Starting phenix.real_space_refine on Thu Feb 22 17:25:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlb_24524/02_2024/7rlb_24524_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlb_24524/02_2024/7rlb_24524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlb_24524/02_2024/7rlb_24524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlb_24524/02_2024/7rlb_24524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlb_24524/02_2024/7rlb_24524_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlb_24524/02_2024/7rlb_24524_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= -0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 180 5.16 5 C 21870 2.51 5 N 6150 2.21 5 O 6660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A ASP 749": "OD1" <-> "OD2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 577": "OD1" <-> "OD2" Residue "B ASP 749": "OD1" <-> "OD2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 577": "OD1" <-> "OD2" Residue "C ASP 749": "OD1" <-> "OD2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 577": "OD1" <-> "OD2" Residue "D ASP 749": "OD1" <-> "OD2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 577": "OD1" <-> "OD2" Residue "E ASP 749": "OD1" <-> "OD2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 577": "OD1" <-> "OD2" Residue "F ASP 749": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34884 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5760 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "B" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5760 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "C" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5760 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "D" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5760 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "E" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5760 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "F" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5760 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.86, per 1000 atoms: 0.54 Number of scatterers: 34884 At special positions: 0 Unit cell: (179.488, 175.338, 106.862, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 24 15.00 O 6660 8.00 N 6150 7.00 C 21870 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 - 3.50 Amino acid : False - 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: 13.51 Conformation dependent library (CDL) restraints added in 7.0 seconds 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8220 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 186 helices and 18 sheets defined 37.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.36 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 removed outlier: 4.215A pdb=" N ASP A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 131 through 134 No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.672A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.788A pdb=" N LYS A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 232 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 272 through 275 No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 282 through 295 removed outlier: 3.645A pdb=" N ALA A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 333 removed outlier: 3.976A pdb=" N ILE A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 381 removed outlier: 3.807A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 399 No H-bonds generated for 'chain 'A' and resid 396 through 399' Processing helix chain 'A' and resid 408 through 427 removed outlier: 3.655A pdb=" N ALA A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 483 through 493 removed outlier: 3.885A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 552 removed outlier: 4.306A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 568 removed outlier: 3.770A pdb=" N GLU A 561 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 567 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 586 removed outlier: 4.130A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 650 through 660 removed outlier: 3.808A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 706 Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.816A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 763 removed outlier: 3.648A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR A 755 " --> pdb=" O ASP A 751 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A 756 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE A 758 " --> pdb=" O LYS A 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 removed outlier: 4.215A pdb=" N ASP B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 No H-bonds generated for 'chain 'B' and resid 89 through 92' Processing helix chain 'B' and resid 131 through 134 No H-bonds generated for 'chain 'B' and resid 131 through 134' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 211 through 225 removed outlier: 3.672A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.789A pdb=" N LYS B 231 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 232 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 272 through 275 No H-bonds generated for 'chain 'B' and resid 272 through 275' Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.645A pdb=" N ALA B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 333 removed outlier: 3.975A pdb=" N ILE B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 381 removed outlier: 3.807A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 399 No H-bonds generated for 'chain 'B' and resid 396 through 399' Processing helix chain 'B' and resid 408 through 427 removed outlier: 3.654A pdb=" N ALA B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 444 No H-bonds generated for 'chain 'B' and resid 442 through 444' Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 483 through 493 removed outlier: 3.884A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 552 removed outlier: 4.306A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 568 removed outlier: 3.769A pdb=" N GLU B 561 " --> pdb=" O ASN B 558 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 567 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 586 removed outlier: 4.130A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 609 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 650 through 660 removed outlier: 3.808A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 706 Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.815A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 763 removed outlier: 3.648A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR B 755 " --> pdb=" O ASP B 751 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU B 756 " --> pdb=" O ILE B 752 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE B 758 " --> pdb=" O LYS B 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 49 removed outlier: 4.216A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 92 No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 131 through 134 No H-bonds generated for 'chain 'C' and resid 131 through 134' Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 211 through 225 removed outlier: 3.672A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.788A pdb=" N LYS C 231 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU C 232 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 272 through 275 No H-bonds generated for 'chain 'C' and resid 272 through 275' Processing helix chain 'C' and resid 282 through 295 removed outlier: 3.645A pdb=" N ALA C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 333 removed outlier: 3.974A pdb=" N ILE C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 381 removed outlier: 3.808A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 399 No H-bonds generated for 'chain 'C' and resid 396 through 399' Processing helix