, 150.7, 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 78 16.00 P 15 15.00 O 6901 8.00 N 6552 7.00 C 23394 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.8 seconds 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8666 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 45 sheets defined 48.4% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 31 through 42 Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.957A pdb=" N LEU A 66 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 139 removed outlier: 3.990A pdb=" N LEU A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ARG A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 148 through 154 removed outlier: 4.264A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 172 removed outlier: 3.945A pdb=" N HIS A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.633A pdb=" N THR A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 241 removed outlier: 3.778A pdb=" N ARG A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N MET A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 247 through 262 removed outlier: 4.018A pdb=" N GLU A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 4.649A pdb=" N GLU A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LYS A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 298 Processing helix chain 'A' and resid 313 through 322 removed outlier: 4.189A pdb=" N ARG A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 344 removed outlier: 3.652A pdb=" N LEU A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 408 through 418 Processing helix chain 'A' and resid 439 through 448 removed outlier: 3.801A pdb=" N ALA A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 489 Processing helix chain 'A' and resid 499 through 510 removed outlier: 4.897A pdb=" N ALA A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 520 removed outlier: 3.842A pdb=" N PHE A 514 " --> pdb=" O PHE A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 539 Processing helix chain 'A' and resid 545 through 566 Processing helix chain 'A' and resid 578 through 584 removed outlier: 3.855A pdb=" N TYR A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 651 removed outlier: 3.990A pdb=" N LYS A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 651 " --> pdb=" O THR A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 666 Processing helix chain 'A' and resid 684 through 698 Processing helix chain 'A' and resid 722 through 733 removed outlier: 3.968A pdb=" N LYS A 726 " --> pdb=" O GLY A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 749 removed outlier: 3.667A pdb=" N ALA A 745 " --> pdb=" O LYS A 742 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ALA A 746 " --> pdb=" O GLU A 743 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 747 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 748 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 749 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 766 through 775 Processing helix chain 'B' and resid 32 through 44 Processing helix chain 'B' and resid 124 through 144 removed outlier: 4.188A pdb=" N LEU B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 178 through 186 removed outlier: 3.992A pdb=" N ILE B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 235 removed outlier: 3.579A pdb=" N ARG B 192 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLU B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 4.302A pdb=" N GLY B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 238 through 243' Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 264 through 281 removed outlier: 4.145A pdb=" N ARG B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 300 Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 327 through 344 removed outlier: 3.521A pdb=" N LEU B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 378 Processing helix chain 'B' and resid 391 through 395 Processing helix chain 'B' and resid 408 through 418 Processing helix chain 'B' and resid 428 through 432 removed outlier: 3.658A pdb=" N LEU B 432 " --> pdb=" O ILE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 448 removed outlier: 3.895A pdb=" N ALA B 443 " --> pdb=" O ASP B 439 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 490 removed outlier: 3.628A pdb=" N MET B 490 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 511 Processing helix chain 'B' and resid 511 through 519 Processing helix chain 'B' and resid 528 through 540 removed outlier: 3.524A pdb=" N THR B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 566 removed outlier: 4.203A pdb=" N GLU B 551 " --> pdb=" O ASN B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 584 Processing helix chain 'B' and resid 636 through 652 removed outlier: 3.963A pdb=" N SER B 641 " --> pdb=" O VAL B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 694 removed outlier: 4.257A pdb=" N ILE B 688 " --> pdb=" O ALA B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 733 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 752 through 759 removed outlier: 3.544A pdb=" N LEU B 756 " --> pdb=" O PRO B 752 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 759 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 772 removed outlier: 3.732A pdb=" N VAL B 770 " --> pdb=" O GLU B 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 42 Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.921A pdb=" N LEU C 66 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 144 removed outlier: 4.026A pdb=" N LEU C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ARG C 126 " --> pdb=" O PRO C 122 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN C 142 " --> pdb=" O ARG C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 154 removed outlier: 4.285A pdb=" N GLN C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 172 removed outlier: 3.857A pdb=" N HIS C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.578A pdb=" N THR C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 239 removed outlier: 3.726A pdb=" N ARG C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 220 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU C 227 " --> pdb=" O GLN C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 262 removed outlier: 3.900A pdb=" N GLY C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 279 removed outlier: 3.788A pdb=" N LYS C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 300 removed outlier: 4.099A pdb=" N THR C 293 " --> pdb=" O THR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 321 removed outlier: 3.556A pdb=" N THR C 316 " --> pdb=" O ASP C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 344 removed outlier: 4.060A pdb=" N ARG C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 377 removed outlier: 3.552A pdb=" N GLY C 370 " --> pdb=" O LYS C 366 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 374 " --> pdb=" O GLY C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 417 Processing helix chain 'C' and resid 428 through 432 removed outlier: 3.761A pdb=" N LEU C 432 " --> pdb=" O ILE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 448 removed outlier: 4.103A pdb=" N GLU C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 499 through 520 removed outlier: 4.332A pdb=" N ALA C 505 " --> pdb=" O HIS C 501 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TRP C 512 " --> pdb=" O ARG C 508 " (cutoff:3.500A) Proline residue: C 513 - end of helix Processing helix chain 'C' and resid 528 through 539 Processing helix chain 'C' and resid 545 through 566 removed outlier: 3.868A pdb=" N ALA C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 565 " --> pdb=" O LYS C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 583 Processing helix chain 'C' and resid 635 through 652 removed outlier: 3.672A pdb=" N SER C 641 " --> pdb=" O VAL C 637 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA C 644 " --> pdb=" O GLU C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 665 Processing helix chain 'C' and resid 684 through 698 Processing helix chain 'C' and resid 722 through 733 Processing helix chain 'C' and resid 741 through 745 removed outlier: 4.057A pdb=" N ALA C 745 " --> pdb=" O LYS C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 775 removed outlier: 3.639A pdb=" N VAL C 770 " --> pdb=" O GLU C 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 42 Processing helix chain 'D' and resid 120 through 140 removed outlier: 3.839A pdb=" N LEU D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ARG D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 154 Processing helix chain 'D' and resid 161 through 172 removed outlier: 4.121A pdb=" N HIS D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 removed outlier: 4.151A pdb=" N THR D 186 " --> pdb=" O THR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.602A pdb=" N ARG D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 242 removed outlier: 3.515A pdb=" N LYS D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 removed outlier: 4.014A pdb=" N ILE D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU D 259 " --> pdb=" O ARG D 255 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY D 262 " --> pdb=" O ILE D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 281 removed outlier: 4.241A pdb=" N LYS D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS D 273 " --> pdb=" O GLU D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 300 removed outlier: 3.722A pdb=" N THR D 289 " --> pdb=" O SER D 285 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL D 290 " --> pdb=" O PRO D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 3.894A pdb=" N THR D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 344 removed outlier: 3.609A pdb=" N LEU D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 366 through 377 removed outlier: 4.019A pdb=" N GLY D 370 " --> pdb=" O LYS D 366 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS D 371 " --> pdb=" O THR D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 418 Processing helix chain 'D' and resid 440 through 448 removed outlier: 4.064A pdb=" N GLU D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 490 Processing helix chain 'D' and resid 499 through 