Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 20 10:22:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wln_8860/10_2023/5wln_8860.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wln_8860/10_2023/5wln_8860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wln_8860/10_2023/5wln_8860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wln_8860/10_2023/5wln_8860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wln_8860/10_2023/5wln_8860.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wln_8860/10_2023/5wln_8860.pdb" } resolution = 3.57 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= 0.004 sd= 0.044 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: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 27585 2.51 5 N 7980 2.21 5 O 8775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 550": "NH1" <-> "NH2" Residue "O ARG 550": "NH1" <-> "NH2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "C ARG 550": "NH1" <-> "NH2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "E ARG 550": "NH1" <-> "NH2" Residue "F ARG 550": "NH1" <-> "NH2" Residue "H ARG 550": "NH1" <-> "NH2" Residue "I ARG 550": "NH1" <-> "NH2" Residue "J ARG 550": "NH1" <-> "NH2" Residue "K ARG 550": "NH1" <-> "NH2" Residue "L ARG 550": "NH1" <-> "NH2" Residue "M ARG 550": "NH1" <-> "NH2" Residue "N ARG 550": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 44415 Number of models: 1 Model: "" Number of chains: 15 Chain: "G" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2961 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 4 Chain: "O" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2961 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 4 Chain: "A" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2961 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 4 Chain: "B" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2961 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 4 Chain: "C" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2961 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 4 Chain: "D" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2961 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 4 Chain: "E" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2961 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 4 Chain: "F" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2961 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 4 Chain: "H" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2961 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 4 Chain: "I" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2961 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 4 Chain: "J" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2961 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 4 Chain: "K" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2961 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 4 Chain: "L" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2961 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 4 Chain: "M" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2961 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 4 Chain: "N" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2961 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 4 Time building chain proxies: 21.32, per 1000 atoms: 0.48 Number of scatterers: 44415 At special positions: 0 Unit cell: (156.88, 156.88, 155.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 8775 8.00 N 7980 7.00 C 27585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.59 Conformation dependent library (CDL) restraints added in 6.4 seconds 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10980 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 90 sheets defined 23.5% alpha, 52.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.43 Creating SS restraints... Processing helix chain 'G' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU G 190 " --> pdb=" O MET G 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN G 194 " --> pdb=" O GLU G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 238 Processing helix chain 'G' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU G 260 " --> pdb=" O ASP G 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR G 263 " --> pdb=" O THR G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 318 Processing helix chain 'G' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU G 377 " --> pdb=" O LEU G 373 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE G 549 " --> pdb=" O GLY G 546 " (cutoff:3.500A) Processing helix chain 'G' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU G 576 " --> pdb=" O ASP G 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE G 590 " --> pdb=" O ASP G 586 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU O 190 " --> pdb=" O MET O 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL O 191 " --> pdb=" O ASP O 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN O 194 " --> pdb=" O GLU O 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 223 through 238 Processing helix chain 'O' and resid 256 through 268 removed outlier: 3.689A pdb=" N LEU O 260 " --> pdb=" O ASP O 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR O 263 " --> pdb=" O THR O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 318 Processing helix chain 'O' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU O 377 " --> pdb=" O LEU O 373 " (cutoff:3.500A) Processing helix chain 'O' and resid 545 through 549 removed outlier: 3.643A pdb=" N PHE O 549 " --> pdb=" O GLY O 546 " (cutoff:3.500A) Processing helix chain 'O' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU O 576 " --> pdb=" O ASP O 572 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE O 590 " --> pdb=" O ASP O 