Starting phenix.real_space_refine on Sat Mar 7 00:52:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y5c_33616/03_2026/7y5c_33616.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5c_33616/03_2026/7y5c_33616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y5c_33616/03_2026/7y5c_33616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5c_33616/03_2026/7y5c_33616.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y5c_33616/03_2026/7y5c_33616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5c_33616/03_2026/7y5c_33616.map" } resolution = 4.7 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= 0.001 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: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 5 5.21 5 S 106 5.16 5 C 22837 2.51 5 N 6247 2.21 5 O 6781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s 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: 35993 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3925 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 22, 'TRANS': 504} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 9} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3777 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 20, 'TRANS': 484} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3790 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 484} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3528 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3503 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3508 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2220 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 862 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 32 Chain: "a" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1604 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "b" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1055 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 141} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "d" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3007 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 11, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 147 Chain: "7" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} 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: "8" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 552 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "9" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 548 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "1" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 564 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "2" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 554 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "3" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "4" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "5" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 573 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 78} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "6" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 564 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.26, per 1000 atoms: 0.23 Number of scatterers: 35993 At special positions: 0 Unit cell: (174.9, 126.5, 237.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 106 16.00 P 17 15.00 Mg 5 11.99 O 6781 8.00 N 6247 7.00 C 22837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.4 seconds 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8732 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 28 sheets defined 59.0% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.933A pdb=" N ASP A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 195 removed outlier: 3.939A pdb=" N VAL A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 200 Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'A' and resid 242 through 264 removed outlier: 3.905A pdb=" N LYS A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Proline residue: A 250 - end of helix removed outlier: 3.777A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A 263 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 298 through 299 No H-bonds generated for 'chain 'A' and resid 298 through 299' Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 339 through 347 removed outlier: 3.824A pdb=" N THR A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 377 through 381 removed outlier: 4.201A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 381 " --> pdb=" O GLY A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 381' Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 392 through 407 Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 440 through 453 removed outlier: 3.525A pdb=" N GLN A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 478 removed outlier: 3.629A pdb=" N GLU A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 473 " --> pdb=" O SER A 469 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 removed outlier: 3.505A pdb=" N ASP A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 Processing helix chain 'B' and resid 12 through 22 removed outlier: 4.346A pdb=" N PHE B 22 " --> pdb=" O TYR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.848A pdb=" N GLN B 141 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 142 " --> pdb=" O VAL B 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 138 through 142' Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.719A pdb=" N ASP B 157 " --> pdb=" O ILE B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 189 through 195 Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.785A pdb=" N LYS B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Proline residue: B 250 - end of helix removed outlier: 3.837A pdb=" N ASN B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 298 through 299 No H-bonds generated for 'chain 'B' and resid 298 through 299' Processing helix chain 'B' and resid 300 through 310 removed outlier: 3.658A pdb=" N GLU B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 362 removed outlier: 3.722A pdb=" N PHE B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 362 " --> pdb=" O ASP B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.567A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 removed outlier: 4.225A pdb=" N GLY B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 405 removed outlier: 3.900A pdb=" N ASP B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 4.560A pdb=" N PHE B 409 " --> pdb=" O PHE B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 432 removed outlier: 3.759A pdb=" N LYS B 432 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 removed outlier: 3.565A pdb=" N GLN B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 479 removed outlier: 3.734A pdb=" N HIS B 479 " --> pdb=" O VAL B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 493 through 510 removed outlier: 3.856A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 22 removed outlier: 3.799A pdb=" N PHE C 22 " --> pdb=" O TYR C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.540A pdb=" N ASP C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 195 removed outlier: 3.841A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 264 removed outlier: 3.778A pdb=" N LYS C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) Proline residue: C 250 - end of helix removed outlier: 3.641A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 298 through 299 No H-bonds generated for 'chain 'C' and resid 298 through 299' Processing helix chain 'C' and resid 300 through 311 removed outlier: 4.193A pdb=" N ARG C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 356 through 363 removed outlier: 3.858A pdb=" N PHE C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 382 removed outlier: 3.934A pdb=" N ALA C 381 " --> pdb=" O GLY C 378 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN C 382 " --> pdb=" O GLY C 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 378 through 382' Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 392 through 404 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 431 Processing helix chain 'C' and resid 440 through 454 Processing helix chain 'C' and resid 463 through 478 Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 493 through 511 Processing helix chain 'D' and resid 126 through 130 Processing helix chain 'D' and resid 141 through 147 Processing helix chain 'D' and resid 165 through 180 removed outlier: 4.012A pdb=" N ARG D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 207 removed outlier: 3.535A pdb=" N ALA D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 211 removed outlier: 3.777A pdb=" N LYS D 211 " --> pdb=" O ASN D 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 208 through 211' Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 229 through 246 removed outlier: 3.522A pdb=" N GLU D 244 " --> pdb=" O PHE D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 271 removed outlier: 3.814A pdb=" N THR D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 292 Processing helix chain 'D' and resid 311 through 314 Processing helix chain 'D' and resid 317 through 325 removed outlier: 3.630A pdb=" N ALA D 321 " --> pdb=" O ASP D 317 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 