Starting phenix.real_space_refine on Fri Feb 16 00:58:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba9_15942/02_2024/8ba9_15942_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba9_15942/02_2024/8ba9_15942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba9_15942/02_2024/8ba9_15942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba9_15942/02_2024/8ba9_15942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba9_15942/02_2024/8ba9_15942_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba9_15942/02_2024/8ba9_15942_trim_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 10 Type Number sf(0) Gaussians K 7 8.98 5 Al 7 5.89 5 P 28 5.49 5 Mg 14 5.21 5 S 294 5.16 5 C 36841 2.51 5 N 10262 2.21 5 O 11977 1.98 5 F 21 1.80 5 H 60991 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ASP 283": "OD1" <-> "OD2" Residue "B TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 461": "OE1" <-> "OE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "E ASP 359": "OD1" <-> "OD2" Residue "E GLU 461": "OE1" <-> "OE2" Residue "F PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 391": "OE1" <-> "OE2" Residue "I GLU 397": "OE1" <-> "OE2" Residue "I GLU 461": "OE1" <-> "OE2" Residue "J TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 52": "OD1" <-> "OD2" Residue "L ASP 11": "OD1" <-> "OD2" Residue "L PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 59": "OE1" <-> "OE2" Residue "L GLU 461": "OE1" <-> "OE2" Residue "M PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M ASP 83": "OD1" <-> "OD2" Residue "M TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 397": "OE1" <-> "OE2" Residue "N ASP 11": "OD1" <-> "OD2" Residue "N ASP 398": "OD1" <-> "OD2" Residue "N ASP 495": "OD1" <-> "OD2" Residue "P ASP 69": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 120442 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7835 Classifications: {'peptide': 524} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "B" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7835 Classifications: {'peptide': 524} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "C" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7835 Classifications: {'peptide': 524} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "D" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7835 Classifications: {'peptide': 524} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "E" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7835 Classifications: {'peptide': 524} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "F" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7835 Classifications: {'peptide': 524} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "G" Number of atoms: 7835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7835 Classifications: {'peptide': 524} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "H" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 7820 Classifications: {'peptide': 523} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain: "I" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 7820 Classifications: {'peptide': 523} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain: "J" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 7820 Classifications: {'peptide': 523} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain: "K" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 7820 Classifications: {'peptide': 523} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain: "L" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 7820 Classifications: {'peptide': 523} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain: "M" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 7820 Classifications: {'peptide': 523} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain: "N" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 7820 Classifications: {'peptide': 523} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain: "O" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1490 Classifications: {'peptide': 97} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "P" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1490 Classifications: {'peptide': 97} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "Q" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1490 Classifications: {'peptide': 97} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "R" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1490 Classifications: {'peptide': 97} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "S" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1490 Classifications: {'peptide': 97} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "T" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1490 Classifications: {'peptide': 97} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "U" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1490 Classifications: {'peptide': 97} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 36.49, per 1000 atoms: 0.30 Number of scatterers: 120442 At special positions: 0 Unit cell: (176.671, 175.822, 222.538, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) K 7 19.00 S 294 16.00 P 28 15.00 Al 7 13.00 Mg 14 11.99 F 21 9.00 O 11977 8.00 N 10262 7.00 C 36841 6.00 H 60991 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 74.23 Conformation dependent library (CDL) restraints added in 8.9 seconds 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14476 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 273 helices and 89 sheets defined 56.6% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 28.61 Creating SS restraints... Processing helix chain 'A' and resid 9 through 28 removed outlier: 3.959A pdb=" N LYS A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.783A pdb=" N GLU A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 85 removed outlier: 3.715A pdb=" N GLY A 70 " --> pdb=" O PHE A 66 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 110 removed outlier: 3.644A pdb=" N ALA A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 140 through 153 Processing helix chain 'A' and resid 155 through 170 removed outlier: 3.541A pdb=" N GLY A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 244 removed outlier: 3.775A pdb=" N MET A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 282 through 297 Processing helix chain 'A' and resid 313 through 318 removed outlier: 5.685A pdb=" N GLY A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 385 through 409 removed outlier: 3.815A pdb=" N GLU A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 428 removed outlier: 3.762A pdb=" N ALA A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASP A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 459 removed outlier: 4.530A pdb=" N GLU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Proline residue: A 450 - end of helix removed outlier: 3.683A pdb=" N CYS A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 473 removed outlier: 3.563A pdb=" N THR A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 496 through 517 removed outlier: 3.951A pdb=" N LEU A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.825A pdb=" N LYS B 15 " --> pdb=" O ASP B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 61 removed outlier: 3.576A pdb=" N VAL B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 85 removed outlier: 4.183A pdb=" N GLY B 70 " --> pdb=" O PHE B 66 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 110 removed outlier: 3.513A pdb=" N ALA B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 135 removed outlier: 3.645A pdb=" N GLU B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 153 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.721A pdb=" N GLY B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 244 removed outlier: 3.986A pdb=" N MET B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 255 through 269 Processing helix chain 'B' and resid 282 through 297 removed outlier: 3.599A pdb=" N LYS B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 removed outlier: 5.518A pdb=" N GLY B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 358 through 374 Processing helix chain 'B' and resid 385 through 409 removed outlier: 3.760A pdb=" N GLU B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 428 removed outlier: 3.651A pdb=" N LYS B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASP B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 459 removed outlier: 3.646A pdb=" N ALA B 443 " --> pdb=" O GLY B 439 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ALA B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) Proline residue: B 450 - end of helix removed outlier: 3.591A pdb=" N CYS B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 473 removed outlier: 3.651A pdb=" N VAL B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASP B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 496 through 517 removed outlier: 4.060A pdb=" N LEU B 513 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET B 514 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 28 removed outlier: 3.500A pdb=" N ARG C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS C 15 " --> pdb=" O ASP C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 61 removed outlier: 3.774A pdb=" N GLU C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLU C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 85 removed outlier: 4.160A pdb=" N GLY C 70 " --> pdb=" O PHE C 66 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA C 71 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU C 76 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 110 removed outlier: 3.781A pdb=" N ALA C 109 " --> pdb=" O LYS C 105 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 135 removed outlier: 3.626A pdb=" N GLU C 129 " --> pdb=" O THR C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 153 Processing helix chain 'C' and resid 155 through 170 removed outlier: 3.598A pdb=" N GLY C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 244 removed outlier: 4.114A pdb=" N MET C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 255 through 269 removed outlier: 3.558A pdb=" N ARG C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 297 Processing helix chain 'C' and resid 313 through 318 removed outlier: 5.134A pdb=" N GLY C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 358 through 374 removed outlier: 3.618A pdb=" N LYS C 364 " --> pdb=" O TYR C 360 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY C 374 " --> pdb=" O ALA C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 409 removed outlier: 3.800A pdb=" N ALA C 394 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 428 removed outlier: 3.864A pdb=" N ALA C 427 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASP C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 459 removed outlier: 3.699A pdb=" N ALA C 443 " --> pdb=" O GLY C 439 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Proline residue: C 450 - end of helix Processing helix chain 'C' and resid 461 through 473 removed outlier: 3.642A pdb=" N VAL C 465 " --> pdb=" O GLU C 461 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASP C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 496 through 517 removed outlier: 3.945A pdb=" N LEU C 513 " --> pdb=" O SER C 509 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR C 516 " --> pdb=" O GLY C 512 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 28 removed outlier: 3.990A pdb=" N LYS D 15 " --> pdb=" O ASP D 11 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA D 26 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 61 removed outlier: 3.530A pdb=" N VAL D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLU D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 85 removed outlier: 4.109A pdb=" N GLY D 70 " --> pdb=" O PHE D 66 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D 71 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU D 76 " --> pdb=" O GLN D 72 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 110 removed outlier: 3.588A pdb=" N ALA D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 135 removed outlier: 3.559A pdb=" N LEU D 116 " --> pdb=" O ASN D 112 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 129 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 153 Processing helix chain 'D' and resid 155 through 170 removed outlier: 3.633A pdb=" N GLY D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 244 removed outlier: 4.410A pdb=" N MET D 233 " --> pdb=" O ASN D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 282 through 297 removed outlier: 3.519A pdb=" N LYS D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 318 removed outlier: 3.631A pdb=" N LEU D 317 " --> pdb=" O THR D 313 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLY D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 313 through 318' Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 358 