chain 'C' and resid 408 through 427 removed outlier: 3.655A pdb=" N ALA C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 444 No H-bonds generated for 'chain 'C' and resid 442 through 444' Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 483 through 493 removed outlier: 3.885A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 552 removed outlier: 4.305A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.770A pdb=" N GLU C 561 " --> pdb=" O ASN C 558 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 567 " --> pdb=" O ASP C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 586 removed outlier: 4.130A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 609 Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 650 through 660 removed outlier: 3.807A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 706 Processing helix chain 'C' and resid 733 through 742 removed outlier: 3.816A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 763 removed outlier: 3.648A pdb=" N ARG C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR C 755 " --> pdb=" O ASP C 751 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU C 756 " --> pdb=" O ILE C 752 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE C 758 " --> pdb=" O LYS C 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 49 removed outlier: 4.216A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 92 No H-bonds generated for 'chain 'D' and resid 89 through 92' Processing helix chain 'D' and resid 131 through 134 No H-bonds generated for 'chain 'D' and resid 131 through 134' Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 211 through 225 removed outlier: 3.672A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU D 221 " --> pdb=" O LYS D 217 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.789A pdb=" N LYS D 231 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 232 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 272 through 275 No H-bonds generated for 'chain 'D' and resid 272 through 275' Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.647A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 removed outlier: 3.975A pdb=" N ILE D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 381 removed outlier: 3.808A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 399 No H-bonds generated for 'chain 'D' and resid 396 through 399' Processing helix chain 'D' and resid 408 through 427 removed outlier: 3.655A pdb=" N ALA D 412 " --> pdb=" O GLY D 408 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN D 421 " --> pdb=" O GLU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 444 No H-bonds generated for 'chain 'D' and resid 442 through 444' Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 483 through 493 removed outlier: 3.885A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 552 removed outlier: 4.307A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 568 removed outlier: 3.769A pdb=" N GLU D 561 " --> pdb=" O ASN D 558 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG D 567 " --> pdb=" O ASP D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 586 removed outlier: 4.130A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 609 Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 650 through 660 removed outlier: 3.808A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 706 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.815A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 763 removed outlier: 3.648A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR D 755 " --> pdb=" O ASP D 751 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU D 756 " --> pdb=" O ILE D 752 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE D 758 " --> pdb=" O LYS D 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 49 removed outlier: 4.216A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 92 No H-bonds generated for 'chain 'E' and resid 89 through 92' Processing helix chain 'E' and resid 131 through 134 No H-bonds generated for 'chain 'E' and resid 131 through 134' Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 211 through 225 removed outlier: 3.671A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU E 221 " --> pdb=" O LYS E 217 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.788A pdb=" N LYS E 231 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU E 232 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 272 through 275 No H-bonds generated for 'chain 'E' and resid 272 through 275' Processing helix chain 'E' and resid 282 through 295 removed outlier: 3.645A pdb=" N ALA E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU E 294 " --> pdb=" O PHE E 290 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 3.974A pdb=" N ILE E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 381 removed outlier: 3.808A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 399 No H-bonds generated for 'chain 'E' and resid 396 through 399' Processing helix chain 'E' and resid 408 through 427 removed outlier: 3.655A pdb=" N ALA E 412 " --> pdb=" O GLY E 408 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN E 421 " --> pdb=" O GLU E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 444 No H-bonds generated for 'chain 'E' and resid 442 through 444' Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 483 through 493 removed outlier: 3.885A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 552 removed outlier: 4.306A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 568 removed outlier: 3.769A pdb=" N GLU E 561 " --> pdb=" O ASN E 558 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG E 567 " --> pdb=" O ASP E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 586 removed outlier: 4.130A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 609 Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 650 through 660 removed outlier: 3.808A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 706 Processing helix chain 'E' and resid 733 through 742 removed outlier: 3.815A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 763 removed outlier: 3.647A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR E 755 " --> pdb=" O ASP E 751 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU E 756 " --> pdb=" O ILE E 752 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE E 758 " --> pdb=" O LYS E 754 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 49 removed outlier: 4.215A pdb=" N ASP F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 49 " --> pdb=" O LYS F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 92 No H-bonds generated for 'chain 'F' and resid 89 through 92' Processing helix chain 'F' and resid 131 through 134 No H-bonds generated for 'chain 'F' and resid 131 through 134' Processing helix chain 'F' and resid 136 through 138 No H-bonds generated for 'chain 'F' and resid 136 through 138' Processing helix chain 'F' and resid 211 through 225 removed outlier: 3.671A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU F 221 " --> pdb=" O LYS F 217 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.788A pdb=" N LYS F 231 " --> pdb=" O ALA F 228 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU F 232 " --> pdb=" O LEU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 272 through 275 No H-bonds generated for 'chain 'F' and resid 272 through 275' Processing helix chain 'F' and resid 282 through 295 removed outlier: 3.646A pdb=" N ALA F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU F 294 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 removed outlier: 3.976A pdb=" N ILE F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 381 removed outlier: 3.808A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 399 No H-bonds generated for 'chain 'F' and resid 396 through 399' Processing helix chain 'F' and resid 408 through 427 removed outlier: 3.654A