341 removed outlier: 3.831A pdb=" N PHE D 338 " --> pdb=" O SER D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 389 removed outlier: 3.851A pdb=" N TYR D 366 " --> pdb=" O GLY D 362 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 394 Processing helix chain 'D' and resid 395 through 412 Processing helix chain 'D' and resid 416 through 420 Processing helix chain 'D' and resid 431 through 445 removed outlier: 3.728A pdb=" N THR D 435 " --> pdb=" O PRO D 431 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 456 removed outlier: 3.634A pdb=" N PHE D 455 " --> pdb=" O GLU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 471 Processing helix chain 'E' and resid 141 through 148 Processing helix chain 'E' and resid 165 through 180 removed outlier: 3.566A pdb=" N LEU E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 207 Processing helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' Processing helix chain 'E' and resid 223 through 246 removed outlier: 4.025A pdb=" N ARG E 227 " --> pdb=" O PRO E 223 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 270 removed outlier: 3.606A pdb=" N LEU E 270 " --> pdb=" O VAL E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 292 Processing helix chain 'E' and resid 310 through 314 removed outlier: 4.181A pdb=" N ASP E 313 " --> pdb=" O VAL E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 324 Processing helix chain 'E' and resid 325 through 327 No H-bonds generated for 'chain 'E' and resid 325 through 327' Processing helix chain 'E' and resid 335 through 341 Processing helix chain 'E' and resid 347 through 351 removed outlier: 3.934A pdb=" N SER E 351 " --> pdb=" O PRO E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 389 removed outlier: 4.487A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 413 removed outlier: 3.979A pdb=" N SER E 413 " --> pdb=" O GLU E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 431 through 444 removed outlier: 4.159A pdb=" N LYS E 444 " --> pdb=" O ASP E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 456 removed outlier: 3.761A pdb=" N PHE E 456 " --> pdb=" O GLN E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 470 Processing helix chain 'F' and resid 91 through 95 removed outlier: 3.742A pdb=" N VAL F 94 " --> pdb=" O GLY F 91 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS F 95 " --> pdb=" O ASP F 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 91 through 95' Processing helix chain 'F' and resid 141 through 148 removed outlier: 3.916A pdb=" N ASP F 145 " --> pdb=" O LEU F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 181 Processing helix chain 'F' and resid 193 through 207 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 223 through 246 removed outlier: 3.603A pdb=" N ARG F 227 " --> pdb=" O PRO F 223 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN F 245 " --> pdb=" O PHE F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 271 removed outlier: 4.427A pdb=" N PHE F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR F 260 " --> pdb=" O ILE F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 283 through 293 Processing helix chain 'F' and resid 310 through 314 removed outlier: 4.218A pdb=" N ASP F 313 " --> pdb=" O VAL F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 324 removed outlier: 3.761A pdb=" N THR F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 327 No H-bonds generated for 'chain 'F' and resid 325 through 327' Processing helix chain 'F' and resid 334 through 341 removed outlier: 3.512A pdb=" N PHE F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY F 341 " --> pdb=" O VAL F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 387 removed outlier: 4.269A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 412 removed outlier: 4.383A pdb=" N LEU F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.711A pdb=" N ALA F 419 " --> pdb=" O MET F 416 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 445 removed outlier: 3.535A pdb=" N GLY F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 456 removed outlier: 3.575A pdb=" N ALA F 454 " --> pdb=" O PRO F 451 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE F 456 " --> pdb=" O GLN F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 470 Processing helix chain 'G' and resid 5 through 41 removed outlier: 3.690A pdb=" N ALA G 34 " --> pdb=" O THR G 30 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU G 41 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 60 removed outlier: 3.948A pdb=" N ALA G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 108 Processing helix chain 'G' and resid 109 through 111 No H-bonds generated for 'chain 'G' and resid 109 through 111' Processing helix chain 'G' and resid 120 through 130 Processing helix chain 'G' and resid 146 through 163 removed outlier: 4.149A pdb=" N ALA G 150 " --> pdb=" O THR G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 176 Processing helix chain 'G' and resid 227 through 302 Proline residue: G 237 - end of helix removed outlier: 3.661A pdb=" N LEU G 248 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU G 249 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG G 261 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA G 262 " --> pdb=" O SER G 258 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET G 263 " --> pdb=" O ARG G 259 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP G 272 " --> pdb=" O ASP G 268 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU G 273 " --> pdb=" O ASN G 269 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA G 302 " --> pdb=" O GLY G 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 101 removed outlier: 3.765A pdb=" N SER H 101 " --> pdb=" O GLU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 116 Processing helix chain 'a' and resid 33 through 53 removed outlier: 3.854A pdb=" N ALA a 51 " --> pdb=" O PHE a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 79 removed outlier: 4.173A pdb=" N PHE a 65 " --> pdb=" O GLY a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 106 removed outlier: 3.920A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 130 through 152 removed outlier: 3.987A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA a 148 " --> pdb=" O CYS a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 164 Processing helix chain 'a' and resid 170 through 206 Proline residue: a 182 - end of helix removed outlier: 4.390A pdb=" N PHE a 206 " --> pdb=" O LEU a 202 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 246 removed outlier: 3.610A pdb=" N THR a 220 " --> pdb=" O ALA a 216 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU a 246 " --> pdb=" O SER a 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 48 removed outlier: 4.289A pdb=" N VAL b 34 " --> pdb=" O THR b 30 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU b 35 " --> pdb=" O PHE b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 59 removed outlier: 4.033A pdb=" N ILE b 53 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS b 55 " --> pdb=" O PRO b 51 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL b 56 " --> pdb=" O PRO b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 60 through 145 removed outlier: 3.773A pdb=" N SER b 74 " --> pdb=" O ASP b 70 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ALA b 75 " --> pdb=" O ASN b 71 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLN b 131 " --> pdb=" O THR b 127 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER b 134 " --> pdb=" O ASP b 130 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN b 139 " --> pdb=" O ALA b 135 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU b 145 " --> pdb=" O ARG b 141 " (cutoff:3.500A) Processing helix chain 'b' and resid 147 through 161 Processing helix chain 'd' and resid 3 through 18 removed outlier: 4.507A pdb=" N ILE d 9 " --> pdb=" O ILE d 5 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY d 10 " --> pdb=" O GLY d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 19 through 21 No H-bonds generated for 'chain 'd' and resid 19 through 21' Processing helix chain 'd' and resid 22 through 54 removed outlier: 3.714A pdb=" N VAL d 26 " --> pdb=" O VAL d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 136 removed outlier: 4.222A pdb=" N LYS d 60 " --> pdb=" O ALA d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 157 removed outlier: 3.836A pdb=" N GLN d 143 " --> pdb=" O ASP d 139 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER d 144 " --> pdb=" O PRO d 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 191 Processing helix chain 'd' and resid 192 through 194 No H-bonds generated for 'chain 'd' and resid 192 through 194' Processing helix chain 'd' and resid 197 through 216 removed outlier: 3.581A pdb=" N GLU d 216 " --> pdb=" O LEU d 212 " (cutoff:3.500A) Processing helix chain 'd' and resid 216 through 224 removed outlier: 4.241A pdb=" N ASN d 220 " --> pdb=" O GLU d 216 " (cutoff:3.500A) Processing helix chain 'd' and resid 230 through 240 Processing helix chain 'd' and resid 241 through 245 removed outlier: 3.554A pdb=" N LYS d 244 " --> pdb=" O LEU d 241 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL d 245 " --> pdb=" O SER d 