Starting phenix.real_space_refine (version: dev) on Fri Apr 8 14:36:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlb_24524/04_2022/7rlb_24524_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlb_24524/04_2022/7rlb_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_24524/04_2022/7rlb_24524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlb_24524/04_2022/7rlb_24524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlb_24524/04_2022/7rlb_24524_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlb_24524/04_2022/7rlb_24524_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'PTRANS': 37, 'TRANS': 694, 'PCIS': 3} 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: {'PTRANS': 37, 'TRANS': 694, 'PCIS': 3} 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: {'PTRANS': 37, 'TRANS': 694, 'PCIS': 3} 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: {'PTRANS': 37, 'TRANS': 694, 'PCIS': 3} 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: {'PTRANS': 37, 'TRANS': 694, 'PCIS': 3} 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: {'PTRANS': 37, 'TRANS': 694, 'PCIS': 3} 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: 17.83, per 1000 atoms: 0.51 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: 14.25 Conformation dependent library (CDL) restraints added in 4.8 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: 4.35 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: 11.24 Time building geometry restraints manager: 15.31 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 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. 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.360 Check model and map are aligned: 0.540 Convert atoms to be neutral: 0.280 Process input model: 83.430 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 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 % 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 *********************** 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 : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 736 average time/residue: 0.4411 time to fit residues: 536.0049 Evaluate side-chains 405 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 4.036 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7152 ------------------------------------------------------------------------------- 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: 0.8980 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: 3.9990 chunk 132 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 255 optimal weight: 0.7980 chunk 397 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS A 406 HIS ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 ASN A 616 ASN B 406 HIS B 458 GLN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN B 616 ASN 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** D 558 ASN D 616 ASN 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 35484 Z= 0.368 Angle : 0.803 13.422 47976 Z= 0.393 Chirality : 0.052 0.201 5376 Planarity : 0.007 0.087 6306 Dihedral : 8.022 138.045 4920 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.06 % Favored : 94.66 % Rotamer Outliers : 2.21 % 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: -1.74 (0.12), residues: 4386 helix: -1.00 (0.12), residues: 1614 sheet: -0.30 (0.25), residues: 486 loop : -1.41 (0.13), residues: 2286 *********************** 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 459 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 376 time to evaluate : 3.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 30 residues processed: 431 average time/residue: 0.4409 time to fit residues: 316.1817 Evaluate side-chains 303 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 273 time to evaluate : 3.686 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3102 time to fit residues: 23.3752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 331 optimal weight: 0.8980 chunk 270 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 398 optimal weight: 6.9990 chunk 430 optimal weight: 0.7980 chunk 354 optimal weight: 2.9990 chunk 395 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 319 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN B 458 GLN C 317 HIS C 536 GLN C 558 ASN D 317 HIS E 421 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 35484 Z= 0.179 Angle : 0.573 6.826 47976 Z= 0.270 Chirality : 0.044 0.143 5376 Planarity : 0.005 0.062 6306 Dihedral : 7.366 123.171 4920 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.60 % Favored : 96.12 % Rotamer Outliers : 1.54 % 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: -1.24 (0.13), residues: 4386 helix: -0.48 (0.13), residues: 1674 sheet: 0.07 (0.25), residues: 486 loop : -1.26 (0.13), residues: 2226 *********************** 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 343 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 285 time to evaluate : 4.023 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 27 residues processed: 323 average time/residue: 0.4207 time to fit residues: 234.5828 Evaluate side-chains 278 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 251 time to evaluate : 4.290 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2923 time to fit residues: 21.0821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 44 optimal weight: 0.0470 chunk 190 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 399 optimal weight: 0.3980 chunk 423 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 379 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 overall best weight: 1.