pdb=" N ALA F 412 " --> pdb=" O GLY F 408 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN F 421 " --> pdb=" O GLU F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 444 No H-bonds generated for 'chain 'F' and resid 442 through 444' Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'F' and resid 483 through 493 removed outlier: 3.885A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 506 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 552 removed outlier: 4.306A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 568 removed outlier: 3.770A pdb=" N GLU F 561 " --> pdb=" O ASN F 558 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG F 567 " --> pdb=" O ASP F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 586 removed outlier: 4.130A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 609 Processing helix chain 'F' and resid 626 through 628 No H-bonds generated for 'chain 'F' and resid 626 through 628' Processing helix chain 'F' and resid 631 through 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 650 through 660 removed outlier: 3.808A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 706 Processing helix chain 'F' and resid 733 through 742 removed outlier: 3.816A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 763 removed outlier: 3.648A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR F 755 " --> pdb=" O ASP F 751 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU F 756 " --> pdb=" O ILE F 752 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE F 758 " --> pdb=" O LYS F 754 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 66 through 70 removed outlier: 3.692A pdb=" N CYS A 69 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 57 " --> pdb=" O CYS A 69 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR A 56 " --> pdb=" O CYS A 105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 60 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 365 through 367 removed outlier: 3.643A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 641 through 645 removed outlier: 4.176A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 643 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 66 through 70 removed outlier: 3.691A pdb=" N CYS B 69 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 57 " --> pdb=" O CYS B 69 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR B 56 " --> pdb=" O CYS B 105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 60 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 365 through 367 removed outlier: 3.643A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 641 through 645 removed outlier: 4.175A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 643 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 66 through 70 removed outlier: 3.692A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 57 " --> pdb=" O CYS C 69 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR C 56 " --> pdb=" O CYS C 105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 60 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 365 through 367 removed outlier: 3.643A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 641 through 645 removed outlier: 4.175A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 643 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 66 through 70 removed outlier: 3.691A pdb=" N CYS D 69 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 57 " --> pdb=" O CYS D 69 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR D 56 " --> pdb=" O CYS D 105 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS D 60 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 365 through 367 removed outlier: 3.643A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 641 through 645 removed outlier: 4.176A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 643 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 66 through 70 removed outlier: 3.690A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL E 57 " --> pdb=" O CYS E 69 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR E 56 " --> pdb=" O CYS E 105 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS E 60 " --> pdb=" O SER E 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 365 through 367 removed outlier: 3.643A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 641 through 645 removed outlier: 4.176A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE E 643 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 66 through 70 removed outlier: 3.691A pdb=" N CYS F 69 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL F 57 " --> pdb=" O CYS F 69 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR F 56 " --> pdb=" O CYS F 105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS F 60 " --> pdb=" O SER F 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 365 through 367 removed outlier: 3.643A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 641 through 645 removed outlier: 4.175A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 643 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) 804 hydrogen bonds defined for protein. 2178 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: 10.71 Time building geometry restraints manager: 14.74 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: 11963 1.34 - 1.46: 5602 1.46 - 1.58: 17595 1.58 - 1.69: 36 1.69 - 1.81: 288 Bond restraints: 35484 Sorted by residual: bond pdb=" C4 ADP E1001 " pdb=" C5 ADP E1001 " ideal model delta sigma weight residual 1.490 1.439 0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" C4 ADP B1001 " pdb=" C5 ADP B1001 " ideal model delta sigma weight residual 1.490 1.439 0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" C4 ADP A1001 " pdb=" C5 ADP A1001 " ideal model delta sigma weight residual 1.490 1.441 0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" C4 ADP C1001 " pdb=" C5 ADP C1001 " ideal model delta sigma weight residual 1.490 1.441 0.049 2.00e-02 2.50e+03 6.08e+00 bond pdb=" C4 ADP D1001 " pdb=" C5 ADP D1001 " ideal model delta sigma weight residual 1.490 1.441 0.049 2.00e-02 2.50e+03 5.96e+00 ... (remaining 35479 not shown) Histogram of bond angle deviations from ideal: 100.13 - 107.27: 1381 107.27 - 114.40: 20760 114.40 - 121.54: 17111 121.54 - 128.68: 8580 128.68 - 135.81: 144 Bond angle restraints: 47976 Sorted by residual: angle pdb=" CA GLN B 473 " pdb=" CB GLN B 473 " pdb=" CG GLN B 473 " ideal model delta sigma weight residual 114.10 124.78 -10.68 2.00e+00 2.50e-01 2.85e+01 angle pdb=" CA GLN F 473 " pdb=" CB GLN F 473 " pdb=" CG GLN F 473 " ideal model delta sigma weight residual 114.10 124.73 -10.63 2.00e+00 2.50e-01 2.83e+01 angle pdb=" CA GLN D 473 " pdb=" CB GLN D 473 " pdb=" CG GLN D 473 " ideal model delta sigma weight residual 114.10 124.73 -10.63 2.00e+00 2.50e-01 2.83e+01 angle pdb=" CA GLN A 473 " pdb=" CB GLN A 473 " pdb=" CG GLN A 473 " ideal model delta sigma weight residual 114.10 124.72 -10.62 2.00e+00 2.50e-01 2.82e+01 angle pdb=" CA GLN E 473 " pdb=" CB GLN E 473 " pdb=" CG GLN E 473 " ideal model delta sigma weight residual 114.10 124.72 -10.62 2.00e+00 2.50e-01 2.82e+01 ... (remaining 47971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.21: 21333 32.21 - 64.42: 549 64.42 - 96.63: 48 96.63 - 128.84: 6 128.84 - 161.05: 6 Dihedral angle restraints: 21942 sinusoidal: 9258 harmonic: 12684 Sorted by residual: dihedral pdb=" C5' ADP E1001 " pdb=" O5' ADP E1001 " pdb=" PA ADP E1001 " pdb=" O2A ADP E1001 " ideal model delta sinusoidal sigma weight residual 300.00 138.96 161.05 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C5' ADP B1001 " pdb=" O5' ADP B1001 " pdb=" PA ADP B1001 " pdb=" O2A ADP B1001 " ideal model delta sinusoidal sigma weight residual 300.00 139.42 160.58 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C5' ADP D1001 " pdb=" O5' ADP D1001 " pdb=" PA ADP D1001 " pdb=" O2A