through 374 Processing helix chain 'D' and resid 385 through 409 Processing helix chain 'D' and resid 416 through 428 removed outlier: 3.894A pdb=" N LYS D 425 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 426 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ASP D 428 " --> pdb=" O SER D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 459 removed outlier: 4.383A pdb=" N GLU D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA D 449 " --> pdb=" O ARG D 445 " (cutoff:3.500A) Proline residue: D 450 - end of helix removed outlier: 3.801A pdb=" N CYS D 458 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY D 459 " --> pdb=" O VAL D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 473 removed outlier: 3.581A pdb=" N VAL D 465 " --> pdb=" O GLU D 461 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY D 472 " --> pdb=" O THR D 468 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 496 through 517 removed outlier: 3.590A pdb=" N THR D 500 " --> pdb=" O PRO D 496 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N THR D 516 " --> pdb=" O GLY D 512 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 28 removed outlier: 3.568A pdb=" N VAL E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 61 removed outlier: 3.756A pdb=" N GLU E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLU E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 85 removed outlier: 4.166A pdb=" N GLU E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 110 removed outlier: 3.856A pdb=" N ALA E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 135 removed outlier: 3.629A pdb=" N ALA E 133 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 153 Processing helix chain 'E' and resid 155 through 170 Processing helix chain 'E' and resid 229 through 244 removed outlier: 4.192A pdb=" N MET E 233 " --> pdb=" O ASN E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 282 through 297 Processing helix chain 'E' and resid 313 through 318 removed outlier: 5.355A pdb=" N GLY E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 356 Processing helix chain 'E' and resid 358 through 374 removed outlier: 3.772A pdb=" N LYS E 364 " --> pdb=" O TYR E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 409 Processing helix chain 'E' and resid 416 through 428 removed outlier: 3.938A pdb=" N ALA E 427 " --> pdb=" O ALA E 423 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ASP E 428 " --> pdb=" O SER E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 459 removed outlier: 4.663A pdb=" N GLU E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA E 449 " --> pdb=" O ARG E 445 " (cutoff:3.500A) Proline residue: E 450 - end of helix Processing helix chain 'E' and resid 461 through 473 removed outlier: 3.893A pdb=" N VAL E 465 " --> pdb=" O GLU E 461 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASP E 473 " --> pdb=" O VAL E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 492 Processing helix chain 'E' and resid 496 through 517 removed outlier: 3.564A pdb=" N VAL E 510 " --> pdb=" O TYR E 506 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU E 513 " --> pdb=" O SER E 509 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE E 515 " --> pdb=" O ALA E 511 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N THR E 516 " --> pdb=" O GLY E 512 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR E 517 " --> pdb=" O LEU E 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 removed outlier: 3.831A pdb=" N LYS F 15 " --> pdb=" O ASP F 11 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL F 22 " --> pdb=" O ARG F 18 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 23 " --> pdb=" O GLY F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 61 removed outlier: 3.904A pdb=" N GLU F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE F 60 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLU F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 85 removed outlier: 3.921A pdb=" N GLY F 70 " --> pdb=" O PHE F 66 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU F 76 " --> pdb=" O GLN F 72 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 110 removed outlier: 3.700A pdb=" N ALA F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 135 removed outlier: 3.700A pdb=" N GLU F 129 " --> pdb=" O THR F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 153 Processing helix chain 'F' and resid 155 through 170 Processing helix chain 'F' and resid 229 through 244 removed outlier: 4.143A pdb=" N MET F 233 " --> pdb=" O ASN F 229 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.560A pdb=" N GLU F 238 " --> pdb=" O LEU F 234 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 269 Processing helix chain 'F' and resid 282 through 297 Processing helix chain 'F' and resid 313 through 318 removed outlier: 5.467A pdb=" N GLY F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 356 removed outlier: 4.028A pdb=" N GLU F 355 " --> pdb=" O GLN F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 374 Processing helix chain 'F' and resid 385 through 409 removed outlier: 3.751A pdb=" N GLU F 391 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA F 394 " --> pdb=" O LYS F 390 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU F 408 " --> pdb=" O ARG F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 428 removed outlier: 3.722A pdb=" N LYS F 425 " --> pdb=" O ARG F 421 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU F 426 " --> pdb=" O VAL F 422 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA F 427 " --> pdb=" O ALA F 423 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASP F 428 " --> pdb=" O SER F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 459 removed outlier: 4.262A pdb=" N GLU F 448 " --> pdb=" O LEU F 444 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA F 449 " --> pdb=" O ARG F 445 " (cutoff:3.500A) Proline residue: F 450 - end of helix removed outlier: 3.625A pdb=" N CYS F 458 " --> pdb=" O ILE F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 473 removed outlier: 5.118A pdb=" N ASP F 473 " --> pdb=" O VAL F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 487 through 492 Processing helix chain 'F' and resid 496 through 517 removed outlier: 3.748A pdb=" N LEU F 513 " --> pdb=" O SER F 509 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F 515 " --> pdb=" O ALA F 511 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N THR F 516 " --> pdb=" O GLY F 512 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR F 517 " --> pdb=" O LEU F 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 28 removed outlier: 3.694A pdb=" N LYS G 15 " --> pdb=" O ASP G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 61 removed outlier: 3.907A pdb=" N GLU G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE G 60 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLU G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 85 removed outlier: 4.240A pdb=" N GLU G 76 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 110 removed outlier: 3.673A pdb=" N ALA G 109 " --> pdb=" O LYS G 105 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 135 Processing helix chain 'G' and resid 140 through 153 removed outlier: 3.667A pdb=" N GLN G 146 " --> pdb=" O LYS G 142 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL G 147 " --> pdb=" O ALA G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 170 removed outlier: 3.743A pdb=" N GLY G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 244 removed outlier: 4.039A pdb=" N MET G 233 " --> pdb=" O ASN G 229 " (cutoff:3.500A) Proline residue: G 235 - end of helix Processing helix chain 'G' and resid 255 through 269 removed outlier: 3.928A pdb=" N ARG G 268 " --> pdb=" O VAL G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 297 removed outlier: 3.543A pdb=" N LYS G 286 " --> pdb=" O GLY G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 318 removed outlier: 5.513A pdb=" N GLY G 318 " --> pdb=" O LEU G 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 356 Processing helix chain 'G' and resid 358 through 374 removed outlier: 3.541A pdb=" N ARG G 368 " --> pdb=" O LYS G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 409 removed outlier: 3.663A pdb=" N GLU G 408 " --> pdb=" O ARG G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 428 removed outlier: 3.547A pdb=" N LYS G 425 " --> pdb=" O ARG G 421 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA G 427 " --> pdb=" O ALA G 423 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASP G 428 " --> pdb=" O SER G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 459 removed outlier: 4.296A pdb=" N GLU G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA G 449 " --> pdb=" O ARG G 445 " (cutoff:3.500A) Proline residue: G 450 - end of helix removed outlier: 3.674A pdb=" N CYS G 458 " --> pdb=" O ILE G 454 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY G 459 " --> pdb=" O VAL G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 473 removed outlier: 3.760A pdb=" N VAL G 465 " --> pdb=" O GLU G 461 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP G 473 " --> pdb=" O VAL G 469 " (cutoff:3.500A) Processing helix chain 'G' and resid 487 through 492 Processing helix chain 'G' and resid 496 through 517 removed outlier: 3.864A pdb=" N LEU G 513 " --> pdb=" O SER G 509 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE G 515 " --> pdb=" O ALA G 511 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N THR G 516 " --> pdb=" O GLY G 512 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR G 517 " --> pdb=" O LEU G 513 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 28 removed outlier: 4.352A pdb=" N LYS H 15 " --> pdb=" O ASP H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 61 removed outlier: 3.739A pdb=" N GLU H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 86 removed outlier: 4.133A pdb=" N GLY H 70 " --> pdb=" O PHE H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 110 removed outlier: 3.924A pdb=" N GLU H 102 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 135 removed outlier: 3.616A pdb=" N GLU H 129 " --> pdb=" O THR H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 153 Processing helix chain 'H' and resid 155 through 170 removed outlier: 3.845A pdb=" N GLY H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 244 removed outlier: 4.315A pdb=" N LEU H 234 " --> pdb=" O ILE H 230 " (cutoff:3.500A) Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 255 through 267 removed outlier: 4.640A pdb=" N THR H 261 " --> pdb=" O GLU H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 297 Processing helix chain 'H' and resid 308 through 313 removed outlier: 6.246A pdb=" N THR H 313 " --> pdb=" O LEU H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 354 removed outlier: 4.711A pdb=" N GLU H 354 " --> pdb=" O ARG H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 374 removed outlier: 4.692A pdb=" N LEU H 365 " --> pdb=" O ASP H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 409 Processing helix chain 'H' and resid 416 through 427 removed outlier: 3.640A pdb=" N ALA H 427 " --> pdb=" O ALA H 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 459 removed outlier: 3.509A pdb=" N ALA H 443 " --> pdb=" O GLY H 439 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLU H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA H 449 " --> pdb=" O ARG H 445 " (cutoff:3.500A) Proline residue: H 450 - end of helix Processing helix chain 'H' and resid 461 through 473 removed outlier: 3.590A pdb=" N VAL H 465 " --> pdb=" O GLU H 461 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASP H 473 " --> pdb=" O VAL H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 487 through 492 Processing helix chain 'H' and resid 496 through 517 removed outlier: 3.754A pdb=" N THR H 500 " --> pdb=" O PRO H 496 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR H 517 " --> pdb=" O LEU H 513 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 28 removed outlier: 3.618A pdb=" N LYS I 15 " --> pdb=" O ASP I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 61 removed outlier: 5.857A pdb=" N GLU I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 86 removed outlier: 3.740A pdb=" N GLY I 70 " --> pdb=" O PHE I 66 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY I 86 " --> pdb=" O ASN I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 110 removed outlier: 3.782A pdb=" N GLU I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY I 110 " --> pdb=" O ALA I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 140 through 153 Processing helix chain 'I' and resid 155 through 170 removed outlier: 3.715A pdb=" N GLY I 159 " --> pdb=" O ASP I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 244 Proline residue: I 235 - end of helix Processing helix chain 'I' and resid 255 through 267 removed outlier: 4.670A pdb=" N LEU I 262 " --> pdb=" O ALA I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 