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU A 190 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 238 Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 318 Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.953A pdb=" N GLU A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE A 549 " --> pdb=" O GLY A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 592 removed outlier: 3.673A pdb=" N LEU A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU B 190 " --> pdb=" O MET B 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 238 Processing helix chain 'B' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 318 Processing helix chain 'B' and resid 368 through 381 removed outlier: 3.953A pdb=" N GLU B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE B 549 " --> pdb=" O GLY B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 592 removed outlier: 3.673A pdb=" N LEU B 576 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU C 190 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 238 Processing helix chain 'C' and resid 256 through 268 removed outlier: 3.689A pdb=" N LEU C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C 263 " --> pdb=" O THR C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 318 Processing helix chain 'C' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE C 549 " --> pdb=" O GLY C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU C 576 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU D 190 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 238 Processing helix chain 'D' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR D 263 " --> pdb=" O THR D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 318 Processing helix chain 'D' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE D 549 " --> pdb=" O GLY D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU D 576 " --> pdb=" O ASP D 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 194 removed outlier: 4.440A pdb=" N GLU E 190 " --> pdb=" O MET E 186 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN E 194 " --> pdb=" O GLU E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 238 Processing helix chain 'E' and resid 256 through 268 removed outlier: 3.689A pdb=" N LEU E 260 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR E 263 " --> pdb=" O THR E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 318 Processing helix chain 'E' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU E 377 " --> pdb=" O LEU E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 549 removed outlier: 3.645A pdb=" N PHE E 549 " --> pdb=" O GLY E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 592 removed outlier: 3.673A pdb=" N LEU E 576 " --> pdb=" O ASP E 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE E 590 " --> pdb=" O ASP E 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU F 190 " --> pdb=" O MET F 186 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 238 Processing helix chain 'F' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR F 263 " --> pdb=" O THR F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 318 Processing helix chain 'F' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU F 377 " --> pdb=" O LEU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE F 549 " --> pdb=" O GLY F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU F 576 " --> pdb=" O ASP F 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE F 590 " --> pdb=" O ASP F 586 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 194 removed outlier: 4.440A pdb=" N GLU H 190 " --> pdb=" O MET H 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL H 191 " --> pdb=" O ASP H 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN H 194 " --> pdb=" O GLU H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 238 Processing helix chain 'H' and resid 256 through 268 removed outlier: 3.689A pdb=" N LEU H 260 " --> pdb=" O ASP H 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR H 263 " --> pdb=" O THR H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 318 Processing helix chain 'H' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU H 377 " --> pdb=" O LEU H 373 " (cutoff:3.500A) Processing helix chain 'H' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE H 549 " --> pdb=" O GLY H 546 " (cutoff:3.500A) Processing helix chain 'H' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU H 576 " --> pdb=" O ASP H 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE H 590 " --> pdb=" O ASP H 586 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU I 190 " --> pdb=" O MET I 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL I 191 " --> pdb=" O ASP I 187 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN I 194 " --> pdb=" O GLU I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 238 Processing helix chain 'I' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU I 260 " --> pdb=" O ASP I 256 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR I 263 " --> pdb=" O THR I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 318 Processing helix chain 'I' and resid 368 through 381 removed outlier: 3.953A pdb=" N GLU I 377 " --> pdb=" O LEU I 373 " (cutoff:3.500A) Processing helix chain 'I' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE I 549 " --> pdb=" O GLY I 546 " (cutoff:3.500A) Processing helix chain 'I' and resid 572 through 592 removed outlier: 3.673A pdb=" N LEU I 576 " --> pdb=" O ASP I 572 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE I 590 " --> pdb=" O ASP I 586 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU J 190 " --> pdb=" O MET J 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL J 191 " --> pdb=" O ASP J 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN J 194 " --> pdb=" O GLU J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 238 