ADP D1001 " ideal model delta sinusoidal sigma weight residual 300.00 143.97 156.03 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 21939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3393 0.037 - 0.074: 1410 0.074 - 0.111: 487 0.111 - 0.149: 80 0.149 - 0.186: 6 Chirality restraints: 5376 Sorted by residual: chirality pdb=" CG LEU D 381 " pdb=" CB LEU D 381 " pdb=" CD1 LEU D 381 " pdb=" CD2 LEU D 381 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CG LEU E 381 " pdb=" CB LEU E 381 " pdb=" CD1 LEU E 381 " pdb=" CD2 LEU E 381 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CG LEU B 381 " pdb=" CB LEU B 381 " pdb=" CD1 LEU B 381 " pdb=" CD2 LEU B 381 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.32e-01 ... (remaining 5373 not shown) Planarity restraints: 6306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 349 " -0.167 9.50e-02 1.11e+02 7.50e-02 3.66e+00 pdb=" NE ARG A 349 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 349 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 349 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 349 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 349 " -0.167 9.50e-02 1.11e+02 7.49e-02 3.66e+00 pdb=" NE ARG E 349 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E 349 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG E 349 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 349 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 349 " -0.166 9.50e-02 1.11e+02 7.45e-02 3.61e+00 pdb=" NE ARG C 349 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 349 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 349 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 349 " -0.003 2.00e-02 2.50e+03 ... (remaining 6303 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7827 2.79 - 3.32: 32571 3.32 - 3.84: 55993 3.84 - 4.37: 63950 4.37 - 4.90: 107000 Nonbonded interactions: 267341 Sorted by model distance: nonbonded pdb=" CA GLY E 250 " pdb=" O2A ADP E1001 " model vdw 2.259 3.440 nonbonded pdb=" OG1 THR A 448 " pdb=" OD1 ASP A 450 " model vdw 2.270 2.440 nonbonded pdb=" CA GLY B 250 " pdb=" O2A ADP B1001 " model vdw 2.270 3.440 nonbonded pdb=" OG1 THR B 448 " pdb=" OD1 ASP B 450 " model vdw 2.270 2.440 nonbonded pdb=" OG1 THR D 448 " pdb=" OD1 ASP D 450 " model vdw 2.270 2.440 ... (remaining 267336 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.180 Check model and map are aligned: 0.600 Set scattering table: 0.310 Process input model: 90.640 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 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 : 0.004 0.058 35484 Z= 0.246 Angle : 0.746 11.050 47976 Z= 0.397 Chirality : 0.044 0.186 5376 Planarity : 0.004 0.075 6306 Dihedral : 14.610 161.046 13722 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.76 % Favored : 95.96 % Rotamer: Outliers : 0.03 % Allowed : 0.96 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.12), residues: 4386 helix: -0.80 (0.13), residues: 1620 sheet: 0.43 (0.24), residues: 504 loop : -1.70 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 454 HIS 0.006 0.001 HIS E 317 PHE 0.016 0.001 PHE F 516 TYR 0.015 0.002 TYR D 203 ARG 0.009 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 736 time to evaluate : 4.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 ILE cc_start: 0.6558 (mt) cc_final: 0.6309 (mt) REVERT: A 330 THR cc_start: 0.7339 (m) cc_final: 0.7109 (p) REVERT: A 354 ASP cc_start: 0.8006 (t0) cc_final: 0.7738 (t0) REVERT: A 508 MET cc_start: 0.6103 (tmm) cc_final: 0.5793 (ttt) REVERT: B 301 ILE cc_start: 0.6185 (mt) cc_final: 0.5955 (mt) REVERT: B 330 THR cc_start: 0.7284 (m) cc_final: 0.7035 (p) REVERT: B 354 ASP cc_start: 0.7946 (t0) cc_final: 0.7342 (t0) REVERT: B 540 ILE cc_start: 0.6678 (mt) cc_final: 0.6328 (mm) REVERT: C 301 ILE cc_start: 0.6114 (mt) cc_final: 0.5848 (mt) REVERT: C 330 THR cc_start: 0.7368 (m) cc_final: 0.7052 (p) REVERT: C 341 VAL cc_start: 0.7006 (p) cc_final: 0.6690 (p) REVERT: D 99 VAL cc_start: 0.8467 (m) cc_final: 0.8135 (p) REVERT: D 301 ILE cc_start: 0.6121 (mt) cc_final: 0.5832 (mt) REVERT: D 330 THR cc_start: 0.7598 (m) cc_final: 0.7291 (p) REVERT: D 540 ILE cc_start: 0.6572 (mt) cc_final: 0.6063 (mm) REVERT: E 301 ILE cc_start: 0.6270 (mt) cc_final: 0.5960 (mt) REVERT: E 330 THR cc_start: 0.7300 (m) cc_final: 0.7063 (p) REVERT: E 354 ASP cc_start: 0.7922 (t0) cc_final: 0.7358 (t0) REVERT: E 540 ILE cc_start: 0.6855 (mt) cc_final: 0.6498 (mm) REVERT: E 558 ASN cc_start: 0.6400 (m-40) cc_final: 0.6173 (m-40) REVERT: F 69 CYS cc_start: 0.8706 (t) cc_final: 0.8497 (m) REVERT: F 99 VAL cc_start: 0.8279 (m) cc_final: 0.8070 (p) REVERT: F 301 ILE cc_start: 0.6393 (mt) cc_final: 0.6034 (mt) REVERT: F 330 THR cc_start: 0.7600 (m) cc_final: 0.7341 (p) REVERT: F 354 ASP cc_start: 0.7922 (t0) cc_final: 0.7623 (t70) outliers start: 1 outliers final: 0 residues processed: 736 average time/residue: 0.4571 time to fit residues: 550.8780 Evaluate side-chains 421 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 10.0000 chunk 331 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 223 optimal weight: 9.9990 chunk 177 optimal weight: 7.9990 chunk 343 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 255 optimal weight: 0.7980 chunk 397 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS B 458 GLN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS C 458 GLN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 HIS E 406 HIS ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS F 458 GLN ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 35484 Z= 0.431 Angle : 0.866 13.995 47976 Z= 0.427 Chirality : 0.052 0.184 5376 Planarity : 0.007 0.091 6306 Dihedral : 8.211 136.333 4920 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.18 % Favored : 94.55 % Rotamer: Outliers : 2.88 % Allowed : 10.60 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.12), residues: 4386 helix: -1.25 (0.12), residues: 1602 sheet: -0.76 (0.26), residues: 420 loop : -1.38 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.005 TRP A 454 HIS 0.007 0.001 HIS D 384 PHE 0.042 0.003 PHE E 516 TYR 0.019 0.002 TYR D 244 ARG 0.019 0.001 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 353 time to evaluate : 4.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ASN cc_start: 0.8698 (m-40) cc_final: 0.8417 (m-40) REVERT: A 508 MET cc_start: 0.7570 (tmm) cc_final: 0.7321 (ttt) REVERT: A 639 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8530 (mp) REVERT: B 304 ASP cc_start: 0.8193 (t70) cc_final: 0.7878 (t0) REVERT: B 508 MET cc_start: 0.7568 (ttt) cc_final: 0.7349 (ttt) REVERT: C 84 MET cc_start: 0.8087 (tpp) cc_final: 0.7773 (tpt) REVERT: C 317 HIS cc_start: 0.7975 (m90) cc_final: 0.7396 (m-70) REVERT: C 324 ILE cc_start: 0.8820 (mm) cc_final: 0.8596 (tp) REVERT: C 388 MET cc_start: 0.8381 (ppp) cc_final: 0.8157 (ppp) REVERT: D 26 LEU cc_start: 0.7217 (tp) cc_final: 0.6758 (tt) REVERT: D 241 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7797 (mt) REVERT: D 317 HIS cc_start: 0.7877 (m90) cc_final: 0.7264 (m-70) REVERT: D 388 MET cc_start: 0.8322 (ppp) cc_final: 0.8084 (ppp) REVERT: D 516 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.7397 (p90) REVERT: E 304 ASP cc_start: 0.8225 (t70) cc_final: 0.7882 (t0) REVERT: E 508 MET cc_start: 0.7447 (ttt) cc_final: 0.7144 (ttt) REVERT: E 639 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8265 (mp) REVERT: F 84 MET cc_start: 0.7637 (tpt) cc_final: 0.7419 (tpt) REVERT: F 426 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7534 (tmtt) REVERT: F 516 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8719 (p90) outliers start: 108 outliers final: 39 residues processed: 426 average time/residue: 0.4543 time to fit residues: 318.4232 Evaluate side-chains 306 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 262 time to evaluate : 4.