511 Processing helix chain 'D' and resid 511 through 518 Processing helix chain 'D' and resid 528 through 539 Processing helix chain 'D' and resid 545 through 555 Processing helix chain 'D' and resid 557 through 566 Processing helix chain 'D' and resid 577 through 583 removed outlier: 3.840A pdb=" N LEU D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 652 Processing helix chain 'D' and resid 661 through 666 Processing helix chain 'D' and resid 681 through 683 No H-bonds generated for 'chain 'D' and resid 681 through 683' Processing helix chain 'D' and resid 684 through 697 Processing helix chain 'D' and resid 722 through 733 removed outlier: 3.903A pdb=" N LYS D 726 " --> pdb=" O GLY D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 746 removed outlier: 3.778A pdb=" N ALA D 746 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 759 removed outlier: 3.595A pdb=" N LEU D 756 " --> pdb=" O PRO D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 775 removed outlier: 3.723A pdb=" N LEU D 773 " --> pdb=" O GLU D 769 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 42 Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.945A pdb=" N LEU E 66 " --> pdb=" O PRO E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 144 removed outlier: 4.010A pdb=" N LEU E 124 " --> pdb=" O LYS E 120 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ARG E 126 " --> pdb=" O PRO E 122 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL E 127 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU E 140 " --> pdb=" O PHE E 136 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN E 141 " --> pdb=" O GLU E 137 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN E 142 " --> pdb=" O ARG E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 154 removed outlier: 4.270A pdb=" N GLN E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 172 removed outlier: 3.892A pdb=" N HIS E 172 " --> pdb=" O LEU E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 186 removed outlier: 3.640A pdb=" N THR E 186 " --> pdb=" O THR E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 241 removed outlier: 3.677A pdb=" N ARG E 192 " --> pdb=" O GLU E 188 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN E 224 " --> pdb=" O GLN E 220 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU E 227 " --> pdb=" O GLN E 223 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU E 241 " --> pdb=" O ILE E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 248 No H-bonds generated for 'chain 'E' and resid 246 through 248' Processing helix chain 'E' and resid 249 through 262 removed outlier: 4.214A pdb=" N LEU E 254 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG E 255 " --> pdb=" O ILE E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 279 removed outlier: 4.165A pdb=" N LYS E 270 " --> pdb=" O PRO E 266 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA E 271 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 301 removed outlier: 3.649A pdb=" N SER E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL E 301 " --> pdb=" O TRP E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 318 Processing helix chain 'E' and resid 327 through 344 removed outlier: 4.081A pdb=" N GLU E 332 " --> pdb=" O LYS E 328 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR E 337 " --> pdb=" O ARG E 333 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL E 340 " --> pdb=" O GLU E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 378 Processing helix chain 'E' and resid 391 through 396 removed outlier: 3.903A pdb=" N ILE E 395 " --> pdb=" O ASP E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 418 removed outlier: 3.686A pdb=" N VAL E 417 " --> pdb=" O GLY E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 447 removed outlier: 4.585A pdb=" N ALA E 443 " --> pdb=" O ASP E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 454 removed outlier: 3.771A pdb=" N HIS E 454 " --> pdb=" O PRO E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 487 Processing helix chain 'E' and resid 499 through 511 removed outlier: 3.714A pdb=" N LYS E 503 " --> pdb=" O THR E 499 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA E 507 " --> pdb=" O LYS E 503 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ARG E 508 " --> pdb=" O ARG E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 520 Processing helix chain 'E' and resid 528 through 539 Processing helix chain 'E' and resid 547 through 566 removed outlier: 3.760A pdb=" N LYS E 566 " --> pdb=" O ASP E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 577 No H-bonds generated for 'chain 'E' and resid 575 through 577' Processing helix chain 'E' and resid 578 through 583 Processing helix chain 'E' and resid 637 through 652 Processing helix chain 'E' and resid 653 through 656 removed outlier: 4.079A pdb=" N TRP E 656 " --> pdb=" O ARG E 653 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 653 through 656' Processing helix chain 'E' and resid 672 through 677 removed outlier: 3.548A pdb=" N GLY E 675 " --> pdb=" O VAL E 672 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA E 676 " --> pdb=" O PRO E 673 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 698 removed outlier: 4.063A pdb=" N THR E 697 " --> pdb=" O ALA E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 722 through 733 removed outlier: 3.723A pdb=" N LYS E 726 " --> pdb=" O GLY E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 744 through 750 Processing helix chain 'E' and resid 752 through 757 Processing helix chain 'E' and resid 766 through 775 removed outlier: 3.873A pdb=" N VAL E 770 " --> pdb=" O GLU E 766 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 43 removed outlier: 4.288A pdb=" N SER F 43 " --> pdb=" O GLU F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 138 removed outlier: 4.642A pdb=" N ARG F 126 " --> pdb=" O PRO F 122 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL F 127 " --> pdb=" O GLU F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 144 removed outlier: 3.643A pdb=" N ASN F 142 " --> pdb=" O ARG F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 154 removed outlier: 3.648A pdb=" N TYR F 151 " --> pdb=" O ARG F 147 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 173 removed outlier: 3.719A pdb=" N ALA F 173 " --> pdb=" O VAL F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 186 removed outlier: 3.603A pdb=" N LYS F 180 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR F 186 " --> pdb=" O THR F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 242 removed outlier: 4.352A pdb=" N ARG F 202 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP F 203 " --> pdb=" O LEU F 199 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN F 225 " --> pdb=" O MET F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 258 removed outlier: 3.643A pdb=" N ILE F 251 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU F 254 " --> pdb=" O GLU F 250 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG F 255 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU F 256 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 279 Processing helix chain 'F' and resid 287 through 301 removed outlier: 3.984A pdb=" N VAL F 301 " --> pdb=" O TRP F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 324 removed outlier: 3.665A pdb=" N ASP F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 343 removed outlier: 3.797A pdb=" N LYS F 331 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 377 Processing helix chain 'F' and resid 391 through 396 Processing helix chain 'F' and resid 408 through 418 removed outlier: 3.596A pdb=" N GLN F 416 " --> pdb=" O GLN F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 432 Processing helix chain 'F' and resid 444 through 449 Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 483 through 488 Processing helix chain 'F' and resid 499 through 510 Processing helix chain 'F' and resid 510 through 519 removed outlier: 3.764A pdb=" N PHE F 514 " --> pdb=" O PHE F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 528 through 539 Processing helix chain 'F' and resid 546 through 564 removed outlier: 3.741A pdb=" N ASP F 562 " --> pdb=" O LYS F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 576 through 580 removed outlier: 3.513A pdb=" N LEU F 579 " --> pdb=" O ALA F 576 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU F 580 " --> pdb=" O GLU F 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 576 through 580' Processing helix chain 'F' and resid 636 through 652 Processing helix chain 'F' and resid 684 through 698 Processing helix chain 'F' and resid 723 through 731 removed outlier: 4.976A pdb=" N ALA F 729 " --> pdb=" O GLU F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 757 removed outlier: 3.886A pdb=" N LEU F 756 " --> pdb=" O PRO F 752 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS F 757 " --> pdb=" O GLU F 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 752 through 757' Processing helix chain 'F' and resid 766 through 775 removed outlier: 4.001A pdb=" N VAL F 770 " --> pdb=" O GLU F 766 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU F 775 " --> pdb=" O LEU F 771 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 removed outlier: 3.942A pdb=" N VAL A 51 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A 71 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N THR A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL A 69 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL A 74 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA A 92 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS A 76 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL A 90 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ALA A 78 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL A 88 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ARG A 80 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU A 86 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.162A pdb=" N VAL A 110 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 381 through 384 removed outlier: 7.104A pdb=" N HIS A 382 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 526 through 527 removed outlier: 7.299A pdb=" N