297 removed outlier: 4.226A pdb=" N THR I 294 " --> pdb=" O GLN I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 313 removed outlier: 6.671A pdb=" N THR I 313 " --> pdb=" O LEU I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 354 Processing helix chain 'I' and resid 359 through 374 removed outlier: 4.308A pdb=" N LYS I 364 " --> pdb=" O TYR I 360 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG I 368 " --> pdb=" O LYS I 364 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY I 374 " --> pdb=" O ALA I 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 409 Processing helix chain 'I' and resid 416 through 427 removed outlier: 3.914A pdb=" N ALA I 427 " --> pdb=" O ALA I 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 459 removed outlier: 4.366A pdb=" N GLU I 448 " --> pdb=" O LEU I 444 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA I 449 " --> pdb=" O ARG I 445 " (cutoff:3.500A) Proline residue: I 450 - end of helix removed outlier: 3.757A pdb=" N CYS I 458 " --> pdb=" O ILE I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 473 removed outlier: 3.587A pdb=" N VAL I 465 " --> pdb=" O GLU I 461 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP I 473 " --> pdb=" O VAL I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 487 through 492 Processing helix chain 'I' and resid 496 through 517 removed outlier: 3.668A pdb=" N THR I 500 " --> pdb=" O PRO I 496 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR I 516 " --> pdb=" O GLY I 512 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR I 517 " --> pdb=" O LEU I 513 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 28 removed outlier: 3.803A pdb=" N LYS M 15 " --> pdb=" O ASP M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 61 removed outlier: 3.828A pdb=" N VAL M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU M 59 " --> pdb=" O SER M 55 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLU M 61 " --> pdb=" O ALA M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 86 removed outlier: 4.303A pdb=" N GLY M 70 " --> pdb=" O PHE M 66 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA M 71 " --> pdb=" O GLU M 67 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL M 74 " --> pdb=" O GLY M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 110 removed outlier: 3.905A pdb=" N GLU M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY M 110 " --> pdb=" O ALA M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 135 Processing helix chain 'M' and resid 140 through 153 removed outlier: 3.656A pdb=" N ASN M 153 " --> pdb=" O THR M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 170 removed outlier: 3.598A pdb=" N GLY M 159 " --> pdb=" O ASP M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 230 through 244 removed outlier: 4.446A pdb=" N LEU M 234 " --> pdb=" O ILE M 230 " (cutoff:3.500A) Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 255 through 267 removed outlier: 4.348A pdb=" N THR M 261 " --> pdb=" O GLU M 257 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 297 removed outlier: 3.644A pdb=" N LYS M 286 " --> pdb=" O GLY M 282 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP M 291 " --> pdb=" O ALA M 287 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR M 294 " --> pdb=" O GLN M 290 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 313 removed outlier: 5.956A pdb=" N THR M 313 " --> pdb=" O LEU M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 354 removed outlier: 4.396A pdb=" N GLU M 354 " --> pdb=" O ARG M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 374 removed outlier: 5.975A pdb=" N GLY M 374 " --> pdb=" O ALA M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 409 Processing helix chain 'M' and resid 416 through 427 removed outlier: 3.905A pdb=" N ALA M 427 " --> pdb=" O ALA M 423 " (cutoff:3.500A) Processing helix chain 'M' and resid 433 through 459 removed outlier: 4.183A pdb=" N GLU M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA M 449 " --> pdb=" O ARG M 445 " (cutoff:3.500A) Proline residue: M 450 - end of helix Processing helix chain 'M' and resid 461 through 473 removed outlier: 3.643A pdb=" N VAL M 465 " --> pdb=" O GLU M 461 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASP M 473 " --> pdb=" O VAL M 469 " (cutoff:3.500A) Processing helix chain 'M' and resid 487 through 492 Processing helix chain 'M' and resid 496 through 517 removed outlier: 3.650A pdb=" N THR M 500 " --> pdb=" O PRO M 496 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR M 516 " --> pdb=" O GLY M 512 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR M 517 " --> pdb=" O LEU M 513 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 31 removed outlier: 3.830A pdb=" N LYS J 15 " --> pdb=" O ASP J 11 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N THR J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU J 31 " --> pdb=" O VAL J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 60 removed outlier: 3.936A pdb=" N GLU J 59 " --> pdb=" O SER J 55 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 85 removed outlier: 3.793A pdb=" N VAL J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 110 removed outlier: 3.724A pdb=" N GLU J 102 " --> pdb=" O ALA J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 135 removed outlier: 3.991A pdb=" N GLU J 129 " --> pdb=" O THR J 125 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU J 130 " --> pdb=" O ALA J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 153 Processing helix chain 'J' and resid 155 through 170 removed outlier: 3.752A pdb=" N GLY J 159 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 230 through 242 removed outlier: 3.848A pdb=" N LEU J 234 " --> pdb=" O ILE J 230 " (cutoff:3.500A) Proline residue: J 235 - end of helix removed outlier: 3.950A pdb=" N LYS J 242 " --> pdb=" O GLU J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 268 removed outlier: 5.281A pdb=" N ARG J 268 " --> pdb=" O VAL J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 297 Processing helix chain 'J' and resid 308 through 313 removed outlier: 5.382A pdb=" N THR J 313 " --> pdb=" O LEU J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 356 removed outlier: 4.587A pdb=" N ILE J 342 " --> pdb=" O GLU J 338 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU J 354 " --> pdb=" O ARG J 350 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU J 355 " --> pdb=" O GLN J 351 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 375 removed outlier: 3.657A pdb=" N LYS J 364 " --> pdb=" O TYR J 360 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU J 367 " --> pdb=" O GLU J 363 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG J 368 " --> pdb=" O LYS J 364 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL J 369 " --> pdb=" O LEU J 365 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA J 370 " --> pdb=" O GLN J 366 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY J 374 " --> pdb=" O ALA J 370 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLY J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 410 Processing helix chain 'J' and resid 416 through 428 removed outlier: 3.658A pdb=" N ALA J 427 " --> pdb=" O ALA J 423 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASP J 428 " --> pdb=" O SER J 424 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 459 removed outlier: 3.954A pdb=" N GLU J 448 " --> pdb=" O LEU J 444 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA J 449 " --> pdb=" O ARG J 445 " (cutoff:3.500A) Proline residue: J 450 - end of helix Processing helix chain 'J' and resid 461 through 473 removed outlier: 3.641A pdb=" N VAL J 465 " --> pdb=" O GLU J 461 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASP J 473 " --> pdb=" O VAL J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 487 through 492 Processing helix chain 'J' and resid 496 through 517 removed outlier: 3.570A pdb=" N THR J 500 " --> pdb=" O PRO J 496 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR J 516 " --> pdb=" O GLY J 512 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR J 517 " --> pdb=" O LEU J 513 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 31 removed outlier: 3.986A pdb=" N LYS K 15 " --> pdb=" O ASP K 11 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA K 26 " --> pdb=" O VAL K 22 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU K 31 " --> pdb=" O VAL K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 60 removed outlier: 4.201A pdb=" N GLU K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE K 60 " --> pdb=" O VAL K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 85 removed outlier: 3.737A pdb=" N MET K 69 " --> pdb=" O LYS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 110 removed outlier: 4.063A pdb=" N GLU K 102 " --> pdb=" O ALA K 98 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY K 110 " --> pdb=" O ALA K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 135 removed outlier: 3.891A pdb=" N GLU K 129 " --> pdb=" O THR K 125 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU K 130 " --> pdb=" O ALA K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 153 Processing helix chain 'K' and resid 155 through 170 removed outlier: 3.877A pdb=" N GLY K 159 " --> pdb=" O ASP K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 230 through 242 Proline residue: K 235 - end of helix removed outlier: 3.937A pdb=" N LYS K 242 " --> pdb=" O GLU K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 268 removed outlier: 5.246A pdb=" N ARG K 268 " --> pdb=" O VAL K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 297 Processing helix chain 'K' and resid 308 through 313 removed outlier: 5.529A pdb=" N THR K 313 " --> pdb=" O LEU K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 356 removed outlier: 4.165A pdb=" N ILE K 342 " --> pdb=" O GLU K 338 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU K 354 " --> pdb=" O ARG K 350 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU K 355 " --> pdb=" O GLN K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 375 removed outlier: 3.818A pdb=" N ARG K 362 " --> pdb=" O SER K 358 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS K 364 " --> pdb=" O TYR K 360 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA K 370 " --> pdb=" O GLN K 366 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLY K 374 " --> pdb=" O ALA K 370 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLY K 375 " --> pdb=" O LYS K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 410 Processing helix chain 'K' and resid 416 through 428 removed outlier: 3.669A pdb=" N SER K 424 " --> pdb=" O ILE K 420 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS K 425 " --> pdb=" O ARG K 421 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA K 427 " --> pdb=" O ALA K 423 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP K 428 " --> pdb=" O SER K 424 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 459 removed outlier: 4.094A pdb=" N GLU K 448 " --> pdb=" O LEU K 444 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA K 449 " --> pdb=" O ARG K 445 " (cutoff:3.500A) Proline residue: K 450 - end of helix removed outlier: 3.563A pdb=" N GLY K 459 " --> pdb=" O VAL K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 473 removed outlier: 3.727A pdb=" N VAL K 465 " --> pdb=" O GLU K 461 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP K 473 " --> pdb=" O VAL K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 487 through 492 Processing helix chain 'K' and resid 496 through 517 removed outlier: 3.633A pdb=" N THR K 516 " --> pdb=" O GLY K 512 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR K 517 " --> pdb=" O LEU K 513 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 31 removed outlier: 4.481A pdb=" N LYS L 15 " --> pdb=" O ASP L 11 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N THR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU L 31 " --> pdb=" O VAL L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 60 removed outlier: 3.740A pdb=" N GLU L 59 " --> pdb=" O SER L 55 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE L 60 " --> pdb=" O VAL L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 85 removed outlier: 3.740A pdb=" N VAL L 74 " --> pdb=" O GLY L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 110 removed outlier: 4.013A pdb=" N GLU L 102 " --> pdb=" O ALA L 98 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 135 removed outlier: 3.695A pdb=" N GLU L 129 " --> pdb=" O THR L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 153 Processing helix chain 'L' and resid 155 through 170 removed outlier: 3.935A pdb=" N GLY L 159 " --> pdb=" O ASP L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 242 removed outlier: 3.504A pdb=" N LEU L 234 " --> pdb=" O ILE L 230 " (cutoff:3.500A) Proline residue: L 235 - end of helix removed outlier: 4.045A pdb=" N LYS L 242 " --> pdb=" O GLU