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 241 through 245' Processing helix chain 'd' and resid 246 through 259 Processing helix chain 'd' and resid 263 through 285 removed outlier: 3.708A pdb=" N VAL d 271 " --> pdb=" O LEU d 267 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU d 272 " --> pdb=" O ILE d 268 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 306 removed outlier: 3.745A pdb=" N GLU d 306 " --> pdb=" O VAL d 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 313 removed outlier: 3.805A pdb=" N SER d 310 " --> pdb=" O GLU d 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 321 through 331 Processing helix chain 'd' and resid 338 through 352 Processing helix chain 'd' and resid 356 through 372 removed outlier: 3.978A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 386 through 401 Processing helix chain 'd' and resid 431 through 442 Processing helix chain '7' and resid 6 through 46 removed outlier: 3.739A pdb=" N ALA 7 44 " --> pdb=" O ILE 7 40 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG 7 45 " --> pdb=" O SER 7 41 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN 7 46 " --> pdb=" O GLY 7 42 " (cutoff:3.500A) Processing helix chain '7' and resid 49 through 52 Processing helix chain '7' and resid 53 through 81 removed outlier: 3.679A pdb=" N VAL 7 64 " --> pdb=" O THR 7 60 " (cutoff:3.500A) Processing helix chain '8' and resid 6 through 46 Processing helix chain '8' and resid 50 through 80 removed outlier: 4.485A pdb=" N THR 8 55 " --> pdb=" O GLY 8 51 " (cutoff:3.500A) Proline residue: 8 56 - end of helix removed outlier: 4.203A pdb=" N PHE 8 80 " --> pdb=" O ALA 8 76 " (cutoff:3.500A) Processing helix chain '9' and resid 6 through 46 Processing helix chain '9' and resid 53 through 81 removed outlier: 4.032A pdb=" N PHE 9 57 " --> pdb=" O LEU 9 53 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE 9 80 " --> pdb=" O ALA 9 76 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA 9 81 " --> pdb=" O LEU 9 77 " (cutoff:3.500A) Processing helix chain '1' and resid 6 through 46 Processing helix chain '1' and resid 54 through 79 removed outlier: 3.792A pdb=" N ALA 1 67 " --> pdb=" O LEU 1 63 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR 1 68 " --> pdb=" O VAL 1 64 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU 1 77 " --> pdb=" O ALA 1 73 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE 1 78 " --> pdb=" O PHE 1 74 " (cutoff:3.500A) Processing helix chain '2' and resid 6 through 43 removed outlier: 3.791A pdb=" N ILE 2 43 " --> pdb=" O LEU 2 39 " (cutoff:3.500A) Processing helix chain '2' and resid 54 through 81 Processing helix chain '3' and resid 6 through 46 removed outlier: 3.712A pdb=" N ARG 3 45 " --> pdb=" O SER 3 41 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN 3 46 " --> pdb=" O GLY 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 49 through 52 Processing helix chain '3' and resid 53 through 81 removed outlier: 3.946A pdb=" N PHE 3 57 " --> pdb=" O LEU 3 53 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU 3 63 " --> pdb=" O ILE 3 59 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL 3 64 " --> pdb=" O THR 3 60 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA 3 81 " --> pdb=" O LEU 3 77 " (cutoff:3.500A) Processing helix chain '4' and resid 6 through 46 removed outlier: 4.097A pdb=" N THR 4 10 " --> pdb=" O ASN 4 6 " (cutoff:3.500A) Processing helix chain '4' and resid 54 through 81 Processing helix chain '5' and resid 4 through 43 removed outlier: 4.196A pdb=" N ILE 5 8 " --> pdb=" O ASP 5 4 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 52 Processing helix chain '5' and resid 53 through 82 removed outlier: 3.876A pdb=" N PHE 5 57 " --> pdb=" O LEU 5 53 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU 5 63 " --> pdb=" O ILE 5 59 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL 5 64 " --> pdb=" O THR 5 60 " (cutoff:3.500A) Processing helix chain '6' and resid 7 through 46 removed outlier: 4.168A pdb=" N ALA 6 11 " --> pdb=" O ALA 6 7 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY 6 12 " --> pdb=" O ILE 6 8 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN 6 46 " --> pdb=" O GLY 6 42 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 81 removed outlier: 3.582A pdb=" N PHE 6 57 " --> pdb=" O LEU 6 53 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA 6 81 " --> pdb=" O LEU 6 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 4.652A pdb=" N GLU A 29 " --> pdb=" O VAL d 427 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL d 427 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 38 removed outlier: 6.367A pdb=" N VAL A 34 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 36 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 68 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL A 77 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA A 66 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU A 54 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU A 55 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 92 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 102 removed outlier: 3.688A pdb=" N THR A 128 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.229A pdb=" N VAL A 111 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 233 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A 271 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331 removed outlier: 6.463A pdb=" N ILE A 170 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 171 " --> pdb=" O CYS A 353 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 534 through 535 removed outlier: 6.950A pdb=" N GLU A 534 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR G 197 " --> pdb=" O GLU G 189 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 13.442A pdb=" N PHE G 190 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N TRP G 138 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL G 118 " --> pdb=" O TRP G 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 540 removed outlier: 5.893A pdb=" N VAL A 538 " --> pdb=" O GLU G 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 31 through 38 removed outlier: 5.286A pdb=" N VAL B 34 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 41 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 42 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 102 Processing sheet with id=AB1, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.087A pdb=" N ALA B 236 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 233 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 270 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 325 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 271 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 329 through 331 removed outlier: 6.556A pdb=" N ILE B 170 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE B 171 " --> pdb=" O LEU B 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 44 through 45 removed outlier: 3.523A pdb=" N GLU C 45 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY C 32 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 91 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 57 " --> pdb=" O LYS C 92 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR C 94 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU C 55 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU C 63 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 99 through 102 removed outlier: 3.562A pdb=" N VAL C 100 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG C 130 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 110 through 111 removed outlier: 3.608A pdb=" N THR C 233 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 207 " --> pdb=" O VAL C 270 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 11 through 16 removed outlier: 3.646A pdb=" N VAL D 13 " --> pdb=" O ASP D 21 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL D 53 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS D 47 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE D 40 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 87 through 89 removed outlier: 3.512A pdb=" N TRP D 118 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 98 through 99 removed outlier: 6.453A pdb=" N PHE D 99 " --> pdb=" O PHE D 217 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA D 307 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE D 156 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL D 308 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU D 158 " --> pdb=" O VAL D 308 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LYS D 155 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR D 331 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ALA D 157 " --> pdb=" O THR D 331 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 16 removed outlier: 5.608A pdb=" N VAL E 12 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU E 23 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG E 14 " --> pdb=" O ASP E 21 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE E 65 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU E 52 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS E 47 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU E 39 