GLU A 526 " --> pdb=" O VAL A 574 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 608 removed outlier: 3.707A pdb=" N ALA A 606 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 613 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 611 " --> pdb=" O THR A 608 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 618 " --> pdb=" O HIS A 671 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 620 " --> pdb=" O HIS A 669 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS A 669 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 629 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 705 through 707 Processing sheet with id=AA7, first strand: chain 'A' and resid 710 through 711 removed outlier: 3.854A pdb=" N GLU A 710 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 718 " --> pdb=" O GLU A 710 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 29 removed outlier: 3.745A pdb=" N THR B 25 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU B 86 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ARG B 80 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL B 88 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ALA B 78 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL B 90 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LYS B 76 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ALA B 92 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL B 74 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL B 69 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N THR B 52 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 51 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 14 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 9 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 110 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 423 through 426 removed outlier: 6.012A pdb=" N LEU B 356 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL B 359 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 456 through 457 removed outlier: 3.857A pdb=" N PHE B 456 " --> pdb=" O TYR B 465 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 526 through 527 removed outlier: 7.386A pdb=" N GLU B 526 " --> pdb=" O VAL B 574 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 601 through 608 removed outlier: 3.914A pdb=" N ALA B 606 " --> pdb=" O THR B 613 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 705 through 707 removed outlier: 7.845A pdb=" N VAL B 764 " --> pdb=" O VAL B 738 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 740 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 710 through 711 Processing sheet with id=AB6, first strand: chain 'C' and resid 11 through 14 removed outlier: 4.005A pdb=" N VAL C 51 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 14 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 71 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N THR C 52 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL C 69 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER C 94 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL C 74 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ALA C 92 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LYS C 76 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL C 90 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ALA C 78 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL C 88 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG C 80 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU C 86 " --> pdb=" O ARG C 80 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 100 through 102 removed outlier: 4.009A pdb=" N VAL C 110 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL C 102 " --> pdb=" O ARG C 108 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG C 108 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 381 through 385 removed outlier: 7.110A pdb=" N HIS C 382 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASP C 427 " --> pdb=" O HIS C 382 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE C 384 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU C 356 " --> pdb=" O THR C 474 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 359 " --> pdb=" O ILE C 493 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 525 through 527 removed outlier: 6.748A pdb=" N GLU C 526 " --> pdb=" O VAL C 574 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 618 through 623 removed outlier: 4.421A pdb=" N GLU C 618 " --> pdb=" O HIS C 671 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS C 671 " --> pdb=" O GLU C 618 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS C 669 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASN C 629 " --> pdb=" O ILE C 670 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 705 through 707 removed outlier: 6.565A pdb=" N ALA C 706 " --> pdb=" O ILE C 739 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 710 through 711 Processing sheet with id=AC4, first strand: chain 'D' and resid 9 through 10 removed outlier: 4.067A pdb=" N LEU D 9 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 109 " --> pdb=" O LEU D 9 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 24 through 29 removed outlier: 3.610A pdb=" N LEU D 86 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL D 90 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LYS D 76 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ALA D 92 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL D 74 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 381 through 385 removed outlier: 3.535A pdb=" N HIS D 382 " --> pdb=" O VAL D 423 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N PHE D 424 " --> pdb=" O ILE D 473 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR D 475 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU D 426 " --> pdb=" O THR D 475 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU D 356 " --> pdb=" O THR D 474 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA D 476 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE D 358 " --> pdb=" O ALA D 476 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 525 through 527 removed outlier: 7.067A pdb=" N GLU D 526 " --> pdb=" O VAL D 574 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 597 through 598 Processing sheet with id=AC9, first strand: chain 'D' and resid 601 through 605 Processing sheet with id=AD1, first strand: chain 'D' and resid 739 through 740 Processing sheet with id=AD2, first strand: chain 'E' and resid 11 through 14 removed outlier: 4.031A pdb=" N VAL E 51 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 14 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR E 71 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N THR E 52 " --> pdb=" O VAL E 69 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL E 69 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL E 74 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA E 92 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LYS E 76 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL E 90 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA E 78 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL E 88 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG E 80 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU E 86 " --> pdb=" O ARG E 80 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 380 through 385 removed outlier: 6.777A pdb=" N ARG E 380 " --> pdb=" O VAL E 423 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU E 425 " --> pdb=" O ARG E 380 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS E 382 " --> pdb=" O LEU E 425 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP E 427 " --> pdb=" O HIS E 382 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE E 384 " --> pdb=" O ASP E 427 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU E 356 " --> pdb=" O THR E 474 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 456 through 458 removed outlier: 3.753A pdb=" N ASP E 458 " --> pdb=" O VAL E 463 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL E 463 " --> pdb=" O ASP E 458 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 526 through 527 removed outlier: 7.368A pdb=" N GLU E 526 " --> pdb=" O VAL E 574 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 603 through 604 removed outlier: 3.570A pdb=" N GLY E 604 " --> pdb=" O LEU E 615 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 607 through 608 removed outlier: 3.575A pdb=" N THR E 608 " --> pdb=" O GLY E 611 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY E 611 " --> pdb=" O THR E 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 710 through 711 removed outlier: 3.742A pdb=" N GLU E 710 " --> pdb=" O LEU E 718 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 737 through 741 Processing sheet with id=AE1, first strand: chain 'F' and resid 24 through 29 removed outlier: 3.931A pdb=" N THR F 25 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 90 " --> pdb=" O THR F 25 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU F 86 " --> pdb=" O ARG F 80 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ARG F 80 " --> pdb=" O LEU F 86 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL F 88 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA F 78 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL F 90 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LYS F 76 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ALA F 92 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL F 74 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER F 94 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL F 69 " --> pdb=" O THR F 52 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR F 52 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR F 71 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU F 107 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ARG F 108 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL F 102 " --> pdb=" O ARG F 108 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL F 110 " --> pdb=" O SER F 100 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 358 through 359 Processing sheet with id=AE3, first strand: chain 'F' and resid 381 through 384 removed outlier: 3.643A pdb=" N HIS F 382 " --> pdb=" O VAL F 423 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 525 through 527 Processing sheet with id=AE5, first strand: chain 'F' and resid 602 through 603 removed outlier: 3.536A pdb=" N ALA F 602 " --> pdb=" O ILE F 617 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 617 " --> pdb=" O ALA F 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'F' and resid 606 through 608 removed outlier: 4.212A pdb=" N ALA F 606 " --> pdb=" O THR F 613 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR F 613 " --> pdb=" O ALA F 606 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 619 through 622 removed outlier: 4.193A pdb=" N VAL F 620 " --> pdb=" O HIS F 669 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N HIS F 669 " --> pdb=" O VAL F 620 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 705 through 707 removed outlier: 6.858A pdb=" N VAL F 738 " --> pdb=" O HIS F 762 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL F 764 " --> pdb=" O VAL F 738 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU F 740 " --> pdb=" O VAL F 764 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 710 through 711 1538 hydrogen bonds defined for protein. 