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 8.9990 chunk 123 optimal weight: 0.7980 chunk 331 optimal weight: 3.9990 chunk 270 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 398 optimal weight: 1.9990 chunk 430 optimal weight: 2.9990 chunk 354 optimal weight: 0.0270 chunk 395 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 319 optimal weight: 0.5980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN A 490 GLN B 36 ASN B 490 GLN C 490 GLN C 536 GLN C 558 ASN D 490 GLN E 36 ASN E 421 GLN E 490 GLN F 490 GLN F 536 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 35484 Z= 0.157 Angle : 0.568 8.185 47976 Z= 0.266 Chirality : 0.044 0.143 5376 Planarity : 0.004 0.058 6306 Dihedral : 7.468 124.042 4920 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.06 % Favored : 95.80 % Rotamer: Outliers : 1.52 % Allowed : 13.98 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 4386 helix: -0.58 (0.13), residues: 1668 sheet: -0.09 (0.25), residues: 462 loop : -1.21 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 454 HIS 0.005 0.001 HIS F 317 PHE 0.024 0.001 PHE D 771 TYR 0.010 0.001 TYR E 244 ARG 0.014 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 281 time to evaluate : 3.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 HIS cc_start: 0.8351 (OUTLIER) cc_final: 0.7575 (m-70) REVERT: A 387 ASN cc_start: 0.8697 (m-40) cc_final: 0.8339 (t0) REVERT: A 639 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8050 (mp) REVERT: A 678 MET cc_start: 0.8767 (tpp) cc_final: 0.8509 (tpp) REVERT: B 304 ASP cc_start: 0.8155 (t70) cc_final: 0.7805 (t0) REVERT: B 317 HIS cc_start: 0.8294 (OUTLIER) cc_final: 0.7628 (m90) REVERT: B 388 MET cc_start: 0.8161 (ppp) cc_final: 0.7258 (ppp) REVERT: B 508 MET cc_start: 0.7715 (ttt) cc_final: 0.7438 (ttt) REVERT: B 619 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8589 (mt) REVERT: C 84 MET cc_start: 0.8005 (tpp) cc_final: 0.7737 (tpt) REVERT: C 317 HIS cc_start: 0.8253 (m90) cc_final: 0.7558 (m-70) REVERT: C 388 MET cc_start: 0.8340 (ppp) cc_final: 0.7844 (ppp) REVERT: C 465 ARG cc_start: 0.8896 (ptp-170) cc_final: 0.8546 (ptp-170) REVERT: C 547 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8648 (tp) REVERT: D 26 LEU cc_start: 0.7505 (tp) cc_final: 0.7137 (tt) REVERT: D 317 HIS cc_start: 0.8259 (m90) cc_final: 0.7443 (m-70) REVERT: D 388 MET cc_start: 0.8315 (ppp) cc_final: 0.7809 (ppp) REVERT: D 678 MET cc_start: 0.8810 (tpp) cc_final: 0.8544 (tpp) REVERT: E 317 HIS cc_start: 0.8261 (m90) cc_final: 0.7462 (m-70) REVERT: E 388 MET cc_start: 0.8274 (ppp) cc_final: 0.7124 (ppp) REVERT: E 508 MET cc_start: 0.7629 (ttt) cc_final: 0.7307 (ttt) REVERT: E 639 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7722 (mp) REVERT: F 317 HIS cc_start: 0.8092 (m90) cc_final: 0.7661 (m90) REVERT: F 388 MET cc_start: 0.7960 (ppp) cc_final: 0.7588 (ppp) REVERT: F 426 LYS cc_start: 0.7742 (ttmt) cc_final: 0.7445 (tmtt) REVERT: F 465 ARG cc_start: 0.8910 (ptp-170) cc_final: 0.8623 (ptp-170) REVERT: F 547 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8639 (tp) outliers start: 57 outliers final: 30 residues processed: 316 average time/residue: 0.4289 time to fit residues: 228.3598 Evaluate side-chains 291 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 254 time to evaluate : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 547 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 5.9990 chunk 299 optimal weight: 20.0000 chunk 206 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 399 optimal weight: 0.9980 chunk 423 optimal weight: 0.7980 chunk 208 optimal weight: 0.0020 chunk 379 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN B 616 ASN C 458 GLN D 616 ASN E 458 GLN ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35484 Z= 0.198 Angle : 0.568 9.474 47976 Z= 0.267 Chirality : 0.044 0.228 5376 Planarity : 0.004 0.057 6306 Dihedral : 7.278 132.092 4920 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.86 % Favored : 95.01 % Rotamer: Outliers : 1.97 % Allowed : 14.35 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 4386 helix: -0.37 (0.13), residues: 1662 sheet: 0.07 (0.25), residues: 468 loop : -1.04 (0.14), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 454 HIS 0.003 0.001 HIS B 317 PHE 0.023 0.002 PHE D 516 TYR 0.016 0.001 TYR A 203 ARG 0.007 0.000 ARG C 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 267 time to evaluate : 3.936 Fit side-chains revert: symmetry clash REVERT: A 305 GLU cc_start: 0.6906 (pp20) cc_final: 0.6313 (pp20) REVERT: A 317 HIS cc_start: 0.8324 (OUTLIER) cc_final: 0.7464 (m-70) REVERT: A 387 ASN cc_start: 0.8772 (m-40) cc_final: 0.8451 (t0) REVERT: A 426 LYS cc_start: 0.7934 (ttmt) cc_final: 0.7468 (tmtt) REVERT: A 508 MET cc_start: 0.7899 (tmm) cc_final: 0.7485 (ttt) REVERT: A 516 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.7784 (p90) REVERT: A 639 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8408 (mp) REVERT: B 99 VAL cc_start: 0.8860 (m) cc_final: 0.8631 (p) REVERT: B 304 ASP cc_start: 0.8290 (t70) cc_final: 0.8043 (t0) REVERT: B 317 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7233 (m-70) REVERT: B 388 MET cc_start: 0.8121 (ppp) cc_final: 0.7261 (ppp) REVERT: B 508 MET cc_start: 0.8145 (ttt) cc_final: 0.7797 (ttt) REVERT: C 84 MET cc_start: 0.8039 (tpp) cc_final: 0.7750 (tpt) REVERT: C 275 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7754 (mtp) REVERT: C 317 HIS cc_start: 0.8207 (m90) cc_final: 0.7505 (m-70) REVERT: C 388 MET cc_start: 0.8403 (ppp) cc_final: 0.7717 (ppp) REVERT: C 516 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8514 (p90) REVERT: C 547 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8656 (tp) REVERT: C 564 ASP cc_start: 0.8596 (m-30) cc_final: 0.8253 (m-30) REVERT: D 26 LEU cc_start: 0.7303 (tp) cc_final: 0.6901 (tt) REVERT: D 275 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8097 (mtp) REVERT: D 317 HIS cc_start: 0.8260 (m90) cc_final: 0.7504 (m-70) REVERT: D 388 MET cc_start: 0.8412 (ppp) cc_final: 0.7891 (ppp) REVERT: D 426 LYS cc_start: 0.8008 (ttmt) cc_final: 0.7582 (tmtt) REVERT: E 317 HIS cc_start: 0.8188 (m90) cc_final: 0.7317 (m-70) REVERT: E 388 MET cc_start: 0.8350 (ppp) cc_final: 0.7426 (ppp) REVERT: E 508 MET cc_start: 0.8178 (ttt) cc_final: 0.7837 (ttt) REVERT: E 578 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8332 (mt-10) REVERT: E 639 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8226 (mp) REVERT: F 244 TYR cc_start: 0.7287 (m-80) cc_final: 0.7079 (m-80) REVERT: F 275 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7908 (mtp) REVERT: F 317 HIS cc_start: 0.8119 (m90) cc_final: 0.7534 (m90) REVERT: F 388 MET cc_start: 0.8076 (ppp) cc_final: 0.7581 (ppp) REVERT: F 417 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8240 (pp20) REVERT: F 426 LYS cc_start: 0.7826 (ttmt) cc_final: 0.7539 (tmtt) REVERT: F 561 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7446 (pm20) outliers start: 74 outliers final: 39 residues processed: 314 average time/residue: 0.4273 time to fit residues: 227.0409 Evaluate side-chains 282 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 231 time to evaluate : 3.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 0.6980 chunk 240 optimal weight: 0.4980 chunk 6 optimal weight: 8.9990 chunk 315 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 361 optimal weight: 8.9990 chunk 292 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 216 optimal weight: 5.9990 chunk 380 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 HIS ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN C 735 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 HIS ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 735 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.8562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 35484 Z= 0.381 Angle : 0.688 10.602 47976 Z= 0.342 Chirality : 0.048 0.231 5376 Planarity : 0.006 0.069 6306 Dihedral : 7.575 140.450 4920 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.88 % Favored : 94.98 % Rotamer: Outliers : 3.73 % Allowed : 14.03 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.13), residues: 4386 helix: -0.54 (0.13), residues: 1758 sheet: 0.33 (0.25), residues: 450 loop : -1.02 (0.14), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 454 HIS 0.004 0.001 HIS B 317 PHE 0.033 0.002 PHE D 516 TYR 0.021 0.002 TYR B 244 ARG 0.008 0.001 ARG F 377 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 243 time to evaluate : 4.