Processing helix chain 'J' and resid 256 through 268 removed outlier: 3.689A pdb=" N LEU J 260 " --> pdb=" O ASP J 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR J 263 " --> pdb=" O THR J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 318 Processing helix chain 'J' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU J 377 " --> pdb=" O LEU J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE J 549 " --> pdb=" O GLY J 546 " (cutoff:3.500A) Processing helix chain 'J' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU J 576 " --> pdb=" O ASP J 572 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE J 590 " --> pdb=" O ASP J 586 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU K 190 " --> pdb=" O MET K 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL K 191 " --> pdb=" O ASP K 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN K 194 " --> pdb=" O GLU K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 238 Processing helix chain 'K' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU K 260 " --> pdb=" O ASP K 256 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR K 263 " --> pdb=" O THR K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 318 Processing helix chain 'K' and resid 368 through 381 removed outlier: 3.951A pdb=" N GLU K 377 " --> pdb=" O LEU K 373 " (cutoff:3.500A) Processing helix chain 'K' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE K 549 " --> pdb=" O GLY K 546 " (cutoff:3.500A) Processing helix chain 'K' and resid 572 through 592 removed outlier: 3.673A pdb=" N LEU K 576 " --> pdb=" O ASP K 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE K 590 " --> pdb=" O ASP K 586 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU L 190 " --> pdb=" O MET L 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL L 191 " --> pdb=" O ASP L 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN L 194 " --> pdb=" O GLU L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 238 Processing helix chain 'L' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU L 260 " --> pdb=" O ASP L 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR L 263 " --> pdb=" O THR L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 318 Processing helix chain 'L' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU L 377 " --> pdb=" O LEU L 373 " (cutoff:3.500A) Processing helix chain 'L' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE L 549 " --> pdb=" O GLY L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 592 removed outlier: 3.675A pdb=" N LEU L 576 " --> pdb=" O ASP L 572 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE L 590 " --> pdb=" O ASP L 586 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 194 removed outlier: 4.440A pdb=" N GLU M 190 " --> pdb=" O MET M 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL M 191 " --> pdb=" O ASP M 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN M 194 " --> pdb=" O GLU M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 238 Processing helix chain 'M' and resid 256 through 268 removed outlier: 3.689A pdb=" N LEU M 260 " --> pdb=" O ASP M 256 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR M 263 " --> pdb=" O THR M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 318 Processing helix chain 'M' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU M 377 " --> pdb=" O LEU M 373 " (cutoff:3.500A) Processing helix chain 'M' and resid 545 through 549 removed outlier: 3.645A pdb=" N PHE M 549 " --> pdb=" O GLY M 546 " (cutoff:3.500A) Processing helix chain 'M' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU M 576 " --> pdb=" O ASP M 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE M 590 " --> pdb=" O ASP M 586 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 194 removed outlier: 4.441A pdb=" N GLU N 190 " --> pdb=" O MET N 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL N 191 " --> pdb=" O ASP N 187 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN N 194 " --> pdb=" O GLU N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 238 Processing helix chain 'N' and resid 256 through 268 removed outlier: 3.690A pdb=" N LEU N 260 " --> pdb=" O ASP N 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR N 263 " --> pdb=" O THR N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 306 through 318 Processing helix chain 'N' and resid 368 through 381 removed outlier: 3.952A pdb=" N GLU N 377 " --> pdb=" O LEU N 373 " (cutoff:3.500A) Processing helix chain 'N' and resid 545 through 549 removed outlier: 3.644A pdb=" N PHE N 549 " --> pdb=" O GLY N 546 " (cutoff:3.500A) Processing helix chain 'N' and resid 572 through 592 removed outlier: 3.674A pdb=" N LEU N 576 " --> pdb=" O ASP N 572 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE N 590 " --> pdb=" O ASP N 586 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 175 through 178 Processing sheet with id=AA2, first strand: chain 'G' and resid 247 through 251 Processing sheet with id=AA3, first strand: chain 'G' and resid 326 through 350 removed outlier: 6.278A pdb=" N SER G 551 " --> pdb=" O GLU G 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU G 533 " --> pdb=" O SER G 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS G 553 " --> pdb=" O GLN G 531 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN G 531 " --> pdb=" O LYS G 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR G 555 " --> pdb=" O VAL G 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL G 529 " --> pdb=" O THR G 555 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR G 557 " --> pdb=" O ASP G 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP G 527 " --> pdb=" O THR G 557 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG G 559 " --> pdb=" O ILE G 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE G 525 " --> pdb=" O