4491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.87 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9275 1.33 - 1.46: 7309 1.46 - 1.58: 20892 1.58 - 1.71: 25 1.71 - 1.83: 150 Bond restraints: 37651 Sorted by residual: bond pdb=" N3B ANP C 801 " pdb=" PG ANP C 801 " ideal model delta sigma weight residual 1.795 1.633 0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" O3A ANP D 801 " pdb=" PB ANP D 801 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.563 0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" O3A ANP E 801 " pdb=" PB ANP E 801 " ideal model delta sigma weight residual 1.700 1.563 0.137 2.00e-02 2.50e+03 4.66e+01 ... (remaining 37646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 49844 4.12 - 8.24: 1032 8.24 - 12.37: 151 12.37 - 16.49: 27 16.49 - 20.61: 9 Bond angle restraints: 51063 Sorted by residual: angle pdb=" CA GLU A 336 " pdb=" CB GLU A 336 " pdb=" CG GLU A 336 " ideal model delta sigma weight residual 114.10 129.33 -15.23 2.00e+00 2.50e-01 5.80e+01 angle pdb=" N GLU C 256 " pdb=" CA GLU C 256 " pdb=" CB GLU C 256 " ideal model delta sigma weight residual 110.39 122.27 -11.88 1.66e+00 3.63e-01 5.12e+01 angle pdb=" C PRO A 483 " pdb=" N ARG A 484 " pdb=" CA ARG A 484 " ideal model delta sigma weight residual 120.58 129.91 -9.33 1.32e+00 5.74e-01 4.99e+01 angle pdb=" CA GLU C 256 " pdb=" CB GLU C 256 " pdb=" CG GLU C 256 " ideal model delta sigma weight residual 114.10 128.10 -14.00 2.00e+00 2.50e-01 4.90e+01 angle pdb=" C GLY B 632 " pdb=" N ASN B 633 " pdb=" CA ASN B 633 " ideal model delta sigma weight residual 121.54 134.38 -12.84 1.91e+00 2.74e-01 4.52e+01 ... (remaining 51058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.77: 22303 25.77 - 51.55: 945 51.55 - 77.32: 68 77.32 - 103.09: 14 103.09 - 128.86: 1 Dihedral angle restraints: 23331 sinusoidal: 9902 harmonic: 13429 Sorted by residual: dihedral pdb=" CA ASP D 55 " pdb=" C ASP D 55 " pdb=" N PRO D 56 " pdb=" CA PRO D 56 " ideal model delta harmonic sigma weight residual -180.00 -112.19 -67.81 0 5.00e+00 4.00e-02 1.84e+02 dihedral pdb=" CA ASP B 55 " pdb=" C ASP B 55 " pdb=" N PRO B 56 " pdb=" CA PRO B 56 " ideal model delta harmonic sigma weight residual -180.00 -117.53 -62.47 0 5.00e+00 4.00e-02 1.56e+02 dihedral pdb=" CA ASP A 55 " pdb=" C ASP A 55 " pdb=" N PRO A 56 " pdb=" CA PRO A 56 " ideal model delta harmonic sigma weight residual 180.00 -120.31 -59.69 0 5.00e+00 4.00e-02 1.43e+02 ... (remaining 23328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4980 0.100 - 0.200: 672 0.200 - 0.300: 112 0.300 - 0.400: 21 0.400 - 0.500: 8 Chirality restraints: 5793 Sorted by residual: chirality pdb=" CG LEU B 444 " pdb=" CB LEU B 444 " pdb=" CD1 LEU B 444 " pdb=" CD2 LEU B 444 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" CB VAL C 447 " pdb=" CA VAL C 447 " pdb=" CG1 VAL C 447 " pdb=" CG2 VAL C 447 " both_signs ideal model delta sigma weight residual False -2.63 -2.13 -0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CB VAL D 364 " pdb=" CA VAL D 364 " pdb=" CG1 VAL D 364 " pdb=" CG2 VAL D 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.71e+00 ... (remaining 5790 not shown) Planarity restraints: 6620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 463 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO A 464 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 464 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 464 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 507 " 0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C ALA A 507 " -0.075 2.00e-02 2.50e+03 pdb=" O ALA A 507 " 0.028 2.00e-02 2.50e+03 pdb=" N ARG A 508 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 512 " 0.033 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" CG TRP A 512 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP A 512 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 512 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 512 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP A 512 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 512 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 512 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 512 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 512 " 0.003 2.00e-02 2.50e+03 ... (remaining 6617 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 365 2.63 - 3.19: 28809 3.19 - 3.76: 59868 3.76 - 4.33: 80046 4.33 - 4.90: 127277 Nonbonded interactions: 296365 Sorted by model distance: nonbonded pdb=" O1A ANP C 801 " pdb=" O3' ANP C 801 " model vdw 2.058 3.040 nonbonded pdb=" OG1 THR E 631 " pdb=" O ILE E 670 " model vdw 2.316 3.040 nonbonded pdb=" OG1 THR C 687 " pdb=" O MET C 707 " model vdw 2.317 3.040 nonbonded pdb=" O LEU F 356 " pdb=" OG1 THR F 474 " model vdw 2.317 3.040 nonbonded pdb=" O THR E 289 " pdb=" OG1 THR E 293 " model vdw 2.318 3.040 ... (remaining 296360 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 6 through 476 or resid 478 through 777)) selection = (chain 'B' and (resid 6 through 252 or (resid 253 and (name N or name CA or name \ C or name O or name CB )) or resid 254 through 476 or resid 478 through 777)) selection = (chain 'C' and resid 6 through 777) selection = (chain 'D' and (resid 6 through 252 or (resid 253 and (name N or name CA or name \ C or name O or name CB )) or resid 254 through 476 or resid 478 through 777)) selection = (chain 'E' and (resid 6 through 476 or resid 478 through 777)) selection = (chain 'F' and (resid 6 through 252 or (resid 253 and (name N or name CA or name \ C or name O or name CB )) or resid 254 through 476 or resid 478 through 777)) } 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=0.69 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 35.870 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.100 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 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 : 0.007 0.162 37652 Z= 0.348 Angle : 1.410 20.612 51063 Z= 0.706 Chirality : 0.076 0.500 5793 Planarity : 0.011 0.110 6620 Dihedral : 13.660 128.863 14665 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.28 % Favored : 93.66 % Rotamer: Outliers : 0.03 % Allowed : 0.46 % Favored : 99.51 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.77 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.10), residues: 4618 helix: -3.31 (0.08), residues: 1970 sheet: -1.61 (0.23), residues: 497 loop : -2.31 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG C 546 TYR 0.043 0.003 TYR E 337 PHE 0.048 0.004 PHE D 136 TRP 0.067 0.004 TRP A 512 HIS 0.025 0.002 HIS C 459 Details of bonding type rmsd covalent geometry : bond 0.00719 (37651) covalent geometry : angle 1.40961 (51063) hydrogen bonds : bond 0.16490 ( 1538) hydrogen bonds : angle 8.54646 ( 4491) Misc. bond : bond 0.01119 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 489 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 PHE cc_start: 0.4685 (p90) cc_final: 0.4439 (p90) REVERT: A 537 GLN cc_start: 0.6881 (pt0) cc_final: 0.6474 (tm-30) REVERT: B 79 MET cc_start: -0.1495 (pmm) cc_final: -0.2339 (pmm) REVERT: B 221 MET cc_start: 0.1452 (mmp) cc_final: 0.1236 (mmm) REVERT: B 394 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 720 ILE cc_start: 0.8458 (pt) cc_final: 0.8128 (mt) REVERT: C 221 MET cc_start: -0.0381 (mmp) cc_final: -0.0881 (mmp) REVERT: C 281 MET cc_start: 0.7601 (mpp) cc_final: 0.7334 (mpp) REVERT: C 294 TYR cc_start: 0.8773 (t80) cc_final: 0.8294 (t80) REVERT: C 318 ARG cc_start: 0.7292 (mtm110) cc_final: 0.6888 (ptp-110) REVERT: C 332 GLU cc_start: 0.7232 (tp30) cc_final: 0.6789 (tp30) REVERT: C 462 ASP cc_start: 0.7966 (m-30) cc_final: 0.7464 (m-30) REVERT: C 500 LEU cc_start: 0.8413 (tt) cc_final: 0.8127 (pp) REVERT: C 728 LEU cc_start: 0.8157 (tp) cc_final: 0.7848 (tp) REVERT: D 79 MET cc_start: -0.0103 (ptt) cc_final: -0.0357 (ptt) REVERT: D 221 MET cc_start: 0.1231 (tpp) cc_final: 0.0656 (mmt) REVERT: D 234 MET cc_start: 0.0602 (tpt) cc_final: -0.0306 (tpt) REVERT: D 425 LEU cc_start: 0.8622 (tp) cc_final: 0.8352 (tp) REVERT: D 490 MET cc_start: 0.6857 (mtm) cc_final: 0.6580 (mtm) REVERT: E 318 ARG cc_start: 0.6870 (ptt90) cc_final: 0.6670 (ptt90) REVERT: E 674 GLU cc_start: 0.7527 (pp20) cc_final: 0.7259 (pp20) REVERT: E 692 LEU cc_start: 0.9184 (mp) cc_final: 0.8914 (mp) REVERT: F 89 MET cc_start: 0.1117 (mmt) cc_final: 0.0838 (mmt) REVERT: F 221 MET cc_start: 0.0488 (mmm) cc_final: 0.0143 (tpt) REVERT: F 281 MET cc_start: 0.4141 (mtt) cc_final: 0.3925 (ttm) REVERT: F 342 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7922 (pp30) REVERT: F 414 MET cc_start: 0.8330 (mmm) cc_final: 0.7947 (mmm) outliers start: 1 outliers final: 0 residues processed: 490 average time/residue: 0.2225 time to fit residues: 181.5398 Evaluate side-chains 327 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 342 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 GLN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 ASN ** E 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 731 HIS ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.119167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.103964 restraints weight = 115363.