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.7339 (pp20) cc_final: 0.6961 (pp20) REVERT: A 317 HIS cc_start: 0.8268 (OUTLIER) cc_final: 0.7427 (m-70) REVERT: A 426 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7757 (tmtt) REVERT: A 516 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8073 (p90) REVERT: B 84 MET cc_start: 0.7463 (tpt) cc_final: 0.7179 (tpt) REVERT: B 304 ASP cc_start: 0.8467 (t70) cc_final: 0.8246 (t0) REVERT: B 317 HIS cc_start: 0.8258 (OUTLIER) cc_final: 0.7154 (m-70) REVERT: B 388 MET cc_start: 0.8241 (ppp) cc_final: 0.7359 (ppp) REVERT: B 426 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7939 (tmtt) REVERT: B 516 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8589 (p90) REVERT: C 317 HIS cc_start: 0.8311 (OUTLIER) cc_final: 0.7665 (m-70) REVERT: C 388 MET cc_start: 0.8546 (ppp) cc_final: 0.7932 (ppp) REVERT: C 404 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.7488 (p-80) REVERT: C 516 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.7911 (p90) REVERT: C 547 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8853 (tp) REVERT: C 616 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8148 (p0) REVERT: D 26 LEU cc_start: 0.7257 (tp) cc_final: 0.6767 (tt) REVERT: D 175 ILE cc_start: -0.1783 (OUTLIER) cc_final: -0.2044 (tp) REVERT: D 305 GLU cc_start: 0.7356 (pp20) cc_final: 0.6983 (pp20) REVERT: D 317 HIS cc_start: 0.8389 (OUTLIER) cc_final: 0.7670 (m-70) REVERT: D 417 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8363 (pp20) REVERT: D 426 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7802 (tmtt) REVERT: D 516 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.7755 (p90) REVERT: D 611 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7598 (ptp) REVERT: D 678 MET cc_start: 0.9040 (tpp) cc_final: 0.8700 (tpp) REVERT: E 84 MET cc_start: 0.7734 (tpt) cc_final: 0.7189 (tpt) REVERT: E 304 ASP cc_start: 0.8323 (t0) cc_final: 0.8025 (t0) REVERT: E 344 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8897 (mtm) REVERT: E 388 MET cc_start: 0.8217 (ppp) cc_final: 0.7408 (ppp) REVERT: E 426 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7716 (tmtt) REVERT: E 516 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8285 (p90) REVERT: E 561 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: E 639 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8262 (mp) REVERT: F 84 MET cc_start: 0.7312 (tpt) cc_final: 0.7034 (tpt) REVERT: F 317 HIS cc_start: 0.8194 (m90) cc_final: 0.7558 (m-70) REVERT: F 388 MET cc_start: 0.8355 (ppp) cc_final: 0.7840 (ptt) REVERT: F 426 LYS cc_start: 0.8166 (ttmt) cc_final: 0.7812 (tmtt) REVERT: F 516 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.7683 (p90) outliers start: 140 outliers final: 68 residues processed: 349 average time/residue: 0.4426 time to fit residues: 261.7832 Evaluate side-chains 297 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 210 time to evaluate : 4.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 565 LYS Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 516 PHE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 565 LYS Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 5.9990 chunk 381 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 423 optimal weight: 0.9990 chunk 351 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 222 optimal weight: 20.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN E 536 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.8672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35484 Z= 0.188 Angle : 0.561 9.733 47976 Z= 0.265 Chirality : 0.044 0.134 5376 Planarity : 0.004 0.055 6306 Dihedral : 7.083 137.943 4920 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.26 % Favored : 95.60 % Rotamer: Outliers : 2.45 % Allowed : 15.73 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.13), residues: 4386 helix: -0.39 (0.13), residues: 1728 sheet: 0.62 (0.25), residues: 456 loop : -0.96 (0.14), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 454 HIS 0.003 0.000 HIS B 317 PHE 0.021 0.001 PHE D 516 TYR 0.012 0.001 TYR A 203 ARG 0.004 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 238 time to evaluate : 4.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.7244 (pp20) cc_final: 0.6920 (pp20) REVERT: A 317 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7394 (m-70) REVERT: A 426 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7675 (tmtt) REVERT: A 508 MET cc_start: 0.8619 (tmm) cc_final: 0.8393 (ttt) REVERT: A 516 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.7910 (p90) REVERT: B 84 MET cc_start: 0.7553 (tpt) cc_final: 0.7262 (tpt) REVERT: B 304 ASP cc_start: 0.8352 (t70) cc_final: 0.8119 (t0) REVERT: B 317 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7220 (m-70) REVERT: B 388 MET cc_start: 0.8267 (ppp) cc_final: 0.7410 (ppp) REVERT: B 426 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7955 (tmtt) REVERT: B 561 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: C 317 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7443 (m-70) REVERT: C 388 MET cc_start: 0.8335 (ppp) cc_final: 0.7691 (ppp) REVERT: C 516 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8033 (p90) REVERT: D 26 LEU cc_start: 0.7399 (tp) cc_final: 0.6918 (tt) REVERT: D 305 GLU cc_start: 0.7273 (pp20) cc_final: 0.6934 (pp20) REVERT: D 317 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7576 (m-70) REVERT: D 426 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7767 (tmtt) REVERT: E 84 MET cc_start: 0.7512 (tpt) cc_final: 0.7015 (tpt) REVERT: E 388 MET cc_start: 0.8243 (ppp) cc_final: 0.7369 (ppp) REVERT: E 426 LYS cc_start: 0.8146 (ttmt) cc_final: 0.7740 (tmtt) REVERT: E 516 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8289 (p90) REVERT: E 561 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: E 639 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8243 (mp) REVERT: F 84 MET cc_start: 0.7424 (tpt) cc_final: 0.7154 (tpt) REVERT: F 305 GLU cc_start: 0.7114 (pp20) cc_final: 0.6810 (pp20) REVERT: F 317 HIS cc_start: 0.8112 (m90) cc_final: 0.7484 (m-70) REVERT: F 388 MET cc_start: 0.8346 (ppp) cc_final: 0.7818 (ptt) REVERT: F 426 LYS cc_start: 0.8107 (ttmt) cc_final: 0.7791 (tmtt) REVERT: F 561 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7428 (pm20) outliers start: 92 outliers final: 59 residues processed: 311 average time/residue: 0.4125 time to fit residues: 219.4689 Evaluate side-chains 287 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 217 time to evaluate : 4.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 516 PHE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 241 optimal weight: 0.9980 chunk 309 optimal weight: 7.9990 chunk 239 optimal weight: 3.9990 chunk 356 optimal weight: 5.9990 chunk 236 optimal weight: 0.0060 chunk 422 optimal weight: 7.9990 chunk 264 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 194 optimal weight: 0.3980 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.8845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35484 Z= 0.206 Angle : 0.559 10.757 47976 Z= 0.264 Chirality : 0.044 0.236 5376 Planarity : 0.004 0.056 6306 Dihedral : 6.920 132.250 4920 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.29 % Favored : 95.58 % Rotamer: Outliers : 2.96 % Allowed : 15.76 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 4386 helix: -0.30 (0.13), residues: 1716 sheet: 0.75 (0.26), residues: 456 loop : -0.96 (0.14), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 454 HIS 0.003 0.001 HIS B 317 PHE 0.024 0.001 PHE D 516 TYR 0.014 0.001 TYR F 244 ARG 0.006 0.000 ARG E 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 226 time to evaluate : 4.