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN A 558 ASN B 36 ASN B 490 GLN B 558 ASN C 458 GLN C 490 GLN D 317 HIS D 490 GLN D 558 ASN E 36 ASN ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 490 GLN ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN F 490 GLN F 735 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.6590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.117 35484 Z= 0.273 Angle : 0.644 12.275 47976 Z= 0.309 Chirality : 0.046 0.186 5376 Planarity : 0.005 0.071 6306 Dihedral : 7.520 139.286 4920 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.08 % Favored : 94.78 % Rotamer Outliers : 1.38 % 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: -0.30 (0.13), residues: 1662 sheet: 0.13 (0.25), residues: 468 loop : -1.12 (0.13), residues: 2256 *********************** 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 323 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 271 time to evaluate : 4.382 Fit side-chains outliers start: 52 outliers final: 19 residues processed: 300 average time/residue: 0.4119 time to fit residues: 215.1037 Evaluate side-chains 244 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 225 time to evaluate : 4.174 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3097 time to fit residues: 16.5685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 5.9990 chunk 240 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 315 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 361 optimal weight: 8.9990 chunk 292 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 380 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN 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 536 GLN ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN E 458 GLN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 HIS F 317 HIS ** F 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.8520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 35484 Z= 0.380 Angle : 0.692 10.932 47976 Z= 0.340 Chirality : 0.048 0.245 5376 Planarity : 0.006 0.075 6306 Dihedral : 7.476 141.574 4920 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.54 % Favored : 95.33 % Rotamer Outliers : 2.88 % 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: -1.10 (0.13), residues: 4386 helix: -0.53 (0.13), residues: 1716 sheet: 0.39 (0.26), residues: 450 loop : -1.07 (0.14), residues: 2220 *********************** 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 337 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 229 time to evaluate : 4.094 Fit side-chains outliers start: 108 outliers final: 45 residues processed: 317 average time/residue: 0.4393 time to fit residues: 238.4721 Evaluate side-chains 237 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 192 time to evaluate : 4.468 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.3582 time to fit residues: 36.5039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 6.9990 chunk 381 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 248 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 423 optimal weight: 0.7980 chunk 351 optimal weight: 0.6980 chunk 196 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN E 421 GLN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.8743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 35484 Z= 0.249 Angle : 0.586 10.720 47976 Z= 0.280 Chirality : 0.046 0.220 5376 Planarity : 0.004 0.056 6306 Dihedral : 7.201 139.980 4920 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.88 % Favored : 94.98 % Rotamer Outliers : 1.38 % 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: -1.01 (0.13), residues: 4386 helix: -0.45 (0.13), residues: 1734 sheet: 0.50 (0.26), residues: 450 loop : -1.04 (0.14), residues: 2202 *********************** 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 267 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 215 time to evaluate : 4.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 24 residues processed: 258 average time/residue: 0.4153 time to fit residues: 187.8403 Evaluate side-chains 219 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 3.998 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3503 time to fit residues: 21.7111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 309 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 356 optimal weight: 0.0270 chunk 236 optimal weight: 0.0980 chunk 422 optimal weight: 2.9990 chunk 264 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 194 optimal weight: 0.7980 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.8922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 35484 Z= 0.221 Angle : 0.580 10.513 47976 Z= 0.275 Chirality : 0.045 0.230 5376 Planarity : 0.004 0.059 6306 Dihedral : 7.013 133.552 4920 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.04 % Favored : 95.83 % Rotamer Outliers : 1.09 % 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: -0.89 (0.13), residues: 4386 helix: -0.35 (0.13), residues: 1734 sheet: 0.60 (0.26), residues: 450 loop : -0.98 (0.14), residues: 2202 *********************** 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 255 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 214 time to evaluate : 3.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 18 residues processed: 246 average time/residue: 0.4311 time to fit residues: 183.5775 Evaluate side-chains 217 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 199 time to evaluate : 3.992 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3223 time to fit residues: 16.5162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 268 optimal weight: 0.0970 chunk 287 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 331 optimal weight: 0.