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.106308 restraints weight = 63993.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.107633 restraints weight = 36431.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.107605 restraints weight = 27441.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.107781 restraints weight = 28775.269| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 37652 Z= 0.269 Angle : 0.808 15.790 51063 Z= 0.411 Chirality : 0.049 0.287 5793 Planarity : 0.007 0.081 6620 Dihedral : 8.066 130.196 5292 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.56 % Allowed : 8.35 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.77 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.12), residues: 4618 helix: -1.51 (0.10), residues: 2043 sheet: -1.63 (0.22), residues: 543 loop : -1.84 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 400 TYR 0.030 0.002 TYR D 228 PHE 0.020 0.003 PHE A 471 TRP 0.041 0.003 TRP F 512 HIS 0.010 0.002 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00584 (37651) covalent geometry : angle 0.80764 (51063) hydrogen bonds : bond 0.04432 ( 1538) hydrogen bonds : angle 5.95971 ( 4491) Misc. bond : bond 0.00152 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 320 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.7999 (tmm) cc_final: 0.7223 (ttp) REVERT: A 269 GLU cc_start: 0.8795 (mp0) cc_final: 0.8110 (pm20) REVERT: B 394 GLU cc_start: 0.8699 (tm-30) cc_final: 0.7827 (tm-30) REVERT: B 414 MET cc_start: 0.9393 (mmm) cc_final: 0.8814 (mmt) REVERT: B 462 ASP cc_start: 0.8777 (p0) cc_final: 0.8568 (p0) REVERT: C 234 MET cc_start: 0.1980 (tmm) cc_final: 0.1664 (tmm) REVERT: C 420 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8885 (t) REVERT: C 703 MET cc_start: 0.4546 (mmp) cc_final: 0.4220 (mmt) REVERT: C 707 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7504 (tmm) REVERT: C 714 ARG cc_start: 0.8068 (mtt90) cc_final: 0.7345 (mtt90) REVERT: D 79 MET cc_start: 0.0474 (ptt) cc_final: -0.0066 (ptt) REVERT: D 223 GLN cc_start: 0.1144 (OUTLIER) cc_final: 0.0778 (pp30) REVERT: D 240 GLU cc_start: -0.1819 (OUTLIER) cc_final: -0.2034 (mt-10) REVERT: D 447 VAL cc_start: 0.9534 (t) cc_final: 0.9199 (p) REVERT: F 219 GLU cc_start: -0.0239 (OUTLIER) cc_final: -0.0509 (pm20) REVERT: F 221 MET cc_start: 0.0560 (mmm) cc_final: 0.0271 (mmm) REVERT: F 398 HIS cc_start: 0.5193 (m-70) cc_final: 0.4183 (m-70) REVERT: F 414 MET cc_start: 0.8274 (mmm) cc_final: 0.7740 (mmm) REVERT: F 614 LEU cc_start: 0.8932 (tp) cc_final: 0.8670 (tp) REVERT: F 703 MET cc_start: 0.6368 (mpp) cc_final: 0.5830 (mpp) outliers start: 61 outliers final: 38 residues processed: 360 average time/residue: 0.2128 time to fit residues: 130.3926 Evaluate side-chains 302 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 259 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 707 MET Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 223 GLN Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 325 TYR Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 535 ILE Chi-restraints excluded: chain D residue 703 MET Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 457 THR Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 680 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 240 optimal weight: 0.0030 chunk 172 optimal weight: 50.0000 chunk 381 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 339 optimal weight: 2.9990 chunk 439 optimal weight: 2.9990 chunk 387 optimal weight: 8.9990 chunk 352 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 420 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 HIS B 537 GLN B 731 HIS ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 ASN E 629 ASN ** E 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 GLN F 459 HIS ** F 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 669 HIS ** 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 = 0.3850 r_free = 0.3850 target = 0.117383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.102219 restraints weight = 114648.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.104380 restraints weight = 64228.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.106105 restraints weight = 36547.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.106120 restraints weight = 25228.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.106169 restraints weight = 24969.622| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 37652 Z= 0.212 Angle : 0.709 12.825 51063 Z= 0.355 Chirality : 0.047 0.429 5793 Planarity : 0.006 0.078 6620 Dihedral : 7.582 130.972 5289 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.95 % Rotamer: Outliers : 2.04 % Allowed : 11.62 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.41 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.12), residues: 4618 helix: -0.70 (0.11), residues: 2040 sheet: -1.58 (0.23), residues: 527 loop : -1.66 (0.14), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 396 TYR 0.032 0.002 TYR F 402 PHE 0.020 0.002 PHE A 471 TRP 0.041 0.002 TRP F 512 HIS 0.008 0.001 HIS F 501 Details of bonding type rmsd covalent geometry : bond 0.00472 (37651) covalent geometry : angle 0.70938 (51063) hydrogen bonds : bond 0.04008 ( 1538) hydrogen bonds : angle 5.61162 ( 4491) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 287 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 PHE cc_start: 0.5523 (p90) cc_final: 0.5257 (p90) REVERT: A 263 MET cc_start: 0.8007 (tmm) cc_final: 0.7713 (ttp) REVERT: A 269 GLU cc_start: 0.8737 (mp0) cc_final: 0.8089 (pm20) REVERT: A 279 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7535 (pp20) REVERT: A 377 MET cc_start: 0.8237 (ptp) cc_final: 0.7876 (ptp) REVERT: B 265 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7926 (tp30) REVERT: B 394 GLU cc_start: 0.8705 (tm-30) cc_final: 0.7771 (tm-30) REVERT: B 414 MET cc_start: 0.9286 (mmm) cc_final: 0.8875 (mmt) REVERT: C 294 TYR cc_start: 0.9253 (t80) cc_final: 0.8366 (t80) REVERT: C 420 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.8884 (t) REVERT: C 462 ASP cc_start: 0.8178 (m-30) cc_final: 0.7529 (m-30) REVERT: C 707 MET cc_start: 0.8371 (tmm) cc_final: 0.7918 (ppp) REVERT: C 714 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7298 (mtt90) REVERT: D 79 MET cc_start: 0.0812 (ptt) cc_final: 0.0355 (ptt) REVERT: D 199 LEU cc_start: 0.0010 (OUTLIER) cc_final: -0.0435 (pp) REVERT: D 447 VAL cc_start: 0.9542 (t) cc_final: 0.9263 (p) REVERT: D 487 LEU cc_start: 0.8598 (tp) cc_final: 0.8295 (pp) REVERT: E 258 ILE cc_start: 0.7574 (mt) cc_final: 0.7297 (mm) REVERT: E 533 GLU cc_start: 0.8185 (tt0) cc_final: 0.7867 (pt0) REVERT: E 646 LEU cc_start: 0.9241 (mt) cc_final: 0.8653 (pp) REVERT: F 398 HIS cc_start: 0.5240 (m-70) cc_final: 0.4556 (m-70) REVERT: F 414 MET cc_start: 0.8444 (mmm) cc_final: 0.7905 (mmm) REVERT: F 614 LEU cc_start: 0.8938 (tp) cc_final: 0.8661 (tp) outliers start: 80 outliers final: 50 residues processed: 346 average time/residue: 0.2069 time to fit residues: 123.3774 Evaluate side-chains 306 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 253 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 629 ASN Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 325 TYR Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 535 ILE Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 703 MET Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 457 THR Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 615 LEU Chi-restraints excluded: chain F residue 649 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 126 optimal weight: 0.4980 chunk 209 optimal weight: 2.9990 chunk 320 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 164 optimal weight: 40.0000 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 356 optimal weight: 4.9990 chunk 195 optimal weight: 0.2980 chunk 349 optimal weight: 3.9990 chunk 359 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 HIS ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.118480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.103541 restraints weight = 112906.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.106086 restraints weight = 61096.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.107255 restraints weight = 34094.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.107438 restraints weight = 25049.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.107559 restraints weight = 24448.844| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37652 Z= 0.146 Angle : 0.650 11.329 51063 Z= 0.321 Chirality : 0.045 0.378 5793 Planarity : 0.005 0.077 6620 Dihedral : 7.270 130.538 5289 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.32 % Allowed : 12.44 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.41 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.12), residues: 4618 helix: -0.29 (0.11), residues: 2036 sheet: -1.48 (0.23), residues: 527 loop : -1.59 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 333 TYR 0.027 0.002 TYR D 228 PHE 0.018 0.001 PHE D 510 TRP 0.042 0.002 TRP F 512 HIS 0.008 0.001 HIS F 501 Details of bonding type rmsd covalent geometry : bond 0.00327 (37651) covalent geometry : angle 0.64959 (51063) hydrogen bonds : bond 0.03639 ( 1538) hydrogen bonds : angle 5.37078 ( 4491) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 291 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 PHE cc_start: 0.5451 (p90) cc_final: 0.5155 (p90) REVERT: A 269 GLU cc_start: 0.8677 (mp0) cc_final: 0.8092 (pm20) REVERT: A 279 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7523 (pp20) REVERT: A 336 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7651 (mm-30) REVERT: B 221 MET cc_start: 0.1636 (mmm) cc_final: 0.1367 (mmm) REVERT: B 234 MET cc_start: -0.0849 (ttp) cc_final: -0.1088 (ttp) REVERT: B 401 THR cc_start: 0.9055 (m) cc_final: 0.8847 (m) REVERT: B 494 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7388 (tm-30) REVERT: C 281 MET cc_start: 0.7632 (mpp) cc_final: 0.7246 (mpp) REVERT: C 294 TYR cc_start: 0.9248 (t80) cc_final: 