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.7294 (pp20) cc_final: 0.6802 (pp20) REVERT: A 317 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.7452 (m-70) REVERT: A 426 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7717 (tmtt) REVERT: A 516 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.7967 (p90) REVERT: B 84 MET cc_start: 0.7495 (tpt) cc_final: 0.7198 (tpt) REVERT: B 317 HIS cc_start: 0.8152 (OUTLIER) cc_final: 0.7253 (m-70) REVERT: B 388 MET cc_start: 0.8252 (ppp) cc_final: 0.7395 (ppp) REVERT: B 426 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7975 (tmtt) REVERT: B 561 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: C 305 GLU cc_start: 0.7173 (pp20) cc_final: 0.6789 (pp20) REVERT: C 317 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7528 (m-70) REVERT: C 388 MET cc_start: 0.8363 (ppp) cc_final: 0.7693 (ppp) REVERT: C 516 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8056 (p90) REVERT: D 26 LEU cc_start: 0.7481 (tp) cc_final: 0.7006 (tt) REVERT: D 305 GLU cc_start: 0.7304 (pp20) cc_final: 0.6789 (pp20) REVERT: D 317 HIS cc_start: 0.8341 (m90) cc_final: 0.7571 (m-70) REVERT: D 417 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8287 (pp20) REVERT: D 426 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7764 (tmtt) REVERT: E 84 MET cc_start: 0.7458 (tpt) cc_final: 0.7059 (tpt) REVERT: E 305 GLU cc_start: 0.7073 (pp20) cc_final: 0.6793 (pp20) REVERT: E 317 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7245 (m-70) REVERT: E 388 MET cc_start: 0.8231 (ppp) cc_final: 0.7384 (ppp) REVERT: E 426 LYS cc_start: 0.8092 (ttmt) cc_final: 0.7728 (tmtt) REVERT: E 516 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8210 (p90) REVERT: E 561 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: E 639 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8266 (mp) REVERT: F 26 LEU cc_start: 0.7092 (tp) cc_final: 0.6647 (tt) REVERT: F 84 MET cc_start: 0.7427 (tpt) cc_final: 0.7172 (tpt) REVERT: F 305 GLU cc_start: 0.7176 (pp20) cc_final: 0.6869 (pp20) REVERT: F 317 HIS cc_start: 0.8061 (m90) cc_final: 0.7418 (m-70) REVERT: F 388 MET cc_start: 0.8350 (ppp) cc_final: 0.7689 (ppp) REVERT: F 426 LYS cc_start: 0.8192 (ttmt) cc_final: 0.7820 (tmtt) outliers start: 111 outliers final: 74 residues processed: 317 average time/residue: 0.4641 time to fit residues: 250.5453 Evaluate side-chains 301 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 216 time to evaluate : 4.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 516 PHE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 647 LEU Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 9.9990 chunk 168 optimal weight: 0.9980 chunk 252 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 81 optimal weight: 20.0000 chunk 268 optimal weight: 0.4980 chunk 287 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 331 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.8956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35484 Z= 0.159 Angle : 0.545 10.213 47976 Z= 0.254 Chirality : 0.044 0.222 5376 Planarity : 0.004 0.056 6306 Dihedral : 6.694 127.801 4920 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.10 % Favored : 95.76 % Rotamer: Outliers : 2.50 % Allowed : 16.29 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 4386 helix: -0.25 (0.13), residues: 1716 sheet: 0.85 (0.25), residues: 456 loop : -0.92 (0.14), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 454 HIS 0.003 0.000 HIS B 317 PHE 0.019 0.001 PHE D 516 TYR 0.011 0.001 TYR B 138 ARG 0.006 0.000 ARG F 560 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 238 time to evaluate : 4.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.7225 (pp20) cc_final: 0.6689 (pp20) REVERT: A 317 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7527 (m-70) REVERT: A 426 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7693 (tmtt) REVERT: A 516 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.7848 (p90) REVERT: A 678 MET cc_start: 0.8685 (tpp) cc_final: 0.8354 (mpp) REVERT: B 305 GLU cc_start: 0.7113 (pp20) cc_final: 0.6738 (pp20) REVERT: B 317 HIS cc_start: 0.8130 (m90) cc_final: 0.7314 (m-70) REVERT: B 388 MET cc_start: 0.8222 (ppp) cc_final: 0.7380 (ppp) REVERT: B 426 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7958 (tmtt) REVERT: B 561 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: C 305 GLU cc_start: 0.7173 (pp20) cc_final: 0.6760 (pp20) REVERT: C 317 HIS cc_start: 0.8193 (OUTLIER) cc_final: 0.7518 (m-70) REVERT: C 388 MET cc_start: 0.8329 (ppp) cc_final: 0.7678 (ppp) REVERT: C 516 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.7985 (p90) REVERT: D 26 LEU cc_start: 0.7510 (tp) cc_final: 0.7041 (tt) REVERT: D 305 GLU cc_start: 0.7248 (pp20) cc_final: 0.6684 (pp20) REVERT: D 317 HIS cc_start: 0.8231 (m90) cc_final: 0.7643 (m-70) REVERT: D 417 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8268 (pp20) REVERT: D 426 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7736 (tmtt) REVERT: E 84 MET cc_start: 0.7520 (tpt) cc_final: 0.7150 (tpt) REVERT: E 305 GLU cc_start: 0.7035 (pp20) cc_final: 0.6813 (pp20) REVERT: E 388 MET cc_start: 0.8229 (ppp) cc_final: 0.7367 (ppp) REVERT: E 426 LYS cc_start: 0.8082 (ttmt) cc_final: 0.7728 (tmtt) REVERT: E 516 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8217 (p90) REVERT: E 561 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: E 639 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8218 (mp) REVERT: F 26 LEU cc_start: 0.7156 (tp) cc_final: 0.6705 (tt) REVERT: F 84 MET cc_start: 0.7392 (tpt) cc_final: 0.7119 (tpt) REVERT: F 305 GLU cc_start: 0.7159 (pp20) cc_final: 0.6761 (pp20) REVERT: F 317 HIS cc_start: 0.8090 (m90) cc_final: 0.7474 (m-70) REVERT: F 388 MET cc_start: 0.8351 (ppp) cc_final: 0.7658 (ppp) REVERT: F 426 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7819 (tmtt) REVERT: F 456 LEU cc_start: 0.8839 (pp) cc_final: 0.8465 (pp) REVERT: F 516 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.7809 (p90) outliers start: 94 outliers final: 68 residues processed: 309 average time/residue: 0.4431 time to fit residues: 230.9328 Evaluate side-chains 304 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 226 time to evaluate : 3.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 516 PHE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 5.9990 chunk 404 optimal weight: 0.9990 chunk 368 optimal weight: 30.0000 chunk 393 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 chunk 171 optimal weight: 0.1980 chunk 308 optimal weight: 6.9990 chunk 120 optimal weight: 0.1980 chunk 355 optimal weight: 4.9990 chunk 372 optimal weight: 10.0000 chunk 392 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 HIS ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.9200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35484 Z= 0.224 Angle : 0.568 11.491 47976 Z= 0.267 Chirality : 0.045 0.214 5376 Planarity : 0.004 0.059 6306 Dihedral : 6.773 129.910 4920 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.31 % Favored : 95.55 % Rotamer: Outliers : 2.82 % Allowed : 16.27 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 4386 helix: -0.24 (0.13), residues: 1734 sheet: 0.71 (0.27), residues: 408 loop : -0.87 (0.14), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 454 HIS 0.003 0.001 HIS B 317 PHE 0.023 0.001 PHE D 516 TYR 0.012 0.001 TYR A 203 ARG 0.009 0.000 ARG C 465 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 226 time to evaluate : 4.