L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 268 removed outlier: 5.298A pdb=" N ARG L 268 " --> pdb=" O VAL L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 297 Processing helix chain 'L' and resid 308 through 313 removed outlier: 5.334A pdb=" N THR L 313 " --> pdb=" O LEU L 309 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 356 removed outlier: 4.149A pdb=" N ILE L 342 " --> pdb=" O GLU L 338 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU L 354 " --> pdb=" O ARG L 350 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU L 355 " --> pdb=" O GLN L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 375 removed outlier: 4.059A pdb=" N ARG L 362 " --> pdb=" O SER L 358 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU L 363 " --> pdb=" O ASP L 359 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS L 364 " --> pdb=" O TYR L 360 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA L 370 " --> pdb=" O GLN L 366 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLY L 374 " --> pdb=" O ALA L 370 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY L 375 " --> pdb=" O LYS L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 410 Processing helix chain 'L' and resid 416 through 428 removed outlier: 3.583A pdb=" N ALA L 427 " --> pdb=" O ALA L 423 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASP L 428 " --> pdb=" O SER L 424 " (cutoff:3.500A) Processing helix chain 'L' and resid 433 through 459 removed outlier: 4.048A pdb=" N GLU L 448 " --> pdb=" O LEU L 444 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA L 449 " --> pdb=" O ARG L 445 " (cutoff:3.500A) Proline residue: L 450 - end of helix Processing helix chain 'L' and resid 461 through 473 removed outlier: 3.600A pdb=" N VAL L 465 " --> pdb=" O GLU L 461 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASP L 473 " --> pdb=" O VAL L 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 487 through 492 Processing helix chain 'L' and resid 496 through 517 removed outlier: 4.009A pdb=" N THR L 516 " --> pdb=" O GLY L 512 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR L 517 " --> pdb=" O LEU L 513 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 28 removed outlier: 3.608A pdb=" N LYS N 15 " --> pdb=" O ASP N 11 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 60 removed outlier: 3.763A pdb=" N GLU N 59 " --> pdb=" O SER N 55 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE N 60 " --> pdb=" O VAL N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 86 removed outlier: 3.616A pdb=" N GLY N 70 " --> pdb=" O PHE N 66 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL N 74 " --> pdb=" O GLY N 70 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY N 86 " --> pdb=" O ASN N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 110 removed outlier: 3.811A pdb=" N GLU N 102 " --> pdb=" O ALA N 98 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY N 110 " --> pdb=" O ALA N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 135 removed outlier: 3.535A pdb=" N ALA N 123 " --> pdb=" O GLY N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 153 Processing helix chain 'N' and resid 155 through 170 removed outlier: 3.681A pdb=" N GLY N 159 " --> pdb=" O ASP N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 244 removed outlier: 4.733A pdb=" N MET N 233 " --> pdb=" O ASN N 229 " (cutoff:3.500A) Proline residue: N 235 - end of helix removed outlier: 3.746A pdb=" N ALA N 243 " --> pdb=" O ALA N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 268 removed outlier: 5.360A pdb=" N ARG N 268 " --> pdb=" O VAL N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 282 through 297 Processing helix chain 'N' and resid 313 through 318 removed outlier: 5.452A pdb=" N GLY N 318 " --> pdb=" O LEU N 314 " (cutoff:3.500A) Processing helix chain 'N' and resid 338 through 356 removed outlier: 3.721A pdb=" N GLU N 354 " --> pdb=" O ARG N 350 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 372 Processing helix chain 'N' and resid 386 through 410 Processing helix chain 'N' and resid 416 through 427 removed outlier: 3.523A pdb=" N SER N 424 " --> pdb=" O ILE N 420 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS N 425 " --> pdb=" O ARG N 421 " (cutoff:3.500A) Processing helix chain 'N' and resid 433 through 459 removed outlier: 4.282A pdb=" N GLU N 448 " --> pdb=" O LEU N 444 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA N 449 " --> pdb=" O ARG N 445 " (cutoff:3.500A) Proline residue: N 450 - end of helix removed outlier: 3.544A pdb=" N CYS N 458 " --> pdb=" O ILE N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 461 through 473 removed outlier: 4.846A pdb=" N ASP N 473 " --> pdb=" O VAL N 469 " (cutoff:3.500A) Processing helix chain 'N' and resid 487 through 492 Processing helix chain 'N' and resid 496 through 517 removed outlier: 3.659A pdb=" N THR N 500 " --> pdb=" O PRO N 496 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR N 516 " --> pdb=" O GLY N 512 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 92 removed outlier: 3.987A pdb=" N ILE O 91 " --> pdb=" O SER O 87 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU O 92 " --> pdb=" O GLU O 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 87 through 92' Processing helix chain 'P' and resid 87 through 92 removed outlier: 3.554A pdb=" N ILE P 91 " --> pdb=" O SER P 87 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU P 92 " --> pdb=" O GLU P 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 87 through 92' Processing helix chain 'Q' and resid 87 through 92 removed outlier: 4.129A pdb=" N ILE Q 91 " --> pdb=" O SER Q 87 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU Q 92 " --> pdb=" O GLU Q 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 87 through 92' Processing helix chain 'R' and resid 87 through 92 removed outlier: 4.378A pdb=" N ILE R 91 " --> pdb=" O SER R 87 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU R 92 " --> pdb=" O GLU R 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 87 through 92' Processing helix chain 'S' and resid 87 through 92 removed outlier: 4.167A pdb=" N ILE S 91 " --> pdb=" O SER S 87 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU S 92 " --> pdb=" O GLU S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 92' Processing helix chain 'T' and resid 87 through 92 removed outlier: 3.916A pdb=" N ILE T 91 " --> pdb=" O SER T 87 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU T 92 " --> pdb=" O GLU T 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 87 through 92' Processing helix chain 'U' and resid 87 through 92 removed outlier: 4.021A pdb=" N ILE U 91 " --> pdb=" O SER U 87 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU U 92 " --> pdb=" O GLU U 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 87 through 92' Processing sheet with id= 1, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= 2, first strand: chain 'A' and resid 37 through 41 Processing sheet with id= 3, first strand: chain 'A' and resid 184 through 190 removed outlier: 4.480A pdb=" N GLN A 184 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 382 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 193 through 197 removed outlier: 3.930A pdb=" N MET A 193 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASP A 328 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR A 329 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG A 322 " --> pdb=" O ILE A 333 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 218 through 223 Processing sheet with id= 6, first strand: chain 'A' and resid 477 through 480 Processing sheet with id= 7, first strand: chain 'B' and resid 4 through 8 Processing sheet with id= 8, first strand: chain 'B' and resid 37 through 41 Processing sheet with id= 9, first strand: chain 'B' and resid 184 through 190 removed outlier: 5.365A pdb=" N GLN B 184 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY B 382 " --> pdb=" O GLN B 184 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 193 through 197 removed outlier: 3.751A pdb=" N MET B 193 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASP B 328 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 329 " --> pdb=" O ASN B 326 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 322 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 218 through 223 Processing sheet with id= 12, first strand: chain 'B' and resid 477 through 480 removed outlier: 3.531A pdb=" N GLU B 484 " --> pdb=" O ASN B 479 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= 14, first strand: chain 'C' and resid 37 through 41 Processing sheet with id= 15, first strand: chain 'C' and resid 184 through 190 removed outlier: 5.208A pdb=" N GLN C 184 " --> pdb=" O GLY C 382 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY C 382 " --> pdb=" O GLN C 184 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'C' and resid 193 through 197 removed outlier: 3.620A pdb=" N MET C 193 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 197 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ASP C 328 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C 329 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'C' and resid 218 through 223 Processing sheet with id= 18, first strand: chain 'C' and resid 477 through 480 Processing sheet with id= 19, first strand: chain 'D' and resid 4 through 8 Processing sheet with id= 20, first strand: chain 'D' and resid 37 through 41 Processing sheet with id= 21, first strand: chain 'D' and resid 184 through 190 removed outlier: 4.629A pdb=" N GLN D 184 " --> pdb=" O GLY D 382 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY D 382 " --> pdb=" O GLN D 184 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'D' and resid 193 through 197 removed outlier: 3.512A pdb=" N MET D 193 " --> pdb=" O ILE D 332 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG D 197 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP D 328 " --> pdb=" O ARG D 197 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR D 329 " --> pdb=" O ASN D 326 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D 322 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 218 through 223 Processing sheet with id= 24, first strand: chain 'D' and resid 477 through 480 Processing sheet with id= 25, first strand: chain 'E' and resid 4 through 8 Processing sheet with id= 26, first strand: chain 'E' and resid 37 through 41 Processing sheet with id= 27, first strand: chain 'E' and resid 184 through 190 removed outlier: 5.090A pdb=" N GLN E 184 " --> pdb=" O GLY E 382 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY E 382 " --> pdb=" O GLN E 184 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'E' and resid 193 through 197 removed outlier: 3.947A pdb=" N MET E 193 " --> pdb=" O ILE E 332 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASP E 328 " --> pdb=" O ARG E 197 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR E 329 " --> pdb=" O ASN E 326 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG E 322 " --> pdb=" O ILE E 333 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'E' and resid 218 through 223 Processing sheet with id= 30, first strand: chain 'E' and resid 477 through 480 removed outlier: 3.541A pdb=" N GLU E 484 " --> pdb=" O ASN E 479 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= 32, first strand: chain 'F' and resid 37 through 41 Processing sheet with id= 33, first strand: chain 'F' and resid 184 through 190 removed outlier: 5.216A pdb=" N GLN F 184 " --> pdb=" O GLY F 382 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY F 382 " --> pdb=" O GLN F 184 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'F' and resid 193 through 197 removed outlier: 3.749A pdb=" N MET F 193 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE F 195 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASP F 328 " --> pdb=" O ARG F 197 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR F 329 " --> pdb=" O ASN F 326 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG F 322 " --> pdb=" O ILE F 333 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'F' and resid 218 through 223 Processing sheet with id= 36, first strand: chain 'F' and resid 477 through 480 removed outlier: 3.645A pdb=" N GLU F 484 " --> pdb=" O ASN F 479 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'G' and resid 4 through 8 Processing sheet with id= 38, first strand: chain 'G' and resid 37 through 41 Processing sheet with id= 39, first strand: chain 'G' and resid 184 through 190 removed outlier: 5.332A pdb=" N GLN G 184 " --> pdb=" O GLY G 382 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY G 382 " --> pdb=" O GLN G 184 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU G 186 " --> pdb=" O LYS G 380 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'G' and resid 193 through 197 removed outlier: 3.744A pdb=" N MET G 193 " --> pdb=" O ILE G 332 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASP G 328 " --> pdb=" O ARG G 197 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR G 329 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG G 322 " --> pdb=" O ILE G 333 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'G' and resid 218 through 223 removed outlier: 3.510A pdb=" N ALA G 274 " --> pdb=" O LEU G 247 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'G' and resid 477 through 480 removed outlier: 3.635A pdb=" N GLU G 484 " --> pdb=" O ASN G 479 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'H' and resid 4 through 8 Processing sheet with id= 44, first strand: chain 'H' and resid 37 through 41 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain 'H' and resid 174 through 179 removed outlier: 5.689A pdb=" N VAL H 174 " --> pdb=" O GLY H 375 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'H' and resid 212 through 215 removed outlier: 6.673A pdb=" N ARG H 322 " --> pdb=" O ILE H 333 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR H 329 " --> pdb=" O ASN H 326 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'H' and resid 272 through 276 Processing sheet with id= 48, first strand: chain 'H' and resid 477 through 480 removed outlier: 6.863A pdb=" N TYR H 478 " --> pdb=" O TYR H 485 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR H 485 " --> pdb=" O TYR H 478 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA H 480 " --> pdb=" O GLU H 483 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= 50, first strand: chain 'I' and resid 37 through 41 No H-bonds generated for sheet with id= 50 Processing sheet with id= 51, first strand: chain 'I' and resid 174 through 179 removed outlier: 4.417A pdb=" N VAL I 174 " --> pdb=" O GLY I 375 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA I 377 " --> pdb=" O VAL I 174 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'I' and resid 212 through 215 removed outlier: 6.605A pdb=" N ARG I 322 " --> pdb=" O ILE I 333 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR I 329 " --> pdb=" O ASN I 326 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'I' and resid 272 through 276 Processing sheet with id= 54, first strand: chain 'I' and resid 477 through 480 removed outlier: 7.019A pdb=" N TYR I 478 " --> pdb=" O TYR I 485 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR I 485 " --> pdb=" O TYR I 478 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ALA I 480 " --> pdb=" O GLU I 483 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU I 483 " --> pdb=" O ALA I 480 " (cutoff:3.500A) No H-bonds generated for sheet with id= 54 Processing sheet with id= 55, first strand: chain 'M' and resid 4 through 8 Processing sheet with id= 56, first strand: chain 'M' and resid 37 through 41 No H-bonds generated for sheet with id= 56 Processing sheet with id= 57, first strand: chain 'M' and resid 174 through 179 removed outlier: 4.050A pdb=" N VAL M 174 " --> pdb=" O GLY M 375 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'M' and resid 212 through 215 removed outlier: 6.782A pdb=" N ARG M 322 " --> pdb=" O ILE M 333 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR M 329 " --> pdb=" O ASN M 326 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'M' and resid 272 through 276 Processing sheet with id= 60, first strand: chain 'M' and resid 477 through 480 removed outlier: 6.921A pdb=" N TYR M 478 " --> pdb=" O TYR M 485 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR M 485 " --> pdb=" O TYR M 478 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA M 480 " --> pdb=" O GLU M 483 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU M 483 " --> pdb=" O ALA M 480 " (cutoff:3.500A) No H-bonds generated for sheet with id= 60 Processing sheet with id= 61, first strand: chain 'J' and resid 5 through 8 removed outlier: 3.557A pdb=" N ASP J 5 " --> pdb=" O THR J 522 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS J 7 " --> pdb=" O MET J 520 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'J' and resid 37 through 41 removed outlier: 6.170A pdb=" N LEU J 40 " --> pdb=" O THR J 48 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'J' and resid 174 through 178 removed outlier: 3.878A pdb=" N ALA J 377 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL J 381 " --> pdb=" O GLU J 178 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP J 188 " --> pdb=" O VAL J 378 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY J 382 " --> pdb=" O GLN J 184 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLN J 184 " --> pdb=" O GLY J 382 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE J 333 " --> pdb=" O GLY J 192 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN J 194 " --> pdb=" O THR J 331 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR J 331 " --> pdb=" O GLN J 194 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP J 196 " --> pdb=" O THR J 329 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N THR J 329 " --> pdb=" O ASP J 196 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG J 322 " --> pdb=" O ILE J 333 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'J' and resid 272 through 277 Processing sheet with id= 65, first strand: chain 'J' and resid 477 through 480 No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain 'K' and resid 5 through 8 removed outlier: 3.652A pdb=" N ASP K 5 " --> pdb=" O THR K 522 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS K 7 " --> pdb=" O MET K 520 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'K' and resid 37 through 41 Processing sheet with id= 68, first strand: chain 'K' and resid 174 through 178 removed outlier: 3.727A pdb=" N ALA K 377 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL K 381 " --> pdb=" O GLU K 178 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP K 188 " --> pdb=" O VAL K 378 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY K 382 " --> pdb=" O GLN K 184 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLN K 184 " --> pdb=" O GLY K 382 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE K 333 " --> pdb=" O GLY K 192 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLN K 194 " --> pdb=" O THR K 331 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR K 331 " --> pdb=" O GLN K 194 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASP K 196 " --> pdb=" O THR K 329 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N THR K 329 " --> pdb=" O ASP K 196 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ARG K 322 " --> pdb=" O ILE K 333 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'K' and resid 272 through 277 Processing sheet with id= 70, first strand: chain 'K' and resid 477 through 480 No H-bonds generated for sheet with id= 70 Processing sheet with id= 71, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= 72, first strand: chain 'L' and resid 37 through 41 removed outlier: 6.049A pdb=" N LEU L 40 " --> pdb=" O THR L 48 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'L' and resid 174 through 178 removed outlier: 3.569A pdb=" N ALA L 377 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL L 381 " --> pdb=" O GLU L 178 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY L 382 " --> pdb=" O GLN L 184 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN L 184 " --> pdb=" O GLY L 382 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE L 333 " --> pdb=" O GLY L 192 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLN L 194 " --> pdb=" O THR L 331 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR L 331 " --> pdb=" O GLN L 194 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP L 196 " --> pdb=" O THR L 329 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N THR L 329 " --> pdb=" O ASP L 196 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG L 322 " --> pdb=" O ILE L 333 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'L' and resid 272 through 277 Processing sheet with id= 75, first strand: chain 'L' and resid 477 through 480 No H-bonds generated for sheet with id= 75 Processing sheet with id= 76, first strand: chain 'N' and resid 4 through 8 Processing sheet with id= 77, first strand: chain 'N' and resid 37 through 41 Processing sheet with id= 78, first strand: chain 'N' and resid 174 through 179 removed outlier: 5.320A pdb=" N VAL N 174 " --> pdb=" O GLY N 375 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY N 382 " --> pdb=" O GLN N 184 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLN N 184 " --> pdb=" O GLY N 382 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'N' and resid 212 through 216 removed outlier: 3.500A pdb=" N VAL N 323 " --> pdb=" O LEU N 215 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ARG N 322 " --> pdb=" O ILE N 333 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE N 333 " --> pdb=" O ARG N 322 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR N 329 " --> pdb=" O ASN N 326 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'N' and resid 218 through 223 removed outlier: 3.685A pdb=" N ILE N 250 " --> pdb=" O LEU N 221 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'N' and resid 225 through 228 Processing sheet with id= 82, first strand: chain 'N' and resid 477 through 480 removed outlier: 6.815A pdb=" N TYR N 478 " --> pdb=" O TYR N 485 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR N 485 " --> pdb=" O TYR N 478 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA N 480 " --> pdb=" O GLU N 483 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'O' and resid 63 through 66 removed outlier: 4.712A pdb=" N ASP O 63 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG O 37 " --> pdb=" O LYS O 15 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE O 11 " --> pdb=" O LEU O 41 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG O 14 " --> pdb=" O GLU O 82 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N GLU O 82 " --> pdb=" O ARG O 14 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'P' and resid 63 through 66 removed outlier: 4.519A pdb=" N ASP P 63 " --> pdb=" O VAL P 40 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG P 37 " --> pdb=" O LYS P 15 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE P 11 " --> pdb=" O LEU P 41 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ARG P 14 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU P 82 " --> pdb=" O ARG P 14 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'Q' and resid 63 through 66 removed outlier: 4.535A pdb=" N ASP Q 63 " --> pdb=" O VAL Q 40 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG Q 37 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE Q 11 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ARG Q 14 " --> pdb=" O GLU Q 82 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLU Q 82 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'R' and resid 63 through 66 removed outlier: 4.406A pdb=" N ASP R 63 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY R 38 " --> pdb=" O VAL R 65 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ARG R 37 " --> pdb=" O LYS R 15 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE R 11 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ARG R 14 " --> pdb=" O GLU R 82 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLU R 82 " --> pdb=" O ARG R 14 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'S' and resid 63 through 66 removed outlier: 4.265A pdb=" N ASP S 63 " --> pdb=" O VAL S 40 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG S 37 " --> pdb=" O LYS S 15 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE S 11 " --> pdb=" O LEU S 41 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG S 14 " --> pdb=" O GLU S 82 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLU S 82 " --> pdb=" O ARG S 14 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'T' and resid 63 through 66 removed outlier: 4.802A pdb=" N ASP T 63 " --> pdb=" O VAL T 40 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG T 37 " --> pdb=" O LYS T 15 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE T 11 " --> pdb=" O LEU T 41 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ARG T 14 " --> pdb=" O GLU T 82 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N GLU T 82 " --> pdb=" O ARG T 14 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'U' and resid 63 through 66 removed outlier: 4.603A pdb=" N ASP U 63 " --> pdb=" O VAL U 40 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG U 37 " --> pdb=" O LYS U 15 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE U 11 " --> pdb=" O LEU U 41 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ARG U 14 " --> pdb=" O GLU U 82 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLU U 82 " --> pdb=" O ARG U 14 " (cutoff:3.500A) 3528 hydrogen bonds defined for protein. 10500 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: 45.55 Time building geometry restraints manager: 78.