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLU E 78 " --> pdb=" O GLU E 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 87 through 90 Processing sheet with id=AC2, first strand: chain 'E' and resid 136 through 137 removed outlier: 4.358A pdb=" N TYR E 150 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 213 through 217 removed outlier: 3.750A pdb=" N ALA E 214 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE E 156 " --> pdb=" O GLN E 306 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA E 329 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR E 330 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER E 352 " --> pdb=" O THR E 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 16 removed outlier: 5.683A pdb=" N VAL F 12 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU F 23 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG F 14 " --> pdb=" O ASP F 21 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU F 61 " --> pdb=" O HIS F 56 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N HIS F 56 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG F 63 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 87 through 90 Processing sheet with id=AC6, first strand: chain 'F' and resid 98 through 99 removed outlier: 3.549A pdb=" N VAL F 216 " --> pdb=" O PHE F 187 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 98 through 99 removed outlier: 3.549A pdb=" N VAL F 216 " --> pdb=" O PHE F 187 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE F 156 " --> pdb=" O GLN F 306 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 136 through 137 removed outlier: 3.738A pdb=" N TYR F 150 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 223 through 224 removed outlier: 4.214A pdb=" N VAL H 42 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU H 80 " --> pdb=" O PHE H 69 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER H 71 " --> pdb=" O ARG H 78 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG H 78 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL H 9 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU H 4 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TRP H 16 " --> pdb=" O ILE H 8 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 31 through 33 removed outlier: 3.603A pdb=" N THR H 25 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE H 22 " --> pdb=" O GLU H 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA H 49 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA H 64 " --> pdb=" O GLN H 85 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN H 85 " --> pdb=" O ALA H 64 " (cutoff:3.500A) 2196 hydrogen bonds defined for protein. 6396 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: 7.26 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12067 1.34 - 1.46: 5398 1.46 - 1.58: 18911 1.58 - 1.70: 27 1.70 - 1.82: 192 Bond restraints: 36595 Sorted by residual: bond pdb=" N GLU A 295 " pdb=" CA GLU A 295 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.50e+00 bond pdb=" C PRO b 51 " pdb=" N PRO b 52 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.27e+00 bond pdb=" CA GLY B 363 " pdb=" C GLY B 363 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.51e+00 bond pdb=" CA PRO F 223 " pdb=" C PRO F 223 " ideal model delta sigma weight residual 1.514 1.523 -0.009 5.50e-03 3.31e+04 2.49e+00 bond pdb=" CG1 ILE 7 26 " pdb=" CD1 ILE 7 26 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.92e+00 ... (remaining 36590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 49094 2.28 - 4.55: 487 4.55 - 6.83: 91 6.83 - 9.11: 14 9.11 - 11.39: 1 Bond angle restraints: 49687 Sorted by residual: angle pdb=" N ILE E 458 " pdb=" CA ILE E 458 " pdb=" C ILE E 458 " ideal model delta sigma weight residual 113.71 108.35 5.36 9.50e-01 1.11e+00 3.18e+01 angle pdb=" N VAL E 209 " pdb=" CA VAL E 209 " pdb=" C VAL E 209 " ideal model delta sigma weight residual 113.20 108.53 4.67 9.60e-01 1.09e+00 2.37e+01 angle pdb=" N ILE B 337 " pdb=" CA ILE B 337 " pdb=" C ILE B 337 " ideal model delta sigma weight residual 113.53 109.64 3.89 9.80e-01 1.04e+00 1.58e+01 angle pdb=" C PHE 1 74 " pdb=" N MET 1 75 " pdb=" CA MET 1 75 " ideal model delta sigma weight residual 122.06 115.48 6.58 1.86e+00 2.89e-01 1.25e+01 angle pdb=" N ILE D 355 " pdb=" CA ILE D 355 " pdb=" C ILE D 355 " ideal model delta sigma weight residual 113.20 109.97 3.23 9.60e-01 1.09e+00 1.13e+01 ... (remaining 49682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.14: 20720 26.14 - 52.28: 1040 52.28 - 78.42: 123 78.42 - 104.56: 18 104.56 - 130.70: 1 Dihedral angle restraints: 21902 sinusoidal: 8272 harmonic: 13630 Sorted by residual: dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual 300.00 169.30 130.70 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" CA ARG A 294 " pdb=" C ARG A 294 " pdb=" N GLU A 295 " pdb=" CA GLU A 295 " ideal model delta harmonic sigma weight residual -180.00 -157.04 -22.96 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" O2A ADP E 501 " pdb=" O3A ADP E 501 " pdb=" PA ADP E 501 " pdb=" PB ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 -134.55 74.55 1 2.00e+01 2.50e-03 1.76e+01 ... (remaining 21899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 4201 0.039 - 0.077: 1169 0.077 - 0.116: 397 0.116 - 0.154: 57 0.154 - 0.193: 4 Chirality restraints: 5828 Sorted by residual: chirality pdb=" CA GLU A 295 " pdb=" N GLU A 295 " pdb=" C GLU A 295 " pdb=" CB GLU A 295 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CB ILE 6 20 " pdb=" CA ILE 6 20 " pdb=" CG1 ILE 6 20 " pdb=" CG2 ILE 6 20 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CA LYS a 181 " pdb=" N LYS a 181 " pdb=" C LYS a 181 " pdb=" CB LYS a 181 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 5825 not shown) Planarity restraints: 6459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE 4 54 " 0.025 2.00e-02 2.50e+03 2.11e-02 7.77e+00 pdb=" CG PHE 4 54 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE 4 54 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE 4 54 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE 4 54 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE 4 54 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE 4 54 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 257 " -0.015 2.00e-02 2.50e+03 1.88e-02 6.20e+00 pdb=" CG PHE D 257 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE D 257 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE D 257 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE D 257 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 257 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 257 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP 6 32 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C ASP 6 32 " 0.041 2.00e-02 2.50e+03 pdb=" O ASP 6 32 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY 6 33 " -0.014 2.00e-02 2.50e+03 ... (remaining 6456 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 219 2.51 - 3.11: 27618 3.11 - 3.71: 56901 3.71 - 4.30: 70530 4.30 - 4.90: 116957 Nonbonded interactions: 272225 Sorted by model distance: nonbonded pdb="MG MG D 500 " pdb=" O2A ATP D 501 " model vdw 1.916 2.170 nonbonded pdb="MG MG D 500 " pdb=" O1B ATP D 501 " model vdw 1.925 2.170 nonbonded pdb="MG MG F 500 " pdb=" O3B ATP F 501 " model vdw 1.963 2.170 nonbonded pdb="MG MG A 600 " pdb=" O1G ATP A 601 " model vdw 2.005 2.170 nonbonded pdb="MG MG B 600 " pdb=" O1A ATP B 601 " model vdw 2.008 2.170 ... (remaining 272220 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 '1' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '2' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 49 or (resid 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '3' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '4' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '5' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '6' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '7' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '8' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 84)) selection = (chain '9' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) } ncs_group { reference = (chain 'A' and (resid 11 through 18 or (resid 19 and (name N or name CA or name \ C or name O or name CB )) or resid 20 through 22 or resid 28 through 190 or (res \ id 191 through 192 and (name N or name CA or name C or name O or name CB )) or r \ esid 193 through 316 or (resid 317 through 318 and (name N or name CA or name C \ or name O or name CB )) or resid 319 through 400 or (resid 401 through 402 and ( \ name N or name CA or name C or name O or name CB )) or resid 403 through 456 or \ (resid 457 and (name N or name CA or name C or name O or name CB )) or resid 458 \ through 469 or (resid 470 and (name N or name CA or name C or name O or name CB \ )) or resid 471 through 493 or (resid 494 through 499 and (name N or name CA or \ name C or name O or name CB )) or resid 500 through 516 or resid 537 through 53 \ 8 or resid 540 or resid 600 through 601)) selection = (chain 'B' and ((resid 11 through 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 through 355 or (resid 356 and (name N \ or name CA or name C or name O or name CB )) or resid 357 or (resid 