0.8085 (t80) REVERT: C 420 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8856 (t) REVERT: C 462 ASP cc_start: 0.8134 (m-30) cc_final: 0.7254 (m-30) REVERT: C 487 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8699 (tp) REVERT: C 666 TYR cc_start: 0.6411 (OUTLIER) cc_final: 0.5644 (t80) REVERT: C 686 ILE cc_start: 0.9384 (pt) cc_final: 0.9172 (pp) REVERT: C 707 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7915 (ppp) REVERT: D 447 VAL cc_start: 0.9516 (t) cc_final: 0.9294 (p) REVERT: D 487 LEU cc_start: 0.8563 (tp) cc_final: 0.8289 (pp) REVERT: E 258 ILE cc_start: 0.7496 (mt) cc_final: 0.7237 (mm) REVERT: E 414 MET cc_start: 0.7100 (tmm) cc_final: 0.6490 (tmm) REVERT: E 533 GLU cc_start: 0.8169 (tt0) cc_final: 0.7874 (pt0) REVERT: E 646 LEU cc_start: 0.9285 (mt) cc_final: 0.8669 (pp) REVERT: E 747 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7287 (pm20) REVERT: F 219 GLU cc_start: -0.1323 (OUTLIER) cc_final: -0.1590 (pm20) REVERT: F 414 MET cc_start: 0.8408 (mmm) cc_final: 0.7890 (mmm) REVERT: F 614 LEU cc_start: 0.8904 (tp) cc_final: 0.8628 (tp) REVERT: F 725 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7533 (tp30) outliers start: 91 outliers final: 49 residues processed: 357 average time/residue: 0.1987 time to fit residues: 123.6970 Evaluate side-chains 323 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 265 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 666 TYR Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 707 MET Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 325 TYR Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 535 ILE Chi-restraints excluded: chain D residue 703 MET Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 628 VAL Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain E residue 747 GLU Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 457 THR Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 725 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 145 optimal weight: 0.7980 chunk 369 optimal weight: 9.9990 chunk 263 optimal weight: 0.8980 chunk 460 optimal weight: 7.9990 chunk 456 optimal weight: 5.9990 chunk 275 optimal weight: 0.7980 chunk 363 optimal weight: 7.9990 chunk 364 optimal weight: 7.9990 chunk 331 optimal weight: 20.0000 chunk 159 optimal weight: 9.9990 chunk 218 optimal weight: 0.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.117709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.102725 restraints weight = 113258.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.105158 restraints weight = 62552.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.106676 restraints weight = 35044.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.106845 restraints weight = 24665.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.106866 restraints weight = 23200.699| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 37652 Z= 0.155 Angle : 0.646 11.079 51063 Z= 0.319 Chirality : 0.045 0.356 5793 Planarity : 0.005 0.080 6620 Dihedral : 7.052 122.794 5289 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.50 % Allowed : 14.00 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.41 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.13), residues: 4618 helix: -0.06 (0.12), residues: 2036 sheet: -1.47 (0.23), residues: 531 loop : -1.50 (0.14), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 231 TYR 0.028 0.001 TYR F 402 PHE 0.021 0.001 PHE D 510 TRP 0.044 0.002 TRP F 512 HIS 0.008 0.001 HIS E 324 Details of bonding type rmsd covalent geometry : bond 0.00353 (37651) covalent geometry : angle 0.64591 (51063) hydrogen bonds : bond 0.03534 ( 1538) hydrogen bonds : angle 5.23259 ( 4491) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 299 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 PHE cc_start: 0.5568 (p90) cc_final: 0.5276 (p90) REVERT: A 269 GLU cc_start: 0.8671 (mp0) cc_final: 0.8129 (pm20) REVERT: A 279 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7548 (pp20) REVERT: A 336 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7655 (mm-30) REVERT: A 377 MET cc_start: 0.8061 (ptp) cc_final: 0.7854 (ptp) REVERT: A 548 LEU cc_start: 0.9281 (tt) cc_final: 0.8912 (tp) REVERT: B 57 GLU cc_start: -0.1322 (OUTLIER) cc_final: -0.1692 (pm20) REVERT: B 221 MET cc_start: 0.1371 (mmm) cc_final: 0.1144 (mmm) REVERT: B 265 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7924 (tp30) REVERT: B 494 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7529 (tm-30) REVERT: B 550 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8380 (mpp80) REVERT: B 595 LYS cc_start: 0.9001 (tptt) cc_final: 0.8794 (tppt) REVERT: C 294 TYR cc_start: 0.9263 (t80) cc_final: 0.8135 (t80) REVERT: C 420 VAL cc_start: 0.9170 (OUTLIER) cc_final: 0.8835 (t) REVERT: C 462 ASP cc_start: 0.8149 (m-30) cc_final: 0.7448 (m-30) REVERT: C 666 TYR cc_start: 0.6480 (OUTLIER) cc_final: 0.5806 (t80) REVERT: C 703 MET cc_start: 0.4676 (mmp) cc_final: 0.4236 (tpp) REVERT: C 707 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7916 (tmm) REVERT: D 447 VAL cc_start: 0.9512 (t) cc_final: 0.9310 (p) REVERT: E 258 ILE cc_start: 0.7562 (mt) cc_final: 0.7330 (mm) REVERT: E 424 PHE cc_start: 0.7115 (t80) cc_final: 0.6324 (t80) REVERT: E 646 LEU cc_start: 0.9306 (mt) cc_final: 0.8690 (pp) REVERT: E 747 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7354 (pm20) REVERT: F 398 HIS cc_start: 0.5334 (m-70) cc_final: 0.4722 (t70) REVERT: F 414 MET cc_start: 0.8475 (mmm) cc_final: 0.7928 (mmm) REVERT: F 614 LEU cc_start: 0.8928 (tp) cc_final: 0.8649 (tp) REVERT: F 703 MET cc_start: 0.6631 (mtm) cc_final: 0.6371 (mtm) REVERT: F 725 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7543 (tp30) outliers start: 98 outliers final: 59 residues processed: 371 average time/residue: 0.1985 time to fit residues: 128.3225 Evaluate side-chains 336 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 268 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 666 TYR Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 707 MET Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 325 TYR Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 535 ILE Chi-restraints excluded: chain D residue 703 MET Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 628 VAL Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain E residue 747 GLU Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 457 THR Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 680 ASP Chi-restraints excluded: chain F residue 725 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 204 optimal weight: 1.9990 chunk 166 optimal weight: 30.0000 chunk 152 optimal weight: 9.9990 chunk 342 optimal weight: 6.9990 chunk 164 optimal weight: 30.0000 chunk 96 optimal weight: 30.0000 chunk 387 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 441 optimal weight: 5.9990 chunk 221 optimal weight: 0.4980 chunk 168 optimal weight: 50.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 HIS ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN E 547 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 HIS ** 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 = 0.3803 r_free = 0.3803 target = 0.114835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.099514 restraints weight = 114067.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.101399 restraints weight = 61646.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.102684 restraints weight = 39661.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.103400 restraints weight = 28752.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.103981 restraints weight = 23381.117| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 37652 Z= 0.221 Angle : 0.700 10.429 51063 Z= 0.347 Chirality : 0.046 0.277 5793 Planarity : 0.005 0.081 6620 Dihedral : 6.969 114.004 5289 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.86 % Allowed : 15.02 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.13), residues: 4618 helix: 0.01 (0.12), residues: 2040 sheet: -1.57 (0.22), residues: 552 loop : -1.52 (0.14), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 231 TYR 0.027 0.002 TYR A 294 PHE 0.022 0.002 PHE C 247 TRP 0.054 0.002 TRP F 512 HIS 0.008 0.001 HIS F 398 Details of bonding type rmsd covalent geometry : bond 0.00496 (37651) covalent geometry : angle 0.70040 (51063) hydrogen bonds : bond 0.03753 ( 1538) hydrogen bonds : angle 5.28111 ( 4491) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 282 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 PHE cc_start: 0.5547 (p90) cc_final: 0.5304 (p90) REVERT: A 263 MET cc_start: 0.7706 (ppp) cc_final: 0.7464 (ttp) REVERT: A 269 GLU cc_start: 0.8726 (mp0) cc_final: 0.8252 (pm20) REVERT: A 279 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7598 (pp20) REVERT: A 336 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7592 (mm-30) REVERT: B 394 GLU cc_start: 0.8789 (tm-30) cc_final: 0.7961 (tm-30) REVERT: B 494 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7815 (tm-30) REVERT: B 550 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8638 (mpp80) REVERT: B 595 LYS cc_start: 0.8976 (tptt) cc_final: 0.8742 (tppt) REVERT: C 275 LEU cc_start: 0.8935 (tp) cc_final: 0.8671 (tp) REVERT: C 420 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.8965 (t) REVERT: C 686 ILE cc_start: 0.9327 (pt) cc_final: 0.9122 (pp) REVERT: C 707 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7874 (ppp) REVERT: E 258 ILE cc_start: 0.7551 (mt) cc_final: 0.7331 (mm) REVERT: E 747 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7342 (pm20) REVERT: F 256 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8233 (pm20) REVERT: F 414 MET cc_start: 0.8482 (mmm) cc_final: 0.8012 (mmm) REVERT: F 515 GLN cc_start: 0.8259 (pp30) cc_final: 0.7936 (pp30) REVERT: F 614 LEU cc_start: 0.9014 (tp) cc_final: 0.8721 (tp) REVERT: F 703 MET cc_start: 0.6559 (OUTLIER) cc_final: 0.6283 (mtm) outliers start: 112 outliers final: 71 residues processed: 365 average time/residue: 0.1960 time to fit residues: 125.7525 Evaluate side-chains 338 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 259 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 629 ASN Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 731 HIS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 666 TYR Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 707 MET Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 325 TYR Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 535 ILE Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain D residue 703 MET Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 599 VAL Chi-restraints excluded: chain E residue 628 VAL Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain E residue 747 GLU Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 457 THR Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 680 ASP Chi-restraints excluded: chain F residue 703 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 60 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 396 optimal weight: 0.0000 chunk 277 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 302 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 418 optimal weight: 10.0000 chunk 311 optimal weight: 10.0000 chunk 157 optimal weight: 50.0000 chunk 377 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.117203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.102929 restraints weight = 113707.