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 60949 1.03 - 1.23: 102 1.23 - 1.43: 22337 1.43 - 1.62: 36900 1.62 - 1.82: 567 Bond restraints: 120855 Sorted by residual: bond pdb=" CB ASP B 41 " pdb=" CG ASP B 41 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.34e+00 bond pdb=" CG GLU B 518 " pdb=" CD GLU B 518 " ideal model delta sigma weight residual 1.516 1.480 0.036 2.50e-02 1.60e+03 2.05e+00 bond pdb=" C4 ADP M 603 " pdb=" C5 ADP M 603 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" CB GLU E 461 " pdb=" CG GLU E 461 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.80e+00 bond pdb=" CB MET K 520 " pdb=" CG MET K 520 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.78e+00 ... (remaining 120850 not shown) Histogram of bond angle deviations from ideal: 73.80 - 86.35: 9 86.35 - 98.91: 10 98.91 - 111.47: 143678 111.47 - 124.02: 69531 124.02 - 136.58: 6971 Bond angle restraints: 220199 Sorted by residual: angle pdb=" C MET O 1 " pdb=" CA MET O 1 " pdb=" HA MET O 1 " ideal model delta sigma weight residual 110.00 74.02 35.98 3.00e+00 1.11e-01 1.44e+02 angle pdb=" C ALA O 32 " pdb=" CA ALA O 32 " pdb=" HA ALA O 32 " ideal model delta sigma weight residual 109.00 73.80 35.20 3.00e+00 1.11e-01 1.38e+02 angle pdb=" N MET O 1 " pdb=" CA MET O 1 " pdb=" HA MET O 1 " ideal model delta sigma weight residual 110.00 74.85 35.15 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C ALA Q 97 " pdb=" CA ALA Q 97 " pdb=" HA ALA Q 97 " ideal model delta sigma weight residual 109.00 73.92 35.08 3.00e+00 1.11e-01 1.37e+02 angle pdb=" CB ALA O 32 " pdb=" CA ALA O 32 " pdb=" HA ALA O 32 " ideal model delta sigma weight residual 109.00 74.00 35.00 3.00e+00 1.11e-01 1.36e+02 ... (remaining 220194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 53073 35.88 - 71.77: 2281 71.77 - 107.65: 84 107.65 - 143.54: 17 143.54 - 179.42: 6 Dihedral angle restraints: 55461 sinusoidal: 31885 harmonic: 23576 Sorted by residual: dihedral pdb=" O2A ADP G 603 " pdb=" O3A ADP G 603 " pdb=" PA ADP G 603 " pdb=" PB ADP G 603 " ideal model delta sinusoidal sigma weight residual -60.00 119.42 -179.42 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP D 602 " pdb=" O3A ADP D 602 " pdb=" PA ADP D 602 " pdb=" PB ADP D 602 " ideal model delta sinusoidal sigma weight residual 300.00 123.11 176.90 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PA ADP B 601 " pdb=" PB ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 110.83 -170.83 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 55458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 9056 0.086 - 0.171: 751 0.171 - 0.257: 11 0.257 - 0.342: 0 0.342 - 0.428: 3 Chirality restraints: 9821 Sorted by residual: chirality pdb=" CA MET O 1 " pdb=" N MET O 1 " pdb=" C MET O 1 " pdb=" CB MET O 1 " both_signs ideal model delta sigma weight residual False 2.57 2.14 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CA ALA Q 97 " pdb=" N ALA Q 97 " pdb=" C ALA Q 97 " pdb=" CB ALA Q 97 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CA ALA O 32 " pdb=" N ALA O 32 " pdb=" C ALA O 32 " pdb=" CB ALA O 32 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 9818 not shown) Planarity restraints: 18305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 58 " -0.270 9.50e-02 1.11e+02 9.13e-02 1.27e+01 pdb=" NE ARG I 58 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG I 58 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG I 58 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG I 58 " 0.026 2.00e-02 2.50e+03 pdb="HH11 ARG I 58 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG I 58 " -0.007 2.00e-02 2.50e+03 pdb="HH21 ARG I 58 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG I 58 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN J 290 " 0.023 2.00e-02 2.50e+03 2.88e-02 1.25e+01 pdb=" CD GLN J 290 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN J 290 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN J 290 " -0.047 2.00e-02 2.50e+03 pdb="HE21 GLN J 290 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN J 290 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER N 217 " -0.056 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO N 218 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO N 218 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO N 218 " -0.047 5.00e-02 4.00e+02 ... (remaining 18302 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.98: 1395 1.98 - 2.77: 246879 2.77 - 3.56: 447686 3.56 - 4.35: 667375 4.35 - 5.14: 1119340 Nonbonded interactions: 2482675 Sorted by model distance: nonbonded pdb=" F1 AF3 A 601 " pdb=" O1B ADP A 602 " model vdw 1.191 2.270 nonbonded pdb=" F2 AF3 E 601 " pdb=" O1B ADP E 603 " model vdw 1.247 2.270 nonbonded pdb=" OE1 GLU C 232 " pdb=" H GLU C 232 " model vdw 1.419 1.850 nonbonded pdb=" OE1 GLU E 303 " pdb=" H GLU E 303 " model vdw 1.430 1.850 nonbonded pdb=" OE1 GLU G 303 " pdb=" H GLU G 303 " model vdw 1.455 1.850 ... (remaining 2482670 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' and resid 2 through 524) selection = (chain 'B' and resid 2 through 524) selection = (chain 'C' and resid 2 through 524) selection = (chain 'D' and resid 2 through 524) selection = (chain 'E' and resid 2 through 524) selection = (chain 'F' and resid 2 through 524) selection = (chain 'G' and resid 2 through 524) selection = (chain 'H' and resid 2 through 524) selection = (chain 'I' and resid 2 through 524) selection = (chain 'J' and resid 2 through 524) selection = (chain 'K' and resid 2 through 524) selection = (chain 'L' and resid 2 through 524) selection = (chain 'M' and resid 2 through 524) selection = (chain 'N' and resid 2 through 524) } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 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: 1.320 Extract box with map and model: 20.830 Check model and map are aligned: 1.300 Set scattering table: 0.830 Process input model: 312.760 Find NCS groups from input model: 5.510 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 349.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 59864 Z= 0.205 Angle : 0.754 11.213 80878 Z= 0.376 Chirality : 0.045 0.428 9821 Planarity : 0.006 0.104 10521 Dihedral : 15.682 179.423 22596 Min Nonbonded Distance : 1.191 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.10 % Allowed : 16.88 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.84 (0.09), residues: 7966 helix: -0.68 (0.07), residues: 3890 sheet: 0.07 (0.15), residues: 1010 loop : -0.33 (0.11), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS S 7 PHE 0.016 0.001 PHE H 8 TYR 0.016 0.002 TYR I 199 ARG 0.020 0.002 ARG N 395 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 561 time to evaluate : 6.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8290 (mtt) cc_final: 0.8081 (mtt) REVERT: C 111 MET cc_start: 0.7907 (mmm) cc_final: 0.7173 (mmm) REVERT: R 2 ASN cc_start: 0.6966 (p0) cc_final: 0.6398 (m-40) REVERT: T 74 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8564 (tppp) REVERT: U 3 ILE cc_start: 0.9360 (tp) cc_final: 0.9099 (tp) outliers start: 6 outliers final: 5 residues processed: 562 average time/residue: 1.4532 time to fit residues: 1324.9327 Evaluate side-chains 497 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 492 time to evaluate : 6.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 389 MET Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain U residue 27 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 667 optimal weight: 0.8980 chunk 599 optimal weight: 6.9990 chunk 332 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 404 optimal weight: 4.9990 chunk 320 optimal weight: 3.9990 chunk 619 optimal weight: 6.9990 chunk 239 optimal weight: 8.9990 chunk 376 optimal weight: 4.9990 chunk 461 optimal weight: 0.6980 chunk 718 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 352 GLN ** F 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 59864 Z= 0.229 Angle : 0.668 10.579 80878 Z= 0.348 Chirality : 0.045 0.432 9821 Planarity : 0.004 0.061 10521 Dihedral : 8.991 176.766 8614 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.28 % Favored : 97.70 % Rotamer: Outliers : 0.87 % Allowed : 14.38 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.09), residues: 7966 helix: 0.73 (0.08), residues: 4131 sheet: 0.32 (0.16), residues: 933 loop : -0.31 (0.11), residues: 2902 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS S 7 PHE 0.012 0.001 PHE E 195 TYR 0.016 0.001 TYR K 360 ARG 0.008 0.000 ARG T 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 521 time to evaluate : 6.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 MET cc_start: 0.7861 (mmm) cc_final: 0.7242 (mmm) REVERT: C 518 GLU cc_start: 0.8758 (tp30) cc_final: 0.8517 (tp30) REVERT: H 114 MET cc_start: 0.8774 (mmt) cc_final: 0.8468 (mmt) REVERT: H 131 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8610 (mp) REVERT: N 398 ASP cc_start: 0.8672 (m-30) cc_final: 0.8397 (t0) REVERT: O 94 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7376 (tp) REVERT: R 1 MET cc_start: 0.4378 (tpt) cc_final: 0.3771 (tpt) REVERT: T 74 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8676 (tppp) outliers start: 54 outliers final: 28 residues processed: 561 average time/residue: 1.4480 time to fit residues: 1354.1573 Evaluate side-chains 515 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 485 time to evaluate : 6.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain J residue 343 GLN Chi-restraints excluded: chain J residue 360 TYR Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 458 CYS Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 195 PHE Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 376 VAL Chi-restraints excluded: chain N residue 519 CYS Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain S residue 71 TYR Chi-restraints excluded: chain T residue 8 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 20.0000 chunk 222 optimal weight: 2.9990 chunk 597 optimal weight: 50.0000 chunk 489 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 719 optimal weight: 2.9990 chunk 777 optimal weight: 8.9990 chunk 640 optimal weight: 7.9990 chunk 713 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 577 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN C 457 ASN F 348 GLN ** F 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 59864 Z= 0.336 Angle : 0.654 10.453 80878 Z= 0.343 Chirality : 0.045 0.457 9821 Planarity : 0.004 0.051 10521 Dihedral : 8.212 172.597 8607 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 1.55 % Allowed : 13.64 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.09), residues: 7966 helix: 1.00 (0.08), residues: 4131 sheet: 0.11 (0.16), residues: 978 loop : -0.38 (0.11), residues: 2857 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS S 7 PHE 0.025 0.001 PHE C 219 TYR 0.016 0.001 TYR K 360 ARG 0.015 0.001 ARG S 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 507 time to evaluate : 6.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9054 (mt) REVERT: B 111 MET cc_start: 0.8036 (mpp) cc_final: 0.7726 (mmt) REVERT: C 111 MET cc_start: 0.7985 (mmm) cc_final: 0.7589 (mmm) REVERT: H 288 MET cc_start: 0.8131 (mmm) cc_final: 0.7898 (mmm) REVERT: I 203 TYR cc_start: 0.7614 (m-80) cc_final: 0.6733 (m-80) REVERT: J 193 MET cc_start: 0.6885 (tpt) cc_final: 0.6641 (tpt) REVERT: J 195 PHE cc_start: 0.8553 (p90) cc_final: 0.8258 (p90) REVERT: J 447 MET cc_start: 0.9051 (mtp) cc_final: 0.8848 (mtp) REVERT: L 334 ASP cc_start: 0.5387 (OUTLIER) cc_final: 0.4954 (p0) REVERT: L 389 MET cc_start: 0.9099 (tpp) cc_final: 0.8802 (mpp) REVERT: M 221 LEU cc_start: 0.8537 (tp) cc_final: 0.8325 (tt) REVERT: M 454 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8442 (tt) REVERT: N 11 ASP cc_start: 0.8186 (t0) cc_final: 0.7969 (t0) REVERT: N 389 MET cc_start: 0.7547 (tpp) cc_final: 0.7150 (tpp) REVERT: N 398 ASP cc_start: 0.8708 (m-30) cc_final: 0.8409 (t0) REVERT: Q 68 ASN cc_start: 0.7943 (t0) cc_final: 0.7654 (t0) REVERT: R 1 MET cc_start: 0.3838 (tpt) cc_final: 0.3195 (tpt) REVERT: R 2 ASN cc_start: 0.6494 (p0) cc_final: 0.6110 (m-40) REVERT: T 74 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8705 (tppp) REVERT: U 20 LYS cc_start: 0.7996 (pptt) cc_final: 0.7565 (ptmm) outliers start: 96 outliers final: 52 residues processed: 582 average time/residue: 1.2796 time to fit residues: 1237.8021 Evaluate side-chains 528 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 473 time to evaluate : 6.