358 and (nam \ e N or name CA or name C or name O or name CB )) or resid 359 through 400 or (re \ sid 401 through 402 and (name N or name CA or name C or name O or name CB )) or \ resid 403 through 411 or (resid 412 and (name N or name CA or name C or name O o \ r name CB )) or resid 413 through 416 or (resid 417 through 419 and (name N or n \ ame CA or name C or name O or name CB )) or resid 420 through 461 or (resid 462 \ through 463 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 4 through 467 or (resid 468 and (name N or name CA or name C or name O or name C \ B )) or resid 469 or (resid 470 and (name N or name CA or name C or name O or na \ me CB )) or resid 471 through 494 or (resid 495 through 499 and (name N or name \ CA or name C or name O or name CB )) or resid 500 through 505 or (resid 506 and \ (name N or name CA or name C or name O or name CB )) or resid 507 through 516 or \ resid 518 through 601)) selection = (chain 'C' and ((resid 11 through 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 through 190 or (resid 191 through 192 \ and (name N or name CA or name C or name O or name CB )) or resid 193 through 31 \ 6 or (resid 317 through 318 and (name N or name CA or name C or name O or name C \ B )) or resid 319 through 355 or (resid 356 and (name N or name CA or name C or \ name O or name CB )) or resid 357 or (resid 358 and (name N or name CA or name C \ or name O or name CB )) or resid 359 through 401 or (resid 402 and (name N or n \ ame CA or name C or name O or name CB )) or resid 403 through 411 or (resid 412 \ and (name N or name CA or name C or name O or name CB )) or resid 413 through 41 \ 6 or (resid 417 through 419 and (name N or name CA or name C or name O or name C \ B )) or resid 420 through 456 or (resid 457 and (name N or name CA or name C or \ name O or name CB )) or resid 458 through 467 or (resid 468 and (name N or name \ CA or name C or name O or name CB )) or resid 469 through 493 or (resid 494 thro \ ugh 499 and (name N or name CA or name C or name O or name CB )) or resid 500 th \ rough 505 or (resid 506 and (name N or name CA or name C or name O or name CB )) \ or resid 507 through 516 or resid 518 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 103 or (resid 104 and (name N or name CA or name \ C or name O or name CB )) or resid 105 through 134 or (resid 135 and (name N or \ name CA or name C or name O or name CB )) or resid 136 through 198 or (resid 19 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 200 through \ 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) or re \ sid 204 through 220 or (resid 221 through 222 and (name N or name CA or name C o \ r name O or name CB )) or resid 223 through 291 or (resid 292 and (name N or nam \ e CA or name C or name O or name CB )) or resid 293 through 362 or (resid 363 th \ rough 364 and (name N or name CA or name C or name O or name CB )) or resid 365 \ through 369 or (resid 370 through 371 and (name N or name CA or name C or name O \ or name CB )) or resid 372 through 380 or (resid 381 and (name N or name CA or \ name C or name O or name CB )) or resid 382 through 383 or (resid 384 and (name \ N or name CA or name C or name O or name CB )) or resid 385 through 395 or (resi \ d 396 through 398 and (name N or name CA or name C or name O or name CB )) or re \ sid 399 through 402 or (resid 403 and (name N or name CA or name C or name O or \ name CB )) or resid 404 through 432 or (resid 433 and (name N or name CA or name \ C or name O or name CB )) or resid 434 through 461 or (resid 462 and (name N or \ name CA or name C or name O or name CB )) or resid 463 through 465 or (resid 46 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 467 through \ 471)) selection = (chain 'E' and (resid 8 through 103 or (resid 104 and (name N or name CA or name \ C or name O or name CB )) or resid 105 through 106 or (resid 107 and (name N or \ name CA or name C or name O or name CB )) or resid 108 through 198 or (resid 19 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 200 through \ 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) or re \ sid 204 through 285 or (resid 286 and (name N or name CA or name C or name O or \ name CB )) or resid 287 through 362 or (resid 363 through 364 and (name N or nam \ e CA or name C or name O or name CB )) or resid 365 through 369 or (resid 370 th \ rough 371 and (name N or name CA or name C or name O or name CB )) or resid 372 \ through 380 or (resid 381 and (name N or name CA or name C or name O or name CB \ )) or resid 382 through 402 or (resid 403 and (name N or name CA or name C or na \ me O or name CB )) or resid 404 through 424 or (resid 425 and (name N or name CA \ or name C or name O or name CB )) or resid 426 through 471)) selection = (chain 'F' and (resid 8 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 through 220 or (resid 221 through 222 an \ d (name N or name CA or name C or name O or name CB )) or resid 223 through 284 \ or (resid 285 through 286 and (name N or name CA or name C or name O or name CB \ )) or resid 287 through 288 or (resid 289 and (name N or name CA or name C or na \ me O or name CB )) or resid 290 through 291 or (resid 292 and (name N or name CA \ or name C or name O or name CB )) or resid 293 through 370 or (resid 371 and (n \ ame N or name CA or name C or name O or name CB )) or resid 372 through 395 or ( \ resid 396 through 398 and (name N or name CA or name C or name O or name CB )) o \ r resid 399 through 461 or (resid 462 and (name N or name CA or name C or name O \ or name CB )) or resid 463 through 465 or (resid 466 and (name N or name CA or \ name C or name O or name CB )) or resid 467 through 471)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.480 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 32.210 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36595 Z= 0.128 Angle : 0.596 11.386 49687 Z= 0.309 Chirality : 0.040 0.193 5828 Planarity : 0.004 0.053 6459 Dihedral : 14.530 130.699 13170 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.12), residues: 4795 helix: 1.82 (0.11), residues: 2527 sheet: 0.54 (0.24), residues: 470 loop : -0.82 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG d 38 TYR 0.024 0.001 TYR a 240 PHE 0.048 0.001 PHE 4 54 TRP 0.021 0.001 TRP a 66 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00256 (36595) covalent geometry : angle 0.59595 (49687) hydrogen bonds : bond 0.14423 ( 2190) hydrogen bonds : angle 5.47729 ( 6396) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8691 (tpt) cc_final: 0.8407 (tpt) REVERT: B 182 CYS cc_start: 0.8998 (m) cc_final: 0.8779 (m) REVERT: C 51 MET cc_start: 0.6846 (tpp) cc_final: 0.6130 (tpp) REVERT: E 64 CYS cc_start: 0.6716 (m) cc_final: 0.6477 (m) REVERT: G 187 PHE cc_start: 0.7595 (p90) cc_final: 0.7301 (p90) REVERT: a 240 TYR cc_start: 0.7470 (m-80) cc_final: 0.7261 (m-80) REVERT: d 157 MET cc_start: 0.8699 (ppp) cc_final: 0.8201 (ppp) REVERT: 2 65 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7752 (mm-30) REVERT: 2 69 PHE cc_start: 0.8449 (m-10) cc_final: 0.8201 (m-80) REVERT: 5 75 MET cc_start: 0.5811 (mmp) cc_final: 0.5501 (tmm) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1753 time to fit residues: 87.4820 Evaluate side-chains 203 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 470 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 HIS B 361 ASN B 369 ASN C 141 GLN D 55 GLN D 377 GLN E 247 GLN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.068378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.057398 restraints weight = 287847.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.057199 restraints weight = 262990.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.057242 restraints weight = 204690.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.057410 restraints weight = 181538.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.057600 restraints weight = 152851.335| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 36595 Z= 0.118 Angle : 0.545 10.704 49687 Z= 0.278 Chirality : 0.040 0.163 5828 Planarity : 0.004 0.058 6459 Dihedral : 6.753 96.939 5337 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.03 % Allowed : 6.02 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.12), residues: 4795 helix: 2.06 (0.10), residues: 2551 sheet: 0.65 (0.24), residues: 466 loop : -0.80 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 38 TYR 0.020 0.001 TYR a 240 PHE 0.035 0.001 PHE 4 54 TRP 0.014 0.001 TRP a 66 HIS 0.004 0.001 HIS E 365 Details of bonding type rmsd covalent geometry : bond 0.00242 (36595) covalent geometry : angle 0.54477 (49687) hydrogen bonds : bond 0.04428 ( 2190) hydrogen bonds : angle 4.16921 ( 6396) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASN cc_start: 0.8517 (t0) cc_final: 0.8307 (p0) REVERT: B 81 GLU cc_start: 0.5044 (tp30) cc_final: 0.4837 (tp30) REVERT: B 182 CYS cc_start: 0.8938 (m) cc_final: 0.8713 (m) REVERT: B 312 CYS cc_start: 0.8760 (m) cc_final: 0.8554 (m) REVERT: B 324 MET cc_start: 0.8008 (mpp) cc_final: 0.7637 (mpp) REVERT: B 325 THR cc_start: 0.7995 (m) cc_final: 0.7774 (p) REVERT: C 51 MET cc_start: 0.6859 (tpp) cc_final: 0.6346 (tpp) REVERT: C 149 LEU cc_start: 0.8488 (tt) cc_final: 0.8228 (tp) REVERT: C 270 VAL cc_start: 0.8532 (t) cc_final: 0.8265 (p) REVERT: F 21 ASP cc_start: 0.8533 (t0) cc_final: 0.8298 (t0) REVERT: F 67 MET cc_start: 0.8226 (mmp) cc_final: 0.7933 (mmm) REVERT: G 187 PHE cc_start: 0.7643 (p90) cc_final: 0.7310 (p90) REVERT: a 233 PHE cc_start: 0.8832 (t80) cc_final: 0.8472 (t80) REVERT: 1 21 MET cc_start: 0.5701 (tpt) cc_final: 0.5368 (mtt) REVERT: 2 65 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7747 (mm-30) REVERT: 2 69 PHE cc_start: 0.8533 (m-10) cc_final: 0.8269 (m-80) REVERT: 5 75 MET cc_start: 0.5738 (mmp) cc_final: 0.5440 (tmm) outliers start: 1 outliers final: 1 residues processed: 297 average time/residue: 0.1868 time to fit residues: 96.7619 Evaluate side-chains 216 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 242 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 286 optimal weight: 0.0970 chunk 107 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 253 optimal weight: 3.9990 chunk 285 optimal weight: 1.9990 chunk 113 optimal weight: 0.0370 chunk 100 optimal weight: 5.9990 overall best weight: 1.