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.7342 (pp20) cc_final: 0.6850 (pp20) REVERT: A 317 HIS cc_start: 0.8233 (OUTLIER) cc_final: 0.7586 (m-70) REVERT: A 516 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.7966 (p90) REVERT: B 84 MET cc_start: 0.7462 (tpt) cc_final: 0.7207 (tpp) REVERT: B 305 GLU cc_start: 0.7118 (pp20) cc_final: 0.6762 (pp20) REVERT: B 317 HIS cc_start: 0.8131 (m90) cc_final: 0.7375 (m-70) REVERT: B 388 MET cc_start: 0.8193 (ppp) cc_final: 0.7461 (ppp) REVERT: B 561 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: B 639 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8268 (mp) REVERT: C 305 GLU cc_start: 0.7151 (pp20) cc_final: 0.6772 (pp20) REVERT: C 317 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7538 (m-70) REVERT: C 388 MET cc_start: 0.8355 (ppp) cc_final: 0.7689 (ppp) REVERT: C 516 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.7887 (p90) REVERT: D 26 LEU cc_start: 0.7546 (tp) cc_final: 0.7063 (tt) REVERT: D 305 GLU cc_start: 0.7322 (pp20) cc_final: 0.6807 (pp20) REVERT: D 317 HIS cc_start: 0.8237 (m90) cc_final: 0.7675 (m-70) REVERT: D 417 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8278 (pp20) REVERT: E 84 MET cc_start: 0.7492 (tpt) cc_final: 0.7107 (tpt) REVERT: E 388 MET cc_start: 0.8238 (ppp) cc_final: 0.7391 (ppp) REVERT: E 426 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7793 (tmtt) REVERT: E 516 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8213 (p90) REVERT: E 561 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: E 639 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8280 (mp) REVERT: F 26 LEU cc_start: 0.7089 (tp) cc_final: 0.6601 (tt) REVERT: F 84 MET cc_start: 0.7363 (tpt) cc_final: 0.6959 (tpt) REVERT: F 305 GLU cc_start: 0.7132 (pp20) cc_final: 0.6711 (pp20) REVERT: F 317 HIS cc_start: 0.8072 (m90) cc_final: 0.7528 (m-70) REVERT: F 388 MET cc_start: 0.8370 (ppp) cc_final: 0.7851 (ptt) REVERT: F 426 LYS cc_start: 0.8330 (ttmt) cc_final: 0.7952 (tmtt) REVERT: F 516 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.7734 (p90) REVERT: F 578 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8139 (pt0) outliers start: 106 outliers final: 81 residues processed: 310 average time/residue: 0.4317 time to fit residues: 227.9212 Evaluate side-chains 308 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 215 time to evaluate : 4.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 516 PHE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 4.9990 chunk 415 optimal weight: 2.9990 chunk 253 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 289 optimal weight: 0.9980 chunk 436 optimal weight: 0.6980 chunk 401 optimal weight: 5.9990 chunk 347 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.9452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35484 Z= 0.226 Angle : 0.574 9.943 47976 Z= 0.270 Chirality : 0.045 0.209 5376 Planarity : 0.004 0.063 6306 Dihedral : 6.782 129.225 4920 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.31 % Favored : 95.55 % Rotamer: Outliers : 2.69 % Allowed : 16.56 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 4386 helix: -0.25 (0.13), residues: 1734 sheet: 0.74 (0.27), residues: 420 loop : -0.87 (0.14), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 454 HIS 0.002 0.001 HIS B 317 PHE 0.022 0.001 PHE D 516 TYR 0.016 0.001 TYR A 203 ARG 0.006 0.000 ARG E 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 226 time to evaluate : 3.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.5487 (tpt) cc_final: 0.5154 (mmt) REVERT: A 305 GLU cc_start: 0.7358 (pp20) cc_final: 0.6868 (pp20) REVERT: A 317 HIS cc_start: 0.8259 (OUTLIER) cc_final: 0.7677 (m-70) REVERT: A 402 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: A 516 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.7980 (p90) REVERT: A 678 MET cc_start: 0.8673 (tpp) cc_final: 0.8259 (mpp) REVERT: B 84 MET cc_start: 0.7486 (tpt) cc_final: 0.7196 (tpp) REVERT: B 305 GLU cc_start: 0.7116 (pp20) cc_final: 0.6783 (pp20) REVERT: B 317 HIS cc_start: 0.8092 (m90) cc_final: 0.7411 (m-70) REVERT: B 388 MET cc_start: 0.8215 (ppp) cc_final: 0.7547 (ppp) REVERT: B 561 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: B 639 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8222 (mp) REVERT: C 305 GLU cc_start: 0.7164 (pp20) cc_final: 0.6766 (pp20) REVERT: C 317 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7536 (m-70) REVERT: C 388 MET cc_start: 0.8251 (ppp) cc_final: 0.7691 (ppp) REVERT: C 516 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.7901 (p90) REVERT: D 26 LEU cc_start: 0.7543 (tp) cc_final: 0.7060 (tt) REVERT: D 305 GLU cc_start: 0.7343 (pp20) cc_final: 0.6857 (pp20) REVERT: D 317 HIS cc_start: 0.8228 (m90) cc_final: 0.7624 (m-70) REVERT: D 417 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8277 (pp20) REVERT: E 84 MET cc_start: 0.7569 (tpt) cc_final: 0.7270 (tpt) REVERT: E 225 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7538 (ttm-80) REVERT: E 317 HIS cc_start: 0.8005 (OUTLIER) cc_final: 0.7230 (m170) REVERT: E 388 MET cc_start: 0.8173 (ppp) cc_final: 0.7846 (ptt) REVERT: E 516 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8232 (p90) REVERT: E 561 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: E 639 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8260 (mp) REVERT: F 26 LEU cc_start: 0.7087 (tp) cc_final: 0.6594 (tt) REVERT: F 84 MET cc_start: 0.7401 (tpt) cc_final: 0.6922 (tpt) REVERT: F 305 GLU cc_start: 0.7158 (pp20) cc_final: 0.6748 (pp20) REVERT: F 317 HIS cc_start: 0.8033 (m90) cc_final: 0.7410 (m-70) REVERT: F 388 MET cc_start: 0.8228 (ppp) cc_final: 0.7845 (ptt) REVERT: F 417 GLU cc_start: 0.8654 (pp20) cc_final: 0.8018 (pp20) REVERT: F 516 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.7669 (p90) REVERT: F 578 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8085 (pt0) outliers start: 101 outliers final: 80 residues processed: 305 average time/residue: 0.4428 time to fit residues: 228.6706 Evaluate side-chains 309 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 214 time to evaluate : 4.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 307 ASP Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 225 ARG Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 321 GLU Chi-restraints excluded: chain E residue 351 ASN Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 516 PHE Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 578 GLU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 9.9990 chunk 370 optimal weight: 0.0770 chunk 106 optimal weight: 0.1980 chunk 320 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 348 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 chunk 357 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.123907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.079659 restraints weight = 76789.858| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 4.33 r_work: 0.2815 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.9459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35484 Z= 0.147 Angle : 0.557 11.412 47976 Z= 0.259 Chirality : 0.044 0.225 5376 Planarity : 0.004 0.058 6306 Dihedral : 6.547 124.216 4920 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.56 % Favored : 96.31 % Rotamer: Outliers : 2.13 % Allowed : 17.28 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 4386 helix: -0.15 (0.13), residues: 1716 sheet: 0.88 (0.26), residues: 426 loop : -0.87 (0.14), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 454 HIS 0.002 0.000 HIS B 317 PHE 0.023 0.001 PHE B 771 TYR 0.035 0.001 TYR C 138 ARG 0.006 0.000 ARG C 349 =============================================================================== Job complete usr+sys time: 6972.05 seconds wall clock time: 127 minutes 53.24 seconds (7673.24 seconds total)