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 519 CYS Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain I residue 521 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 343 GLN Chi-restraints excluded: chain J residue 360 TYR Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 36 ARG Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 523 ASP Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 195 PHE Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 334 ASP Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain M residue 389 MET Chi-restraints excluded: chain M residue 454 ILE Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 351 GLN Chi-restraints excluded: chain N residue 376 VAL Chi-restraints excluded: chain N residue 519 CYS Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 71 TYR Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain S residue 71 TYR Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain U residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 9.9990 chunk 541 optimal weight: 20.0000 chunk 373 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 343 optimal weight: 7.9990 chunk 483 optimal weight: 4.9990 chunk 722 optimal weight: 1.9990 chunk 764 optimal weight: 4.9990 chunk 377 optimal weight: 5.9990 chunk 684 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 319 GLN ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 59864 Z= 0.280 Angle : 0.610 10.787 80878 Z= 0.316 Chirality : 0.044 0.446 9821 Planarity : 0.003 0.042 10521 Dihedral : 7.657 154.686 8607 Min Nonbonded Distance : 1.568 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 1.56 % Allowed : 13.92 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.09), residues: 7966 helix: 1.25 (0.08), residues: 4134 sheet: 0.05 (0.16), residues: 945 loop : -0.41 (0.11), residues: 2887 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS S 7 PHE 0.021 0.001 PHE C 195 TYR 0.013 0.001 TYR K 360 ARG 0.006 0.000 ARG S 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 488 time to evaluate : 6.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 MET cc_start: 0.8097 (mpp) cc_final: 0.7792 (mmt) REVERT: C 73 MET cc_start: 0.8501 (ttm) cc_final: 0.8266 (ttm) REVERT: C 111 MET cc_start: 0.7772 (mmm) cc_final: 0.7538 (mmm) REVERT: H 389 MET cc_start: 0.7188 (mmm) cc_final: 0.6380 (mmm) REVERT: I 203 TYR cc_start: 0.7636 (m-80) cc_final: 0.6742 (m-80) REVERT: I 295 LEU cc_start: 0.9335 (mm) cc_final: 0.9087 (mm) REVERT: J 398 ASP cc_start: 0.8875 (m-30) cc_final: 0.8373 (t0) REVERT: L 5 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6849 (t0) REVERT: L 334 ASP cc_start: 0.5355 (OUTLIER) cc_final: 0.5016 (p0) REVERT: L 389 MET cc_start: 0.9105 (tpp) cc_final: 0.8773 (mpp) REVERT: M 520 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.6640 (mtt) REVERT: N 11 ASP cc_start: 0.8126 (t0) cc_final: 0.7816 (t0) REVERT: N 389 MET cc_start: 0.7559 (tpp) cc_final: 0.7117 (tpp) REVERT: N 398 ASP cc_start: 0.8657 (m-30) cc_final: 0.8401 (t0) REVERT: O 1 MET cc_start: 0.7853 (tpp) cc_final: 0.7275 (tpt) REVERT: Q 68 ASN cc_start: 0.8060 (t0) cc_final: 0.7702 (t0) REVERT: R 1 MET cc_start: 0.3958 (tpt) cc_final: 0.3325 (tpt) REVERT: R 2 ASN cc_start: 0.6504 (p0) cc_final: 0.6164 (m-40) REVERT: T 74 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8730 (tppp) outliers start: 97 outliers final: 67 residues processed: 560 average time/residue: 1.4427 time to fit residues: 1355.4476 Evaluate side-chains 536 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 466 time to evaluate : 6.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 519 CYS Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 343 GLN Chi-restraints excluded: chain J residue 360 TYR Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 36 ARG Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain L residue 5 ASP Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 195 PHE Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 334 ASP Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 523 ASP Chi-restraints excluded: chain M residue 389 MET Chi-restraints excluded: chain M residue 520 MET Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 351 GLN Chi-restraints excluded: chain N residue 376 VAL Chi-restraints excluded: chain N residue 519 CYS Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 71 TYR Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 71 TYR Chi-restraints excluded: chain T residue 8 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 636 optimal weight: 1.9990 chunk 434 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 569 optimal weight: 3.9990 chunk 315 optimal weight: 0.8980 chunk 652 optimal weight: 30.0000 chunk 528 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 390 optimal weight: 0.0670 chunk 686 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 453 GLN ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 59864 Z= 0.175 Angle : 0.567 10.930 80878 Z= 0.288 Chirality : 0.042 0.441 9821 Planarity : 0.003 0.043 10521 Dihedral : 7.112 137.042 8607 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.87 % Favored : 97.08 % Rotamer: Outliers : 1.40 % Allowed : 13.90 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.09), residues: 7966 helix: 1.65 (0.08), residues: 4131 sheet: 0.03 (0.16), residues: 921 loop : -0.29 (0.11), residues: 2914 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS S 7 PHE 0.016 0.001 PHE D 44 TYR 0.014 0.001 TYR L 199 ARG 0.004 0.000 ARG T 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 502 time to evaluate : 6.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 MET cc_start: 0.8019 (mpp) cc_final: 0.7711 (mmt) REVERT: C 73 MET cc_start: 0.8493 (ttm) cc_final: 0.8260 (ttm) REVERT: H 288 MET cc_start: 0.7622 (mmm) cc_final: 0.7032 (mmt) REVERT: H 389 MET cc_start: 0.7102 (mmm) cc_final: 0.6275 (mmm) REVERT: J 398 ASP cc_start: 0.8866 (m-30) cc_final: 0.8420 (t0) REVERT: L 5 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6780 (t0) REVERT: L 334 ASP cc_start: 0.5334 (OUTLIER) cc_final: 0.4994 (p0) REVERT: L 389 MET cc_start: 0.9105 (tpp) cc_final: 0.8760 (mpp) REVERT: M 63 GLU cc_start: 0.5207 (OUTLIER) cc_final: 0.4186 (mt-10) REVERT: N 11 ASP cc_start: 0.7993 (t0) cc_final: 0.7647 (t0) REVERT: N 398 ASP cc_start: 0.8620 (m-30) cc_final: 0.8385 (t0) REVERT: O 1 MET cc_start: 0.7845 (tpp) cc_final: 0.7273 (tpt) REVERT: Q 68 ASN cc_start: 0.8089 (t0) cc_final: 0.7721 (t0) REVERT: R 1 MET cc_start: 0.3883 (tpt) cc_final: 0.3274 (tpt) REVERT: R 2 ASN cc_start: 0.6385 (p0) cc_final: 0.6087 (m-40) REVERT: T 74 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8691 (tppp) outliers start: 87 outliers final: 60 residues processed: 562 average time/residue: 1.3731 time to fit residues: 1284.4193 Evaluate side-chains 539 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 476 time to evaluate : 6.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 319 GLN Chi-restraints excluded: chain G residue 519 CYS Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 343 GLN Chi-restraints excluded: chain J residue 360 TYR Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 36 ARG Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain L residue 5 ASP Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 195 PHE Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 334 ASP Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain M residue 389 MET Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 351 GLN Chi-restraints excluded: chain N residue 376 VAL Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 71 TYR Chi-restraints excluded: chain O residue 85 ILE Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 71 TYR Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 48 ILE Chi-restraints excluded: chain U residue 86 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 257 optimal weight: 2.9990 chunk 688 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 448 optimal weight: 9.9990 chunk 188 optimal weight: 0.9990 chunk 765 optimal weight: 1.9990 chunk 635 optimal weight: 1.9990 chunk 354 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 253 optimal weight: 3.9990 chunk 401 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 59864 Z= 0.194 Angle : 0.562 10.984 80878 Z= 0.286 Chirality : 0.042 0.440 9821 Planarity : 0.003 0.042 10521 Dihedral : 6.889 136.343 8607 Min Nonbonded Distance : 1.620 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 1.32 % Allowed : 14.21 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.09), residues: 7966 helix: 1.77 (0.08), residues: 4131 sheet: 0.02 (0.16), residues: 921 loop : -0.30 (0.11), residues: 2914 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS S 7 PHE 0.014 0.001 PHE C 195 TYR 0.012 0.001 TYR F 360 ARG 0.005 0.000 ARG J 445 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 490 time to evaluate : 6.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 MET cc_start: 0.8021 (mpp) cc_final: 0.7718 (mmt) REVERT: H 69 MET cc_start: 0.8300 (mtt) cc_final: 0.7941 (mtt) REVERT: H 114 MET cc_start: 0.8544 (mmt) cc_final: 0.8334 (mmt) REVERT: H 288 MET cc_start: 0.7799 (mmm) cc_final: 0.7522 (mmm) REVERT: H 389 MET cc_start: 0.7087 (mmm) cc_final: 0.6270 (mmm) REVERT: H 520 MET cc_start: 0.8703 (mtp) cc_final: 0.8473 (mtp) REVERT: I 295 LEU cc_start: 0.9171 (tp) cc_final: 0.8965 (mm) REVERT: J 398 ASP cc_start: 0.8859 (m-30) cc_final: 0.8418 (t0) REVERT: L 5 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6789 (t0) REVERT: L 40 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8297 (mm) REVERT: L 334 ASP cc_start: 0.5435 (OUTLIER) cc_final: 0.5096 (p0) REVERT: L 389 MET cc_start: 0.9100 (tpp) cc_final: 0.8740 (mpp) REVERT: M 63 GLU cc_start: 0.5251 (OUTLIER) cc_final: 0.4098 (mt-10) REVERT: M 520 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.6672 (mtt) REVERT: N 11 ASP cc_start: 0.7984 (t0) cc_final: 0.7617 (t0) REVERT: O 1 MET cc_start: 0.7881 (tpp) cc_final: 0.7326 (tpt) REVERT: Q 68 ASN cc_start: 0.8138 (t0) cc_final: 0.7725 (t0) REVERT: R 1 MET cc_start: 0.3904 (tpt) cc_final: 0.3306 (tpt) REVERT: R 2 ASN cc_start: 0.6482 (p0) cc_final: 0.6138 (m-40) REVERT: T 74 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8721 (tppp) outliers start: 82 outliers final: 68 residues processed: 547 average time/residue: 1.3909 time to fit residues: 1272.8199 Evaluate side-chains 545 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 472 time to evaluate : 6.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 447 MET Chi-restraints excluded: chain G residue 519 CYS Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 502 SER Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 343 GLN Chi-restraints excluded: chain J residue 360 TYR Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 36 ARG Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain L residue 5 ASP Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 334 ASP Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain M residue 389 MET Chi-restraints excluded: chain M residue 520 MET Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 351 GLN Chi-restraints excluded: chain N residue 376 VAL Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 71 TYR Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 71 TYR Chi-restraints excluded: chain U residue 48 ILE Chi-restraints excluded: chain U residue 86 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 737 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 436 optimal weight: 9.9990 chunk 558 optimal weight: 0.9980 chunk 433 optimal weight: 3.9990 chunk 644 optimal weight: 3.9990 chunk 427 optimal weight: 2.9990 chunk 762 optimal weight: 7.9990 chunk 477 optimal weight: 1.9990 chunk 464 optimal weight: 2.9990 chunk 351 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 59864 Z= 0.252 Angle : 0.577 11.045 80878 Z= 0.296 Chirality : 0.042 0.444 9821 Planarity : 0.003 0.043 10521 Dihedral : 6.805 137.846 8607 Min Nonbonded Distance : 1.613 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.74 % Rotamer: Outliers : 1.47 % Allowed : 14.19 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.11 (0.09), residues: 7966 helix: 1.73 (0.08), residues: 4134 sheet: -0.07 (0.16), residues: 959 loop : -0.37 (0.11), residues: 2873 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS S 7 PHE 0.013 0.001 PHE F 281 TYR 0.013 0.001 TYR I 203 ARG 0.007 0.000 ARG Q 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 478 time to evaluate : 6.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 MET cc_start: 0.8073 (mpp) cc_final: 0.7781 (mmt) REVERT: C 73 MET cc_start: 0.8304 (ttm) cc_final: 0.7929 (ttm) REVERT: H 69 MET cc_start: 0.8348 (mtt) cc_final: 0.8065 (mtt) REVERT: H 389 MET cc_start: 0.7097 (mmm) cc_final: 0.6272 (mmm) REVERT: I 7 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7463 (ptpt) REVERT: I 295 LEU cc_start: 0.9164 (tp) cc_final: 0.8955 (mm) REVERT: J 203 TYR cc_start: 0.8193 (m-80) cc_final: 0.7858 (m-80) REVERT: J 398 ASP cc_start: 0.8863 (m-30) cc_final: 0.8429 (t0) REVERT: L 5 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6854 (t0) REVERT: L 334 ASP cc_start: 0.5480 (OUTLIER) cc_final: 0.5129 (p0) REVERT: L 389 MET cc_start: 0.9145 (tpp) cc_final: 0.8769 (mpp) REVERT: M 63 GLU cc_start: 0.5421 (OUTLIER) cc_final: 0.4286 (mt-10) REVERT: M 520 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.6878 (mtt) REVERT: N 11 ASP cc_start: 0.8053 (t0) cc_final: 0.7702 (t0) REVERT: O 1 MET cc_start: 0.7910 (tpp) cc_final: 0.7360 (tpt) REVERT: Q 68 ASN cc_start: 0.8185 (t0) cc_final: 0.7773 (t0) REVERT: R 1 MET cc_start: 0.4050 (tpt) cc_final: 0.3433 (tpt) REVERT: R 2 ASN cc_start: 0.6540 (p0) cc_final: 0.6204 (m-40) outliers start: 91 outliers final: 77 residues processed: 544 average time/residue: 1.3548 time to fit residues: 1225.8373 Evaluate side-chains 551 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 469 time to evaluate : 6.