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 369 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 GLN D 55 GLN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.067430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.057027 restraints weight = 290298.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.056604 restraints weight = 281530.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.056907 restraints weight = 220705.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.056979 restraints weight = 186932.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.057010 restraints weight = 161602.780| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36595 Z= 0.139 Angle : 0.566 9.022 49687 Z= 0.287 Chirality : 0.041 0.165 5828 Planarity : 0.004 0.063 6459 Dihedral : 6.582 82.852 5337 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.12), residues: 4795 helix: 2.04 (0.10), residues: 2553 sheet: 0.64 (0.24), residues: 476 loop : -0.84 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 52 TYR 0.022 0.001 TYR a 240 PHE 0.035 0.001 PHE 6 69 TRP 0.011 0.001 TRP a 208 HIS 0.005 0.001 HIS E 365 Details of bonding type rmsd covalent geometry : bond 0.00301 (36595) covalent geometry : angle 0.56609 (49687) hydrogen bonds : bond 0.04466 ( 2190) hydrogen bonds : angle 4.10787 ( 6396) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 CYS cc_start: 0.8976 (m) cc_final: 0.8735 (m) REVERT: B 324 MET cc_start: 0.8182 (mpp) cc_final: 0.7882 (mpp) REVERT: C 51 MET cc_start: 0.6856 (tpp) cc_final: 0.6514 (tpp) REVERT: C 270 VAL cc_start: 0.8523 (t) cc_final: 0.8261 (p) REVERT: D 317 ASP cc_start: 0.8080 (t0) cc_final: 0.7859 (t0) REVERT: E 64 CYS cc_start: 0.7059 (m) cc_final: 0.6833 (m) REVERT: F 21 ASP cc_start: 0.8522 (t0) cc_final: 0.8216 (t0) REVERT: a 233 PHE cc_start: 0.8725 (t80) cc_final: 0.8449 (t80) REVERT: 2 65 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7694 (mm-30) REVERT: 2 69 PHE cc_start: 0.8443 (m-10) cc_final: 0.8175 (m-80) REVERT: 5 75 MET cc_start: 0.5962 (mmp) cc_final: 0.5606 (tmm) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.1845 time to fit residues: 91.0323 Evaluate side-chains 204 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 116 optimal weight: 8.9990 chunk 250 optimal weight: 0.9990 chunk 388 optimal weight: 2.9990 chunk 296 optimal weight: 5.9990 chunk 420 optimal weight: 0.9990 chunk 311 optimal weight: 8.9990 chunk 366 optimal weight: 0.0870 chunk 203 optimal weight: 9.9990 chunk 146 optimal weight: 0.5980 chunk 430 optimal weight: 6.9990 chunk 282 optimal weight: 3.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN B 361 ASN B 369 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 GLN C 168 GLN D 55 GLN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 HIS ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 71 ASN ** 1 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.067724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.056975 restraints weight = 289165.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.056490 restraints weight = 294511.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.056792 restraints weight = 225721.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.056969 restraints weight = 184538.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.057043 restraints weight = 162770.449| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36595 Z= 0.118 Angle : 0.553 8.167 49687 Z= 0.277 Chirality : 0.040 0.175 5828 Planarity : 0.004 0.060 6459 Dihedral : 6.344 70.376 5337 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.12), residues: 4795 helix: 2.12 (0.10), residues: 2540 sheet: 0.64 (0.24), residues: 479 loop : -0.80 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 108 TYR 0.022 0.001 TYR a 240 PHE 0.032 0.001 PHE 6 69 TRP 0.021 0.001 TRP E 118 HIS 0.005 0.001 HIS E 365 Details of bonding type rmsd covalent geometry : bond 0.00247 (36595) covalent geometry : angle 0.55349 (49687) hydrogen bonds : bond 0.04155 ( 2190) hydrogen bonds : angle 3.97678 ( 6396) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 GLU cc_start: 0.5732 (tp30) cc_final: 0.5286 (tp30) REVERT: B 182 CYS cc_start: 0.8972 (m) cc_final: 0.8750 (m) REVERT: B 324 MET cc_start: 0.8321 (mpp) cc_final: 0.8096 (mpp) REVERT: B 361 ASN cc_start: 0.9137 (t0) cc_final: 0.8709 (t0) REVERT: C 51 MET cc_start: 0.6976 (tpp) cc_final: 0.6625 (tpp) REVERT: C 270 VAL cc_start: 0.8497 (t) cc_final: 0.8230 (p) REVERT: E 64 CYS cc_start: 0.7088 (m) cc_final: 0.6833 (m) REVERT: F 21 ASP cc_start: 0.8491 (t0) cc_final: 0.8156 (t0) REVERT: F 305 MET cc_start: 0.8503 (ttp) cc_final: 0.8298 (ttp) REVERT: G 193 MET cc_start: 0.2989 (tpt) cc_final: 0.2704 (tpt) REVERT: H 106 THR cc_start: 0.8553 (p) cc_final: 0.8325 (p) REVERT: a 233 PHE cc_start: 0.8743 (t80) cc_final: 0.8474 (t80) REVERT: b 86 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8736 (tp30) REVERT: d 127 ASN cc_start: 0.9171 (t0) cc_final: 0.8914 (m-40) REVERT: 7 65 GLU cc_start: 0.8393 (mp0) cc_final: 0.8094 (mm-30) REVERT: 1 21 MET cc_start: 0.5554 (tpt) cc_final: 0.5283 (mtt) REVERT: 2 65 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7651 (mm-30) REVERT: 2 69 PHE cc_start: 0.8447 (m-10) cc_final: 0.8203 (m-80) REVERT: 5 75 MET cc_start: 0.5541 (mmp) cc_final: 0.5245 (tmm) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1956 time to fit residues: 97.4137 Evaluate side-chains 203 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 240 optimal weight: 9.9990 chunk 371 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 206 optimal weight: 0.1980 chunk 268 optimal weight: 4.9990 chunk 380 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 440 optimal weight: 4.9990 chunk 332 optimal weight: 4.9990 chunk 366 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 GLN C 141 GLN D 55 GLN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 GLN ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 71 ASN 1 71 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.066878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.056123 restraints weight = 291081.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.055715 restraints weight = 298656.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.055916 restraints weight = 225422.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.056095 restraints weight = 190824.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.056185 restraints weight = 168981.544| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36595 Z= 0.137 Angle : 0.574 11.066 49687 Z= 0.289 Chirality : 0.041 0.181 5828 Planarity : 0.004 0.059 6459 Dihedral : 6.244 67.242 5337 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.12), residues: 4795 helix: 2.07 (0.10), residues: 2547 sheet: 0.57 (0.24), residues: 467 loop : -0.82 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG b 158 TYR 0.025 0.001 TYR a 240 PHE 0.035 0.001 PHE b 38 TRP 0.018 0.001 TRP a 66 HIS 0.004 0.001 HIS E 365 Details of bonding type rmsd covalent geometry : bond 0.00297 (36595) covalent geometry : angle 0.57353 (49687) hydrogen bonds : bond 0.04279 ( 2190) hydrogen bonds : angle 4.01918 ( 6396) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 277 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 GLU cc_start: 0.5826 (tp30) cc_final: 0.5253 (tp30) REVERT: B 182 CYS cc_start: 0.8972 (m) cc_final: 0.8754 (m) REVERT: B 361 ASN cc_start: 0.9246 (t0) cc_final: 0.8916 (t0) REVERT: C 51 MET cc_start: 0.7053 (tpp) cc_final: 0.6675 (tpp) REVERT: C 174 ARG cc_start: 0.8204 (ttp80) cc_final: 0.7913 (ttp80) REVERT: C 270 VAL cc_start: 0.8525 (t) cc_final: 0.8274 (p) REVERT: E 64 CYS cc_start: 0.7048 (m) cc_final: 0.6827 (m) REVERT: F 21 ASP cc_start: 0.8403 (t0) cc_final: 0.8104 (t0) REVERT: G 193 MET cc_start: 0.2896 (tpt) cc_final: 0.2606 (tpt) REVERT: a 233 PHE cc_start: 0.8747 (t80) cc_final: 0.8420 (t80) REVERT: 2 65 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7638 (mm-30) REVERT: 2 69 PHE cc_start: 0.8480 (m-10) cc_final: 0.8205 (m-80) REVERT: 5 75 MET cc_start: 0.5504 (mmp) cc_final: 0.5295 (tmm) outliers start: 1 outliers final: 0 residues processed: 278 average time/residue: 0.1857 time to fit residues: 89.8581 Evaluate side-chains 197 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 309 optimal weight: 10.0000 chunk 364 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 292 optimal weight: 9.9990 chunk 407 optimal weight: 6.9990 chunk 70 optimal weight: 0.0980 chunk 387 optimal weight: 4.9990 chunk 413 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 311 optimal weight: 8.