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.104335 restraints weight = 61136.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.105687 restraints weight = 36350.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.105765 restraints weight = 30584.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.105972 restraints weight = 25903.386| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37652 Z= 0.138 Angle : 0.642 10.404 51063 Z= 0.314 Chirality : 0.045 0.194 5793 Planarity : 0.005 0.081 6620 Dihedral : 6.866 114.239 5289 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.02 % Favored : 94.95 % Rotamer: Outliers : 2.38 % Allowed : 16.40 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.13), residues: 4618 helix: 0.16 (0.12), residues: 2049 sheet: -1.48 (0.23), residues: 545 loop : -1.42 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 231 TYR 0.025 0.001 TYR D 228 PHE 0.017 0.001 PHE C 247 TRP 0.041 0.002 TRP F 512 HIS 0.005 0.001 HIS B 671 Details of bonding type rmsd covalent geometry : bond 0.00316 (37651) covalent geometry : angle 0.64229 (51063) hydrogen bonds : bond 0.03396 ( 1538) hydrogen bonds : angle 5.09666 ( 4491) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 297 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 PHE cc_start: 0.5588 (p90) cc_final: 0.5323 (p90) REVERT: A 269 GLU cc_start: 0.8666 (mp0) cc_final: 0.8183 (pm20) REVERT: A 279 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7459 (pp20) REVERT: A 356 LEU cc_start: 0.8659 (tp) cc_final: 0.8446 (tp) REVERT: A 377 MET cc_start: 0.7585 (ptm) cc_final: 0.7247 (ptm) REVERT: A 424 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8483 (m-10) REVERT: A 548 LEU cc_start: 0.9209 (tt) cc_final: 0.8813 (tp) REVERT: B 394 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8017 (tm-30) REVERT: B 494 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7609 (tm-30) REVERT: B 550 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8332 (mpp80) REVERT: B 595 LYS cc_start: 0.8988 (tptt) cc_final: 0.8775 (tppt) REVERT: C 269 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6825 (mt-10) REVERT: C 294 TYR cc_start: 0.9216 (t80) cc_final: 0.8342 (t80) REVERT: C 366 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7979 (mttp) REVERT: C 420 VAL cc_start: 0.9243 (OUTLIER) cc_final: 0.8942 (t) REVERT: C 707 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7999 (ppp) REVERT: D 386 LEU cc_start: 0.9042 (mt) cc_final: 0.8796 (mp) REVERT: D 447 VAL cc_start: 0.9522 (t) cc_final: 0.9307 (p) REVERT: D 449 ASP cc_start: 0.7826 (t0) cc_final: 0.7480 (t0) REVERT: E 258 ILE cc_start: 0.7685 (mt) cc_final: 0.7474 (mm) REVERT: E 318 ARG cc_start: 0.7877 (ptt90) cc_final: 0.7516 (tmm-80) REVERT: E 414 MET cc_start: 0.7261 (tmm) cc_final: 0.6853 (tmm) REVERT: E 747 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7354 (pm20) REVERT: F 79 MET cc_start: -0.1111 (pmm) cc_final: -0.1475 (ptp) REVERT: F 256 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8292 (pm20) REVERT: F 414 MET cc_start: 0.8544 (mmm) cc_final: 0.8135 (mmm) REVERT: F 515 GLN cc_start: 0.8100 (pp30) cc_final: 0.7678 (pp30) REVERT: F 614 LEU cc_start: 0.8973 (tp) cc_final: 0.8715 (tp) REVERT: F 615 LEU cc_start: 0.8365 (tp) cc_final: 0.7796 (tp) REVERT: F 703 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6388 (mtm) outliers start: 93 outliers final: 60 residues processed: 367 average time/residue: 0.2076 time to fit residues: 131.3805 Evaluate side-chains 336 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 267 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 731 HIS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 666 TYR Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 707 MET Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 714 ARG Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 325 TYR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain D residue 703 MET Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 628 VAL Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain E residue 747 GLU Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 457 THR Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 649 LEU Chi-restraints excluded: chain F residue 680 ASP Chi-restraints excluded: chain F residue 703 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 246 optimal weight: 3.9990 chunk 322 optimal weight: 50.0000 chunk 342 optimal weight: 0.0270 chunk 28 optimal weight: 0.9980 chunk 396 optimal weight: 7.9990 chunk 380 optimal weight: 20.0000 chunk 175 optimal weight: 6.9990 chunk 393 optimal weight: 30.0000 chunk 260 optimal weight: 3.9990 chunk 78 optimal weight: 40.0000 chunk 422 optimal weight: 10.0000 overall best weight: 3.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 HIS ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.114483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099326 restraints weight = 113817.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.101247 restraints weight = 60685.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.102492 restraints weight = 38669.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.103339 restraints weight = 27920.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.103772 restraints weight = 22306.147| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 37652 Z= 0.219 Angle : 0.704 10.607 51063 Z= 0.349 Chirality : 0.046 0.218 5793 Planarity : 0.005 0.081 6620 Dihedral : 6.832 107.692 5289 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.81 % Allowed : 16.55 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.13), residues: 4618 helix: 0.14 (0.12), residues: 2065 sheet: -1.50 (0.22), residues: 557 loop : -1.47 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 231 TYR 0.023 0.002 TYR D 228 PHE 0.021 0.002 PHE C 247 TRP 0.043 0.002 TRP F 512 HIS 0.011 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00494 (37651) covalent geometry : angle 0.70438 (51063) hydrogen bonds : bond 0.03618 ( 1538) hydrogen bonds : angle 5.20485 ( 4491) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 279 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 PHE cc_start: 0.5674 (p90) cc_final: 0.5439 (p90) REVERT: A 263 MET cc_start: 0.7697 (ppp) cc_final: 0.7427 (ttp) REVERT: A 269 GLU cc_start: 0.8743 (mp0) cc_final: 0.8355 (pm20) REVERT: A 279 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7581 (pp20) REVERT: A 336 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7561 (mm-30) REVERT: A 338 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8668 (tp) REVERT: B 394 GLU cc_start: 0.8833 (tm-30) cc_final: 0.7990 (tm-30) REVERT: B 490 MET cc_start: 0.7564 (mtm) cc_final: 0.7289 (mtp) REVERT: B 494 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7643 (tm-30) REVERT: B 546 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6077 (mtm110) REVERT: B 550 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8629 (mpp80) REVERT: B 595 LYS cc_start: 0.8996 (tptt) cc_final: 0.8779 (tppt) REVERT: C 234 MET cc_start: 0.1985 (tmm) cc_final: 0.1755 (ptp) REVERT: C 390 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.5941 (ptm-80) REVERT: C 420 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9032 (t) REVERT: C 603 GLN cc_start: 0.5978 (mp-120) cc_final: 0.5718 (mp10) REVERT: C 703 MET cc_start: 0.4298 (mmp) cc_final: 0.3806 (mmt) REVERT: C 707 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7711 (tmm) REVERT: E 414 MET cc_start: 0.7297 (tmm) cc_final: 0.6902 (tmm) REVERT: E 747 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7148 (pm20) REVERT: F 256 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8271 (pm20) REVERT: F 414 MET cc_start: 0.8489 (mmm) cc_final: 0.8047 (mmm) REVERT: F 515 GLN cc_start: 0.8137 (pp30) cc_final: 0.7776 (pp30) REVERT: F 614 LEU cc_start: 0.8960 (tp) cc_final: 0.8642 (tp) REVERT: F 615 LEU cc_start: 0.8213 (tp) cc_final: 0.7791 (tt) outliers start: 110 outliers final: 70 residues processed: 362 average time/residue: 0.2078 time to fit residues: 129.6641 Evaluate side-chains 344 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 264 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 629 ASN Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 666 TYR Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 707 MET Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 325 TYR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain D residue 703 MET Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 547 ASN Chi-restraints excluded: chain E residue 599 VAL Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 628 VAL Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain E residue 747 GLU Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 457 THR Chi-restraints excluded: chain F residue 492 VAL Chi-restraints excluded: chain F residue 514 PHE Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 649 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 37 optimal weight: 3.9990 chunk 358 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 263 optimal weight: 1.9990 chunk 347 optimal weight: 0.8980 chunk 390 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 343 optimal weight: 0.5980 chunk 184 optimal weight: 7.9990 chunk 239 optimal weight: 30.