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 319 GLN Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 447 MET Chi-restraints excluded: chain G residue 519 CYS Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 502 SER Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 343 GLN Chi-restraints excluded: chain J residue 360 TYR Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 36 ARG Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain L residue 5 ASP Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 334 ASP Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain M residue 389 MET Chi-restraints excluded: chain M residue 520 MET Chi-restraints excluded: chain N residue 351 GLN Chi-restraints excluded: chain N residue 376 VAL Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 71 TYR Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 71 TYR Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain U residue 48 ILE Chi-restraints excluded: chain U residue 86 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 0.9980 chunk 304 optimal weight: 2.9990 chunk 455 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 484 optimal weight: 4.9990 chunk 519 optimal weight: 2.9990 chunk 376 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 599 optimal weight: 30.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 59864 Z= 0.202 Angle : 0.563 11.233 80878 Z= 0.285 Chirality : 0.042 0.445 9821 Planarity : 0.003 0.043 10521 Dihedral : 6.597 135.260 8605 Min Nonbonded Distance : 1.636 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % Rotamer: Outliers : 1.40 % Allowed : 14.56 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.09), residues: 7966 helix: 1.83 (0.08), residues: 4141 sheet: -0.06 (0.16), residues: 959 loop : -0.35 (0.11), residues: 2866 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS S 7 PHE 0.012 0.001 PHE C 195 TYR 0.013 0.001 TYR F 360 ARG 0.003 0.000 ARG G 268 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 487 time to evaluate : 6.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 MET cc_start: 0.8021 (mpp) cc_final: 0.7755 (mmt) REVERT: H 69 MET cc_start: 0.8366 (mtt) cc_final: 0.8033 (mtt) REVERT: H 389 MET cc_start: 0.7082 (mmm) cc_final: 0.6244 (mmm) REVERT: I 295 LEU cc_start: 0.9160 (tp) cc_final: 0.8948 (mm) REVERT: J 203 TYR cc_start: 0.8117 (m-80) cc_final: 0.7786 (m-80) REVERT: J 398 ASP cc_start: 0.8852 (m-30) cc_final: 0.8416 (t0) REVERT: L 5 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6809 (t0) REVERT: L 334 ASP cc_start: 0.5491 (OUTLIER) cc_final: 0.5156 (p0) REVERT: M 63 GLU cc_start: 0.5241 (OUTLIER) cc_final: 0.4069 (mt-10) REVERT: N 11 ASP cc_start: 0.8012 (t0) cc_final: 0.7680 (t0) REVERT: O 1 MET cc_start: 0.7882 (tpp) cc_final: 0.7344 (tpt) REVERT: Q 68 ASN cc_start: 0.8206 (t0) cc_final: 0.7795 (t0) REVERT: R 1 MET cc_start: 0.4044 (tpt) cc_final: 0.3424 (tpt) REVERT: R 2 ASN cc_start: 0.6529 (p0) cc_final: 0.6188 (m-40) outliers start: 87 outliers final: 71 residues processed: 549 average time/residue: 1.3675 time to fit residues: 1258.4320 Evaluate side-chains 546 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 472 time to evaluate : 6.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 319 GLN Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 447 MET Chi-restraints excluded: chain G residue 519 CYS Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 391 GLU Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 502 SER Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 343 GLN Chi-restraints excluded: chain J residue 360 TYR Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 36 ARG Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain L residue 5 ASP Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 334 ASP Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain M residue 389 MET Chi-restraints excluded: chain N residue 351 GLN Chi-restraints excluded: chain N residue 376 VAL Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 71 TYR Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 71 TYR Chi-restraints excluded: chain U residue 48 ILE Chi-restraints excluded: chain U residue 86 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 6.9990 chunk 730 optimal weight: 5.9990 chunk 666 optimal weight: 0.8980 chunk 710 optimal weight: 10.0000 chunk 427 optimal weight: 1.9990 chunk 309 optimal weight: 0.6980 chunk 557 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 641 optimal weight: 8.9990 chunk 671 optimal weight: 6.9990 chunk 707 optimal weight: 30.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 GLN ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 59864 Z= 0.277 Angle : 0.590 13.925 80878 Z= 0.303 Chirality : 0.043 0.445 9821 Planarity : 0.003 0.043 10521 Dihedral : 6.599 136.015 8605 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 1.29 % Allowed : 14.61 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.09), residues: 7966 helix: 1.72 (0.08), residues: 4140 sheet: -0.01 (0.16), residues: 929 loop : -0.45 (0.11), residues: 2897 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS S 7 PHE 0.013 0.001 PHE E 44 TYR 0.012 0.001 TYR E 360 ARG 0.004 0.000 ARG G 268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 482 time to evaluate : 6.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 MET cc_start: 0.8050 (mpp) cc_final: 0.7787 (mmt) REVERT: H 69 MET cc_start: 0.8426 (mtt) cc_final: 0.8091 (mtt) REVERT: H 389 MET cc_start: 0.7089 (mmm) cc_final: 0.6274 (mmm) REVERT: I 295 LEU cc_start: 0.9167 (tp) cc_final: 0.8958 (mm) REVERT: J 203 TYR cc_start: 0.8087 (m-80) cc_final: 0.7791 (m-80) REVERT: J 398 ASP cc_start: 0.8856 (m-30) cc_final: 0.8451 (t0) REVERT: L 5 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6853 (t0) REVERT: L 334 ASP cc_start: 0.5546 (OUTLIER) cc_final: 0.5209 (p0) REVERT: L 389 MET cc_start: 0.9134 (tpp) cc_final: 0.8720 (mpp) REVERT: M 63 GLU cc_start: 0.5492 (OUTLIER) cc_final: 0.4190 (mt-10) REVERT: N 11 ASP cc_start: 0.8170 (t0) cc_final: 0.7826 (t0) REVERT: Q 68 ASN cc_start: 0.8267 (t0) cc_final: 0.7850 (t0) REVERT: Q 86 MET cc_start: 0.8051 (pmm) cc_final: 0.7811 (pmm) REVERT: R 1 MET cc_start: 0.4206 (tpt) cc_final: 0.3575 (tpt) REVERT: R 2 ASN cc_start: 0.6565 (p0) cc_final: 0.6304 (m-40) outliers start: 80 outliers final: 73 residues processed: 542 average time/residue: 1.3785 time to fit residues: 1246.8042 Evaluate side-chains 549 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 473 time to evaluate : 6.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 319 GLN Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 447 MET Chi-restraints excluded: chain G residue 519 CYS Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 391 GLU Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 502 SER Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 343 GLN Chi-restraints excluded: chain J residue 360 TYR Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 36 ARG Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain L residue 5 ASP Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 334 ASP Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain M residue 389 MET Chi-restraints excluded: chain N residue 351 GLN Chi-restraints excluded: chain N residue 376 VAL Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 71 TYR Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 71 TYR Chi-restraints excluded: chain T residue 41 LEU Chi-restraints excluded: chain U residue 86 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 466 optimal weight: 2.9990 chunk 751 optimal weight: 6.9990 chunk 458 optimal weight: 2.9990 chunk 356 optimal weight: 2.9990 chunk 522 optimal weight: 0.9990 chunk 788 optimal weight: 0.1980 chunk 725 optimal weight: 3.9990 chunk 627 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 484 optimal weight: 6.9990 chunk 384 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 GLN ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 GLN ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 59864 Z= 0.159 Angle : 0.557 11.378 80878 Z= 0.277 Chirality : 0.042 0.448 9821 Planarity : 0.003 0.043 10521 Dihedral : 6.281 126.117 8605 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.44 % Favored : 97.53 % Rotamer: Outliers : 1.03 % Allowed : 14.88 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.09), residues: 7966 helix: 2.02 (0.08), residues: 4114 sheet: -0.03 (0.16), residues: 943 loop : -0.29 (0.11), residues: 2909 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS S 7 PHE 0.013 0.001 PHE C 195 TYR 0.019 0.001 TYR F 360 ARG 0.003 0.000 ARG N 350 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 490 time to evaluate : 6.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 MET cc_start: 0.7995 (mpp) cc_final: 0.7730 (mmt) REVERT: H 288 MET cc_start: 0.7546 (mmm) cc_final: 0.7240 (mmt) REVERT: H 389 MET cc_start: 0.7004 (mmm) cc_final: 0.6199 (mmm) REVERT: I 295 LEU cc_start: 0.9146 (tp) cc_final: 0.8934 (mm) REVERT: J 97 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8724 (tt0) REVERT: J 114 MET cc_start: 0.7760 (mmt) cc_final: 0.7369 (mmt) REVERT: J 203 TYR cc_start: 0.8063 (m-80) cc_final: 0.7758 (m-80) REVERT: J 398 ASP cc_start: 0.8851 (m-30) cc_final: 0.8421 (t0) REVERT: L 5 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6698 (t0) REVERT: L 334 ASP cc_start: 0.5453 (OUTLIER) cc_final: 0.5133 (p0) REVERT: L 389 MET cc_start: 0.9115 (tpp) cc_final: 0.8741 (mpp) REVERT: M 63 GLU cc_start: 0.5095 (OUTLIER) cc_final: 0.3857 (mt-10) REVERT: N 11 ASP cc_start: 0.7982 (t0) cc_final: 0.7653 (t0) REVERT: Q 68 ASN cc_start: 0.8168 (t0) cc_final: 0.7787 (t0) REVERT: R 1 MET cc_start: 0.4171 (tpt) cc_final: 0.3587 (tpt) REVERT: R 2 ASN cc_start: 0.6558 (p0) cc_final: 0.6279 (m-40) outliers start: 64 outliers final: 54 residues processed: 536 average time/residue: 1.3465 time to fit residues: 1206.1714 Evaluate side-chains 536 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 478 time to evaluate : 6.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain F residue 319 GLN Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 519 CYS Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 398 ASP Chi-restraints excluded: chain H residue 502 SER Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 97 GLN Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 343 GLN Chi-restraints excluded: chain J residue 360 TYR Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 36 ARG Chi-restraints excluded: chain K residue 247 LEU Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain L residue 5 ASP Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 334 ASP Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain M residue 389 MET Chi-restraints excluded: chain N residue 351 GLN Chi-restraints excluded: chain N residue 376 VAL Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 71 TYR Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 71 TYR Chi-restraints excluded: chain T residue 41 LEU Chi-restraints excluded: chain U residue 86 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 498 optimal weight: 40.0000 chunk 668 optimal weight: 0.9980 chunk 192 optimal weight: 9.9990 chunk 578 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 628 optimal weight: 0.5980 chunk 263 optimal weight: 2.9990 chunk 645 optimal weight: 30.0000 chunk 79 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 GLN ** K 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.122578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.082548 restraints weight = 368816.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.081409 restraints weight = 206597.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.081123 restraints weight = 154882.099| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.155 59864 Z= 0.227 Angle : 0.620 59.199 80878 Z= 0.324 Chirality : 0.043 0.447 9821 Planarity : 0.003 0.043 10521 Dihedral : 6.272 126.232 8603 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.57 % Favored : 97.39 % Rotamer: Outliers : 1.05 % Allowed : 15.01 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.09), residues: 7966 helix: 2.02 (0.08), residues: 4114 sheet: -0.04 (0.16), residues: 943 loop : -0.29 (0.11), residues: 2909 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS S 7 PHE 0.012 0.001 PHE C 195 TYR 0.012 0.001 TYR K 360 ARG 0.004 0.000 ARG N 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20242.67 seconds wall clock time: 350 minutes 50.13 seconds (21050.13 seconds total)