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.9041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 35484 Z= 0.184 Angle : 0.571 10.295 47976 Z= 0.268 Chirality : 0.045 0.242 5376 Planarity : 0.004 0.058 6306 Dihedral : 6.848 129.651 4920 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.26 % Favored : 95.60 % Rotamer Outliers : 0.53 % 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: -0.77 (0.13), residues: 4386 helix: -0.26 (0.13), residues: 1704 sheet: 0.73 (0.25), residues: 456 loop : -0.92 (0.14), residues: 2226 *********************** 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 239 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 219 time to evaluate : 4.120 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 236 average time/residue: 0.4377 time to fit residues: 175.8363 Evaluate side-chains 205 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 199 time to evaluate : 4.038 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3071 time to fit residues: 9.3038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 0.9990 chunk 404 optimal weight: 6.9990 chunk 368 optimal weight: 6.9990 chunk 393 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 chunk 171 optimal weight: 0.6980 chunk 308 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 355 optimal weight: 4.9990 chunk 372 optimal weight: 10.0000 chunk 392 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.9246 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= 0.214 Angle : 0.590 12.703 47976 Z= 0.276 Chirality : 0.045 0.241 5376 Planarity : 0.004 0.062 6306 Dihedral : 6.850 129.808 4920 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.15 % Favored : 95.71 % Rotamer Outliers : 0.77 % 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: -0.71 (0.13), residues: 4386 helix: -0.25 (0.13), residues: 1722 sheet: 0.80 (0.26), residues: 450 loop : -0.86 (0.14), residues: 2214 *********************** 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 236 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 207 time to evaluate : 4.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 10 residues processed: 228 average time/residue: 0.4301 time to fit residues: 169.9936 Evaluate side-chains 209 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 199 time to evaluate : 4.018 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3156 time to fit residues: 11.7054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 0.8980 chunk 415 optimal weight: 0.0370 chunk 253 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 289 optimal weight: 0.9980 chunk 436 optimal weight: 0.9990 chunk 401 optimal weight: 1.9990 chunk 347 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 268 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.9292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 35484 Z= 0.162 Angle : 0.574 11.174 47976 Z= 0.269 Chirality : 0.045 0.231 5376 Planarity : 0.004 0.061 6306 Dihedral : 6.695 126.119 4920 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.78 % Favored : 96.08 % Rotamer Outliers : 0.19 % 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: -0.64 (0.13), residues: 4386 helix: -0.19 (0.13), residues: 1716 sheet: 0.91 (0.25), residues: 468 loop : -0.86 (0.14), residues: 2202 ********************** 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 225 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 218 time to evaluate : 4.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 222 average time/residue: 0.4584 time to fit residues: 172.8833 Evaluate side-chains 210 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 206 time to evaluate : 4.247 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3602 time to fit residues: 8.5601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 8.9990 chunk 370 optimal weight: 30.0000 chunk 106 optimal weight: 0.0670 chunk 320 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 348 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 357 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 HIS ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 HIS ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.120659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.076398 restraints weight = 77046.469| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.01 r_work: 0.2939 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work: 0.2906 rms_B_bonded: 3.70 restraints_weight: 0.1250 r_work: 0.2889 rms_B_bonded: 3.75 restraints_weight: 0.0625 r_work: 0.2872 rms_B_bonded: 3.83 restraints_weight: 0.0312 r_work: 0.2854 rms_B_bonded: 3.94 restraints_weight: 0.0156 r_work: 0.2835 rms_B_bonded: 4.08 restraints_weight: 0.0078 r_work: 0.2815 rms_B_bonded: 4.24 restraints_weight: 0.0039 r_work: 0.2795 rms_B_bonded: 4.44 restraints_weight: 0.0020 r_work: 0.2773 rms_B_bonded: 4.67 restraints_weight: 0.0010 r_work: 0.2750 rms_B_bonded: 4.94 restraints_weight: 0.0005 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.9720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 35484 Z= 0.355 Angle : 0.656 11.105 47976 Z= 0.316 Chirality : 0.048 0.236 5376 Planarity : 0.004 0.064 6306 Dihedral : 7.111 133.444 4920 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.74 % Favored : 95.12 % Rotamer Outliers : 0.24 % 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: -0.72 (0.13), residues: 4386 helix: -0.28 (0.13), residues: 1758 sheet: 0.74 (0.25), residues: 480 loop : -0.85 (0.14), residues: 2148 =============================================================================== Job complete usr+sys time: 5921.59 seconds wall clock time: 109 minutes 39.86 seconds (6579.86 seconds total)