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 HIS ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.115293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.100123 restraints weight = 114006.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.102108 restraints weight = 60715.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.103359 restraints weight = 38416.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.104106 restraints weight = 27730.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.104710 restraints weight = 22431.987| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 37652 Z= 0.176 Angle : 0.691 13.512 51063 Z= 0.339 Chirality : 0.046 0.263 5793 Planarity : 0.005 0.080 6620 Dihedral : 6.824 107.166 5289 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.02 % Allowed : 17.68 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.13), residues: 4618 helix: 0.22 (0.12), residues: 2049 sheet: -1.52 (0.22), residues: 560 loop : -1.40 (0.14), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 231 TYR 0.024 0.002 TYR D 228 PHE 0.021 0.002 PHE C 247 TRP 0.037 0.002 TRP F 512 HIS 0.006 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00405 (37651) covalent geometry : angle 0.69100 (51063) hydrogen bonds : bond 0.03514 ( 1538) hydrogen bonds : angle 5.15649 ( 4491) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 277 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 PHE cc_start: 0.5661 (p90) cc_final: 0.5368 (p90) REVERT: A 263 MET cc_start: 0.7644 (ppp) cc_final: 0.7328 (ttp) REVERT: A 269 GLU cc_start: 0.8734 (mp0) cc_final: 0.8273 (pm20) REVERT: A 279 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7533 (pp20) REVERT: A 338 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8613 (tp) REVERT: A 356 LEU cc_start: 0.8682 (tp) cc_final: 0.8461 (tp) REVERT: A 548 LEU cc_start: 0.9252 (tt) cc_final: 0.8878 (tp) REVERT: B 394 GLU cc_start: 0.8813 (tm-30) cc_final: 0.7979 (tm-30) REVERT: B 494 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7626 (tm-30) REVERT: B 546 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.5887 (mtm110) REVERT: B 550 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8551 (mpp80) REVERT: B 595 LYS cc_start: 0.8976 (tptt) cc_final: 0.8709 (tppt) REVERT: C 366 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8308 (mttm) REVERT: C 390 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.5936 (ptm-80) REVERT: C 420 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.8985 (t) REVERT: C 703 MET cc_start: 0.4285 (mmp) cc_final: 0.3839 (mmt) REVERT: E 414 MET cc_start: 0.7349 (tmm) cc_final: 0.7052 (tmm) REVERT: E 533 GLU cc_start: 0.8063 (tt0) cc_final: 0.7858 (pt0) REVERT: E 747 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7107 (pm20) REVERT: F 256 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8296 (pm20) REVERT: F 414 MET cc_start: 0.8505 (mmm) cc_final: 0.8178 (mmm) REVERT: F 515 GLN cc_start: 0.8069 (pp30) cc_final: 0.7694 (pp30) REVERT: F 614 LEU cc_start: 0.8799 (tp) cc_final: 0.8595 (tp) outliers start: 79 outliers final: 60 residues processed: 335 average time/residue: 0.2068 time to fit residues: 120.7243 Evaluate side-chains 336 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 267 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 666 TYR Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 325 TYR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain D residue 703 MET Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 599 VAL Chi-restraints excluded: chain E residue 628 VAL Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain E residue 747 GLU Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 457 THR Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 617 ILE Chi-restraints excluded: chain F residue 649 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 315 optimal weight: 50.0000 chunk 424 optimal weight: 7.9990 chunk 414 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 431 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 ASN ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.117163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.101976 restraints weight = 112926.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.103978 restraints weight = 60128.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.105281 restraints weight = 38091.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.106045 restraints weight = 27489.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.106698 restraints weight = 22202.742| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37652 Z= 0.133 Angle : 0.676 14.084 51063 Z= 0.329 Chirality : 0.045 0.219 5793 Planarity : 0.005 0.081 6620 Dihedral : 6.734 104.317 5289 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.89 % Allowed : 18.03 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.13), residues: 4618 helix: 0.28 (0.12), residues: 2058 sheet: -1.42 (0.23), residues: 545 loop : -1.38 (0.15), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 231 TYR 0.024 0.001 TYR D 228 PHE 0.016 0.001 PHE C 247 TRP 0.059 0.002 TRP E 568 HIS 0.005 0.001 HIS B 671 Details of bonding type rmsd covalent geometry : bond 0.00313 (37651) covalent geometry : angle 0.67565 (51063) hydrogen bonds : bond 0.03392 ( 1538) hydrogen bonds : angle 5.03934 ( 4491) Misc. bond : bond 0.00008 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9236 Ramachandran restraints generated. 4618 Oldfield, 0 Emsley, 4618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 294 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 PHE cc_start: 0.5700 (p90) cc_final: 0.5421 (p90) REVERT: A 263 MET cc_start: 0.7536 (ppp) cc_final: 0.7243 (ttp) REVERT: A 269 GLU cc_start: 0.8716 (mp0) cc_final: 0.8230 (pm20) REVERT: A 336 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7631 (mm-30) REVERT: A 338 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8579 (tp) REVERT: A 356 LEU cc_start: 0.8654 (tp) cc_final: 0.8443 (tp) REVERT: A 548 LEU cc_start: 0.9196 (tt) cc_final: 0.8748 (tp) REVERT: B 494 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7187 (tm-30) REVERT: B 546 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.5818 (mtm110) REVERT: B 550 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8341 (mpp80) REVERT: B 595 LYS cc_start: 0.8954 (tptt) cc_final: 0.8666 (tppt) REVERT: B 638 MET cc_start: 0.8101 (tpp) cc_final: 0.7897 (tpp) REVERT: C 366 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7976 (mttm) REVERT: C 390 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.5766 (ptm-80) REVERT: C 420 VAL cc_start: 0.9242 (OUTLIER) cc_final: 0.8913 (t) REVERT: C 703 MET cc_start: 0.4292 (mmp) cc_final: 0.3771 (mmt) REVERT: D 638 MET cc_start: 0.8269 (pmm) cc_final: 0.8068 (pmm) REVERT: D 694 SER cc_start: 0.8071 (OUTLIER) cc_final: 0.7279 (p) REVERT: D 753 GLU cc_start: 0.7516 (tp30) cc_final: 0.7214 (tp30) REVERT: E 234 MET cc_start: -0.1378 (pmm) cc_final: -0.1674 (pmm) REVERT: E 414 MET cc_start: 0.7544 (tmm) cc_final: 0.7268 (tmm) REVERT: E 533 GLU cc_start: 0.8107 (tt0) cc_final: 0.7899 (pt0) REVERT: E 747 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7123 (pm20) REVERT: F 256 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8277 (pm20) REVERT: F 414 MET cc_start: 0.8529 (mmm) cc_final: 0.8213 (mmm) REVERT: F 515 GLN cc_start: 0.7997 (pp30) cc_final: 0.7693 (pp30) REVERT: F 614 LEU cc_start: 0.8720 (tp) cc_final: 0.8286 (tp) outliers start: 74 outliers final: 48 residues processed: 345 average time/residue: 0.2017 time to fit residues: 120.2051 Evaluate side-chains 338 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 280 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 546 ARG Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 666 TYR Chi-restraints excluded: chain C residue 671 HIS Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 325 TYR Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain D residue 703 MET Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain E residue 599 VAL Chi-restraints excluded: chain E residue 628 VAL Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain E residue 747 GLU Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 342 GLN Chi-restraints excluded: chain F residue 457 THR Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 617 ILE Chi-restraints excluded: chain F residue 649 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 170 optimal weight: 50.0000 chunk 143 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 402 optimal weight: 20.0000 chunk 118 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 221 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.114977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.099730 restraints weight = 113922.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.101689 restraints weight = 61049.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.102899 restraints weight = 38894.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.103785 restraints weight = 28395.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104327 restraints weight = 22559.167| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 37652 Z= 0.196 Angle : 0.705 13.444 51063 Z= 0.346 Chirality : 0.046 0.211 5793 Planarity : 0.005 0.080 6620 Dihedral : 6.706 97.907 5289 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.79 % Allowed : 18.34 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.13), residues: 4618 helix: 0.26 (0.12), residues: 2064 sheet: -1.42 (0.23), residues: 549 loop : -1.42 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 231 TYR 0.023 0.002 TYR F 337 PHE 0.020 0.002 PHE C 247 TRP 0.044 0.002 TRP E 568 HIS 0.006 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00452 (37651) covalent geometry : angle 0.70543 (51063) hydrogen bonds : bond 0.03530 ( 1538) hydrogen bonds : angle 5.11283 ( 4491) Misc. bond : bond 0.00055 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5058.72 seconds wall clock time: 88 minutes 39.02 seconds (5319.02 seconds total)