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 HIS B 201 GLN B 258 GLN B 259 HIS B 305 HIS B 369 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 GLN D 55 GLN F 56 HIS ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 HIS G 301 ASN a 112 GLN ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 222 HIS 1 71 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.064466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.054259 restraints weight = 293216.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053687 restraints weight = 320678.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.053885 restraints weight = 278328.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.053944 restraints weight = 254541.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.054013 restraints weight = 212209.521| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 36595 Z= 0.234 Angle : 0.709 17.576 49687 Z= 0.365 Chirality : 0.045 0.257 5828 Planarity : 0.005 0.074 6459 Dihedral : 6.708 69.150 5337 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.06 % Allowed : 4.04 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.12), residues: 4795 helix: 1.57 (0.10), residues: 2562 sheet: 0.21 (0.24), residues: 458 loop : -1.08 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 294 TYR 0.022 0.002 TYR B 262 PHE 0.048 0.002 PHE 6 69 TRP 0.025 0.002 TRP a 208 HIS 0.010 0.002 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00517 (36595) covalent geometry : angle 0.70902 (49687) hydrogen bonds : bond 0.05374 ( 2190) hydrogen bonds : angle 4.45392 ( 6396) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 249 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 CYS cc_start: 0.9060 (m) cc_final: 0.8811 (m) REVERT: B 324 MET cc_start: 0.8002 (mpp) cc_final: 0.7662 (mpp) REVERT: B 361 ASN cc_start: 0.9200 (t0) cc_final: 0.8909 (t0) REVERT: C 51 MET cc_start: 0.7284 (tpp) cc_final: 0.7079 (tpp) REVERT: C 270 VAL cc_start: 0.8598 (t) cc_final: 0.8320 (p) REVERT: D 327 LEU cc_start: 0.7266 (mm) cc_final: 0.7062 (mm) REVERT: D 412 LEU cc_start: 0.8533 (pt) cc_final: 0.8193 (tt) REVERT: E 64 CYS cc_start: 0.7167 (m) cc_final: 0.6938 (m) REVERT: F 21 ASP cc_start: 0.8483 (t0) cc_final: 0.8212 (t0) REVERT: G 193 MET cc_start: 0.3171 (tpt) cc_final: 0.2840 (tpt) REVERT: H 41 LEU cc_start: 0.5125 (tp) cc_final: 0.4784 (tt) REVERT: H 104 GLU cc_start: 0.8746 (pp20) cc_final: 0.8471 (pp20) REVERT: 1 75 MET cc_start: 0.6407 (pmm) cc_final: 0.5588 (pmm) REVERT: 2 65 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7496 (mm-30) REVERT: 2 69 PHE cc_start: 0.8477 (m-10) cc_final: 0.8166 (m-80) REVERT: 3 75 MET cc_start: 0.5712 (tmm) cc_final: 0.5367 (tmm) REVERT: 5 21 MET cc_start: 0.6519 (mmm) cc_final: 0.6252 (tpt) REVERT: 5 75 MET cc_start: 0.5481 (mmp) cc_final: 0.5177 (tmm) outliers start: 2 outliers final: 1 residues processed: 251 average time/residue: 0.1869 time to fit residues: 81.0102 Evaluate side-chains 191 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 386 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 429 optimal weight: 4.9990 chunk 420 optimal weight: 8.9990 chunk 411 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 304 optimal weight: 0.0770 chunk 456 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 GLN C 435 GLN D 55 GLN E 121 HIS G 301 ASN ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 71 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.066085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.055236 restraints weight = 291381.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.054929 restraints weight = 291089.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.055087 restraints weight = 230307.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.055239 restraints weight = 194633.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.055316 restraints weight = 171091.114| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36595 Z= 0.125 Angle : 0.597 11.353 49687 Z= 0.300 Chirality : 0.041 0.280 5828 Planarity : 0.004 0.058 6459 Dihedral : 6.271 67.853 5337 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.12), residues: 4795 helix: 1.89 (0.10), residues: 2550 sheet: 0.34 (0.23), residues: 459 loop : -1.00 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 108 TYR 0.034 0.001 TYR B 262 PHE 0.041 0.001 PHE D 324 TRP 0.018 0.001 TRP F 118 HIS 0.004 0.001 HIS E 365 Details of bonding type rmsd covalent geometry : bond 0.00261 (36595) covalent geometry : angle 0.59666 (49687) hydrogen bonds : bond 0.04561 ( 2190) hydrogen bonds : angle 4.10794 ( 6396) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 GLU cc_start: 0.5909 (tp30) cc_final: 0.5427 (tp30) REVERT: B 182 CYS cc_start: 0.9007 (m) cc_final: 0.8790 (m) REVERT: B 324 MET cc_start: 0.7980 (mpp) cc_final: 0.7485 (mpp) REVERT: B 361 ASN cc_start: 0.9220 (t0) cc_final: 0.8904 (t0) REVERT: C 51 MET cc_start: 0.7396 (tpp) cc_final: 0.7017 (tpp) REVERT: C 270 VAL cc_start: 0.8453 (t) cc_final: 0.8195 (p) REVERT: D 412 LEU cc_start: 0.8433 (pt) cc_final: 0.7990 (mt) REVERT: E 64 CYS cc_start: 0.7200 (m) cc_final: 0.6971 (m) REVERT: F 21 ASP cc_start: 0.8355 (t0) cc_final: 0.8065 (t0) REVERT: F 392 ASP cc_start: 0.7972 (p0) cc_final: 0.7748 (p0) REVERT: G 151 ARG cc_start: 0.8379 (ttp80) cc_final: 0.8114 (ptm160) REVERT: H 41 LEU cc_start: 0.4931 (tp) cc_final: 0.4586 (tt) REVERT: a 233 PHE cc_start: 0.8743 (t80) cc_final: 0.8215 (t80) REVERT: b 86 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8816 (tp30) REVERT: b 89 MET cc_start: 0.8750 (tmm) cc_final: 0.8363 (tmm) REVERT: 9 21 MET cc_start: 0.4659 (ppp) cc_final: 0.4177 (ppp) REVERT: 1 75 MET cc_start: 0.6454 (pmm) cc_final: 0.5933 (pmm) REVERT: 2 65 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7416 (mm-30) REVERT: 2 69 PHE cc_start: 0.8544 (m-10) cc_final: 0.8259 (m-80) REVERT: 5 21 MET cc_start: 0.6463 (mmm) cc_final: 0.6115 (tpt) REVERT: 5 75 MET cc_start: 0.5394 (mmp) cc_final: 0.5093 (tmm) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1899 time to fit residues: 89.6429 Evaluate side-chains 196 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 283 optimal weight: 5.9990 chunk 269 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 369 optimal weight: 3.9990 chunk 386 optimal weight: 0.4980 chunk 221 optimal weight: 0.9980 chunk 287 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 210 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 GLN D 55 GLN E 56 HIS F 306 GLN ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.066249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.055334 restraints weight = 288364.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.054789 restraints weight = 300114.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.054890 restraints weight = 236381.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.055098 restraints weight = 197579.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.055195 restraints weight = 178544.286| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36595 Z= 0.125 Angle : 0.595 10.508 49687 Z= 0.297 Chirality : 0.041 0.199 5828 Planarity : 0.004 0.057 6459 Dihedral : 6.047 65.052 5337 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.12), residues: 4795 helix: 2.01 (0.10), residues: 2543 sheet: 0.35 (0.23), residues: 466 loop : -0.96 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 108 TYR 0.024 0.001 TYR B 262 PHE 0.033 0.001 PHE 2 74 TRP 0.018 0.001 TRP a 66 HIS 0.006 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00267 (36595) covalent geometry : angle 0.59474 (49687) hydrogen bonds : bond 0.04344 ( 2190) hydrogen bonds : angle 4.01947 ( 6396) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 CYS cc_start: 0.9004 (m) cc_final: 0.8778 (m) REVERT: B 324 MET cc_start: 0.7939 (mpp) cc_final: 0.7333 (mpp) REVERT: B 361 ASN cc_start: 0.9216 (t0) cc_final: 0.8885 (t0) REVERT: C 51 MET cc_start: 0.7390 (tpp) cc_final: 0.7056 (tpp) REVERT: C 270 VAL cc_start: 0.8495 (t) cc_final: 0.8241 (p) REVERT: D 412 LEU cc_start: 0.8356 (pt) cc_final: 0.7960 (mt) REVERT: E 64 CYS cc_start: 0.7208 (m) cc_final: 0.6966 (m) REVERT: E 273 MET cc_start: 0.7877 (mmt) cc_final: 0.7392 (mmt) REVERT: F 21 ASP cc_start: 0.8341 (t0) cc_final: 0.8031 (t0) REVERT: F 392 ASP cc_start: 0.7926 (p0) cc_final: 0.7652 (p0) REVERT: G 151 ARG cc_start: 0.8362 (ttp80) cc_final: 0.8124 (ptm160) REVERT: H 41 LEU cc_start: 0.4872 (tp) cc_final: 0.4566 (tt) REVERT: a 233 PHE cc_start: 0.8773 (t80) cc_final: 0.8249 (t80) REVERT: b 86 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8811 (tp30) REVERT: b 89 MET cc_start: 0.8761 (tmm) cc_final: 0.8313 (tmm) REVERT: d 127 ASN cc_start: 0.9148 (t0) cc_final: 0.8867 (m-40) REVERT: 1 75 MET cc_start: 0.6360 (pmm) cc_final: 0.5414 (pmm) REVERT: 2 65 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7457 (mm-30) REVERT: 2 69 PHE cc_start: 0.8566 (m-10) cc_final: 0.8279 (m-80) REVERT: 5 21 MET cc_start: 0.6503 (mmm) cc_final: 0.6167 (tpt) REVERT: 5 75 MET cc_start: 0.5423 (mmp) cc_final: 0.5115 (tmm) REVERT: 6 53 LEU cc_start: 0.7713 (pp) cc_final: 0.6443 (mm) REVERT: 6 54 PHE cc_start: 0.7900 (m-10) cc_final: 0.7593 (m-10) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1954 time to fit residues: 91.0570 Evaluate side-chains 200 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 77 optimal weight: 0.9980 chunk 334 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 222 optimal weight: 4.9990 chunk 163 optimal weight: 0.0170 chunk 13 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 442 optimal weight: 9.9990 chunk 458 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 352 GLN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 GLN D 55 GLN E 56 HIS G 301 ASN ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 71 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.066666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.056101 restraints weight = 289325.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.055635 restraints weight = 291473.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.055926 restraints weight = 235641.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.055897 restraints weight = 229254.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.055983 restraints weight = 184711.088| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36595 Z= 0.117 Angle : 0.594 9.794 49687 Z= 0.297 Chirality : 0.041 0.183 5828 Planarity : 0.004 0.056 6459 Dihedral : 5.879 67.476 5337 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.03 % Allowed : 0.64 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.12), residues: 4795 helix: 2.03 (0.10), residues: 2543 sheet: 0.49 (0.23), residues: 459 loop : -0.93 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 108 TYR 0.024 0.001 TYR a 240 PHE 0.045 0.001 PHE 6 69 TRP 0.022 0.001 TRP a 66 HIS 0.012 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00241 (36595) covalent geometry : angle 0.59365 (49687) hydrogen bonds : bond 0.04165 ( 2190) hydrogen bonds : angle 4.01176 ( 6396) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 GLU cc_start: 0.5533 (tp30) cc_final: 0.5115 (tp30) REVERT: B 182 CYS cc_start: 0.8988 (m) cc_final: 0.8767 (m) REVERT: B 324 MET cc_start: 0.8021 (mpp) cc_final: 0.7233 (mpp) REVERT: B 361 ASN cc_start: 0.9225 (t0) cc_final: 0.8868 (t0) REVERT: C 51 MET cc_start: 0.7480 (tpp) cc_final: 0.7124 (tpp) REVERT: D 412 LEU cc_start: 0.8162 (pt) cc_final: 0.7779 (mt) REVERT: E 64 CYS cc_start: 0.7269 (m) cc_final: 0.7052 (m) REVERT: E 273 MET cc_start: 0.8331 (mmt) cc_final: 0.8001 (mmt) REVERT: F 21 ASP cc_start: 0.8336 (t0) cc_final: 0.8000 (t0) REVERT: F 392 ASP cc_start: 0.7895 (p0) cc_final: 0.7611 (p0) REVERT: H 41 LEU cc_start: 0.4812 (tp) cc_final: 0.4462 (tt) REVERT: a 233 PHE cc_start: 0.8823 (t80) cc_final: 0.8622 (t80) REVERT: b 86 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8799 (tp30) REVERT: b 89 MET cc_start: 0.8804 (tmm) cc_final: 0.8281 (tmm) REVERT: d 99 LYS cc_start: 0.8618 (tptp) cc_final: 0.7975 (mptt) REVERT: d 127 ASN cc_start: 0.9108 (t0) cc_final: 0.8832 (m-40) REVERT: 9 21 MET cc_start: 0.4749 (ppp) cc_final: 0.4280 (ppp) REVERT: 1 75 MET cc_start: 0.5736 (pmm) cc_final: 0.5241 (pmm) REVERT: 2 65 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7371 (mm-30) REVERT: 2 69 PHE cc_start: 0.8482 (m-10) cc_final: 0.8200 (m-80) REVERT: 5 21 MET cc_start: 0.6509 (mmm) cc_final: 0.6147 (tpt) REVERT: 5 75 MET cc_start: 0.5373 (mmp) cc_final: 0.5072 (tmm) REVERT: 6 53 LEU cc_start: 0.7589 (pp) cc_final: 0.6439 (mm) REVERT: 6 54 PHE cc_start: 0.7876 (m-10) cc_final: 0.7583 (m-10) outliers start: 1 outliers final: 1 residues processed: 277 average time/residue: 0.1905 time to fit residues: 91.1038 Evaluate side-chains 198 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 202 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 452 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 362 optimal weight: 0.6980 chunk 223 optimal weight: 1.9990 chunk 256 optimal weight: 0.3980 chunk 182 optimal weight: 0.9980 chunk 211 optimal weight: 0.7980 chunk 402 optimal weight: 0.0870 chunk 462 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 GLN D 55 GLN G 301 ASN d 32 ASN ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.067070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.056428 restraints weight = 290151.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.055871 restraints weight = 307265.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.056053 restraints weight = 252815.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.056141 restraints weight = 240721.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.056276 restraints weight = 198155.515| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 36595 Z= 0.112 Angle : 0.588 8.915 49687 Z= 0.291 Chirality : 0.041 0.184 5828 Planarity : 0.004 0.056 6459 Dihedral : 5.726 68.451 5337 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.12), residues: 4795 helix: 2.08 (0.10), residues: 2544 sheet: 0.52 (0.23), residues: 459 loop : -0.90 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG b 108 TYR 0.024 0.001 TYR a 240 PHE 0.025 0.001 PHE 4 54 TRP 0.025 0.001 TRP a 66 HIS 0.010 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00230 (36595) covalent geometry : angle 0.58810 (49687) hydrogen bonds : bond 0.03933 ( 2190) hydrogen bonds : angle 3.93101 ( 6396) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 GLU cc_start: 0.5370 (tp30) cc_final: 0.4971 (tp30) REVERT: B 182 CYS cc_start: 0.8940 (m) cc_final: 0.8722 (m) REVERT: B 324 MET cc_start: 0.7875 (mpp) cc_final: 0.7158 (mpp) REVERT: B 361 ASN cc_start: 0.9209 (t0) cc_final: 0.8852 (t0) REVERT: C 51 MET cc_start: 0.7479 (tpp) cc_final: 0.7146 (tpp) REVERT: D 379 TYR cc_start: 0.8024 (t80) cc_final: 0.7688 (t80) REVERT: D 412 LEU cc_start: 0.8169 (pt) cc_final: 0.7726 (mt) REVERT: E 64 CYS cc_start: 0.7279 (m) cc_final: 0.7070 (m) REVERT: E 254 ASP cc_start: 0.3760 (p0) cc_final: 0.3402 (t0) REVERT: E 273 MET cc_start: 0.7737 (mmt) cc_final: 0.7329 (mmt) REVERT: F 21 ASP cc_start: 0.8400 (t0) cc_final: 0.8057 (t0) REVERT: F 392 ASP cc_start: 0.7883 (p0) cc_final: 0.7590 (p0) REVERT: H 41 LEU cc_start: 0.4849 (tp) cc_final: 0.4489 (tt) REVERT: a 239 LEU cc_start: 0.9023 (tp) cc_final: 0.8796 (tp) REVERT: b 86 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8783 (tp30) REVERT: b 89 MET cc_start: 0.8811 (tmm) cc_final: 0.8272 (tmm) REVERT: d 127 ASN cc_start: 0.9152 (t0) cc_final: 0.8886 (m-40) REVERT: 7 75 MET cc_start: 0.7086 (ppp) cc_final: 0.6778 (ppp) REVERT: 8 69 PHE cc_start: 0.8740 (m-80) cc_final: 0.8278 (m-80) REVERT: 1 21 MET cc_start: 0.7213 (mpp) cc_final: 0.6918 (mpp) REVERT: 1 75 MET cc_start: 0.5737 (pmm) cc_final: 0.5204 (pmm) REVERT: 2 65 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7362 (mm-30) REVERT: 2 69 PHE cc_start: 0.8547 (m-10) cc_final: 0.8270 (m-80) REVERT: 3 75 MET cc_start: 0.6093 (tmm) cc_final: 0.5797 (tmm) REVERT: 5 21 MET cc_start: 0.6484 (mmm) cc_final: 0.6218 (tpt) REVERT: 5 75 MET cc_start: 0.5608 (mmp) cc_final: 0.5277 (tmm) REVERT: 6 53 LEU cc_start: 0.7717 (pp) cc_final: 0.6585 (mm) REVERT: 6 54 PHE cc_start: 0.7878 (m-10) cc_final: 0.7561 (m-10) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1887 time to fit residues: 89.7417 Evaluate side-chains 205 residues out of total 3779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 475 optimal weight: 8.9990 chunk 17 optimal weight: 0.0060 chunk 429 optimal weight: 2.9990 chunk 295 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 392 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 410 optimal weight: 0.0470 chunk 320 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 GLN D 55 GLN G 301 ASN ** d 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.065690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.055138 restraints weight = 290306.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.054537 restraints weight = 325725.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.054663 restraints weight = 265385.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.054919 restraints weight = 216621.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.055067 restraints weight = 189845.925| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36595 Z= 0.148 Angle : 0.622 10.469 49687 Z= 0.314 Chirality : 0.042 0.186 5828 Planarity : 0.004 0.060 6459 Dihedral : 5.895 67.559 5337 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.12), residues: 4795 helix: 1.97 (0.10), residues: 2551 sheet: 0.42 (0.23), residues: 461 loop : -0.97 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG b 108 TYR 0.020 0.002 TYR E 379 PHE 0.058 0.001 PHE 6 69 TRP 0.032 0.002 TRP a 66 HIS 0.011 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00324 (36595) covalent geometry : angle 0.62245 (49687) hydrogen bonds : bond 0.04402 ( 2190) hydrogen bonds : angle 4.09770 ( 6396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4462.54 seconds wall clock time: 78 minutes 20.19 seconds (4700.19 seconds total)