ARG G 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU G 561 " --> pdb=" O GLY G 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY G 523 " --> pdb=" O LEU G 561 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL G 563 " --> pdb=" O ILE G 521 " (cutoff:3.500A) removed outlier: 16.934A pdb=" N ILE G 519 " --> pdb=" O LEU H 422 " (cutoff:3.500A) removed outlier: 13.862A pdb=" N LEU H 422 " --> pdb=" O ILE G 519 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE G 521 " --> pdb=" O LEU H 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA H 407 " --> pdb=" O GLN H 341 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER H 551 " --> pdb=" O GLU H 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU H 533 " --> pdb=" O SER H 551 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS H 553 " --> pdb=" O GLN H 531 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN H 531 " --> pdb=" O LYS H 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR H 555 " --> pdb=" O VAL H 529 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL H 529 " --> pdb=" O THR H 555 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR H 557 " --> pdb=" O ASP H 527 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP H 527 " --> pdb=" O THR H 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG H 559 " --> pdb=" O ILE H 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE H 525 " --> pdb=" O ARG H 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU H 561 " --> pdb=" O GLY H 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY H 523 " --> pdb=" O LEU H 561 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL H 563 " --> pdb=" O ILE H 521 " (cutoff:3.500A) removed outlier: 16.784A pdb=" N ILE H 519 " --> pdb=" O LEU I 422 " (cutoff:3.500A) removed outlier: 13.731A pdb=" N LEU I 422 " --> pdb=" O ILE H 519 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE H 521 " --> pdb=" O LEU I 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA I 407 " --> pdb=" O GLN I 341 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER I 551 " --> pdb=" O GLU I 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU I 533 " --> pdb=" O SER I 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS I 553 " --> pdb=" O GLN I 531 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN I 531 " --> pdb=" O LYS I 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR I 555 " --> pdb=" O VAL I 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL I 529 " --> pdb=" O THR I 555 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR I 557 " --> pdb=" O ASP I 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP I 527 " --> pdb=" O THR I 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG I 559 " --> pdb=" O ILE I 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE I 525 " --> pdb=" O ARG I 559 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU I 561 " --> pdb=" O GLY I 523 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY I 523 " --> pdb=" O LEU I 561 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL I 563 " --> pdb=" O ILE I 521 " (cutoff:3.500A) removed outlier: 17.066A pdb=" N ILE I 519 " --> pdb=" O LEU J 422 " (cutoff:3.500A) removed outlier: 13.983A pdb=" N LEU J 422 " --> pdb=" O ILE I 519 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE I 521 " --> pdb=" O LEU J 420 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA J 407 " --> pdb=" O GLN J 341 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER J 551 " --> pdb=" O GLU J 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU J 533 " --> pdb=" O SER J 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS J 553 " --> pdb=" O GLN J 531 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN J 531 " --> pdb=" O LYS J 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR J 555 " --> pdb=" O VAL J 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL J 529 " --> pdb=" O THR J 555 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR J 557 " --> pdb=" O ASP J 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP J 527 " --> pdb=" O THR J 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG J 559 " --> pdb=" O ILE J 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE J 525 " --> pdb=" O ARG J 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU J 561 " --> pdb=" O GLY J 523 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY J 523 " --> pdb=" O LEU J 561 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL J 563 " --> pdb=" O ILE J 521 " (cutoff:3.500A) removed outlier: 16.868A pdb=" N ILE J 519 " --> pdb=" O LEU K 422 " (cutoff:3.500A) removed outlier: 13.838A pdb=" N LEU K 422 " --> pdb=" O ILE J 519 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE J 521 " --> pdb=" O LEU K 420 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN K 408 " --> pdb=" O GLU J 533 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA K 407 " --> pdb=" O GLN K 341 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER K 551 " --> pdb=" O GLU K 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU K 533 " --> pdb=" O SER K 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS K 553 " --> pdb=" O GLN K 531 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN K 531 " --> pdb=" O LYS K 553 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR K 555 " --> pdb=" O VAL K 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL K 529 " --> pdb=" O THR K 555 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR K 557 " --> pdb=" O ASP K 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP K 527 " --> pdb=" O THR K 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG K 559 " --> pdb=" O ILE K 525 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE K 525 " --> pdb=" O ARG K 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU K 561 " --> pdb=" O GLY K 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY K 523 " --> pdb=" O LEU K 561 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL K 563 " --> pdb=" O ILE K 521 " (cutoff:3.500A) removed outlier: 16.947A pdb=" N ILE K 519 " --> pdb=" O LEU L 422 " (cutoff:3.500A) removed outlier: 13.910A pdb=" N LEU L 422 " --> pdb=" O ILE K 519 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE K 521 " --> pdb=" O LEU L 420 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN L 408 " --> pdb=" O GLU K 533 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA L 407 " --> pdb=" O GLN L 341 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER L 551 " --> pdb=" O GLU L 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU L 533 " --> pdb=" O SER L 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS L 553 " --> pdb=" O GLN L 531 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN L 531 " --> pdb=" O LYS L 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR L 555 " --> pdb=" O VAL L 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL L 529 " --> pdb=" O THR L 555 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR L 557 " --> pdb=" O ASP L 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP L 527 " --> pdb=" O THR L 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG L 559 " --> pdb=" O ILE L 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE L 525 " --> pdb=" O ARG L 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU L 561 " --> pdb=" O GLY L 523 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY L 523 " --> pdb=" O LEU L 561 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL L 563 " --> pdb=" O ILE L 521 " (cutoff:3.500A) removed outlier: 17.013A pdb=" N ILE L 519 " --> pdb=" O LEU M 422 " (cutoff:3.500A) removed outlier: 13.965A pdb=" N LEU M 422 " --> pdb=" O ILE L 519 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE L 521 " --> pdb=" O LEU M 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA M 407 " --> pdb=" O GLN M 341 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER M 551 " --> pdb=" O GLU M 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU M 533 " --> pdb=" O SER M 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS M 553 " --> pdb=" O GLN M 531 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN M 531 " --> pdb=" O LYS M 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR M 555 " --> pdb=" O VAL M 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL M 529 " --> pdb=" O THR M 555 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR M 557 " --> pdb=" O ASP M 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP M 527 " --> pdb=" O THR M 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG M 559 " --> pdb=" O ILE M 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE M 525 " --> pdb=" O ARG M 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU M 561 " --> pdb=" O GLY M 523 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY M 523 " --> pdb=" O LEU M 561 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL M 563 " --> pdb=" O ILE M 521 " (cutoff:3.500A) removed outlier: 17.204A pdb=" N ILE M 519 " --> pdb=" O LEU N 422 " (cutoff:3.500A) removed outlier: 14.157A pdb=" N LEU N 422 " --> pdb=" O ILE M 519 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE M 521 " --> pdb=" O LEU N 420 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA N 407 " --> pdb=" O GLN N 341 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER N 551 " --> pdb=" O GLU N 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU N 533 " --> pdb=" O SER N 551 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS N 553 " --> pdb=" O GLN N 531 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN N 531 " --> pdb=" O LYS N 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR N 555 " --> pdb=" O VAL N 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL N 529 " --> pdb=" O THR N 555 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR N 557 " --> pdb=" O ASP N 527 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP N 527 " --> pdb=" O THR N 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG N 559 " --> pdb=" O ILE N 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE N 525 " --> pdb=" O ARG N 559 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU N 561 " --> pdb=" O GLY N 523 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY N 523 " --> pdb=" O LEU N 561 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL N 563 " --> pdb=" O ILE N 521 " (cutoff:3.500A) removed outlier: 16.786A pdb=" N ILE N 519 " --> pdb=" O LEU O 422 " (cutoff:3.500A) removed outlier: 13.602A pdb=" N LEU O 422 " --> pdb=" O ILE N 519 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE N 521 " --> pdb=" O LEU O 420 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN O 408 " --> pdb=" O GLU N 533 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS N 535 " --> pdb=" O SER O 406 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA O 407 " --> pdb=" O GLN O 341 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER O 551 " --> pdb=" O GLU O 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU O 533 " --> pdb=" O SER O 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS O 553 " --> pdb=" O GLN O 531 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN O 531 " --> pdb=" O LYS O 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR O 555 " --> pdb=" O VAL O 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL O 529 " --> pdb=" O THR O 555 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR O 557 " --> pdb=" O ASP O 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP O 527 " --> pdb=" O THR O 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG O 559 " --> pdb=" O ILE O 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE O 525 " --> pdb=" O ARG O 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU O 561 " --> pdb=" O GLY O 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY O 523 " --> pdb=" O LEU O 561 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL O 563 " --> pdb=" O ILE O 521 " (cutoff:3.500A) removed outlier: 16.922A pdb=" N ILE O 519 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 13.859A pdb=" N LEU A 422 " --> pdb=" O ILE O 519 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE O 521 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A 407 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER A 551 " --> pdb=" O GLU A 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A 533 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS A 553 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN A 531 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR A 555 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A 529 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR A 557 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP A 527 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG A 559 " --> pdb=" O ILE A 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A 525 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 561 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY A 523 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 563 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 17.066A pdb=" N ILE A 519 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 13.968A pdb=" N LEU B 422 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE A 521 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B 407 " --> pdb=" O GLN B 341 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER B 551 " --> pdb=" O GLU B 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU B 533 " --> pdb=" O SER B 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS B 553 " --> pdb=" O GLN B 531 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN B 531 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR B 555 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL B 529 " --> pdb=" O THR B 555 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR B 557 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP B 527 " --> pdb=" O THR B 557 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG B 559 " --> pdb=" O ILE B 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE B 525 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU B 561 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY B 523 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL B 563 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP B 527 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 414 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 529 " --> pdb=" O ASN C 412 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN C 412 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 531 " --> pdb=" O LYS C 410 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 410 " --> pdb=" O GLN B 531 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 533 " --> pdb=" O ASN C 408 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN C 408 " --> pdb=" O GLU B 533 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS B 535 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER C 406 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 407 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER C 551 " --> pdb=" O GLU C 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU C 533 " --> pdb=" O SER C 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS C 553 " --> pdb=" O GLN C 531 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN C 531 " --> pdb=" O LYS C 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR C 555 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL C 529 " --> pdb=" O THR C 555 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR C 557 " --> pdb=" O ASP C 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP C 527 " --> pdb=" O THR C 557 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG C 559 " --> pdb=" O ILE C 525 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE C 525 " --> pdb=" O ARG C 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 561 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY C 523 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL C 563 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 16.673A pdb=" N ILE C 519 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 13.429A pdb=" N LEU D 422 " --> pdb=" O ILE C 519 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C 521 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA D 407 " --> pdb=" O GLN D 341 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER D 551 " --> pdb=" O GLU D 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU D 533 " --> pdb=" O SER D 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS D 553 " --> pdb=" O GLN D 531 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN D 531 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR D 555 " --> pdb=" O VAL D 529 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL D 529 " --> pdb=" O THR D 555 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR D 557 " --> pdb=" O ASP D 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP D 527 " --> pdb=" O THR D 557 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG D 559 " --> pdb=" O ILE D 525 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE D 525 " --> pdb=" O ARG D 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU D 561 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY D 523 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL D 563 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 17.532A pdb=" N ILE D 519 " --> pdb=" O LEU E 422 " (cutoff:3.500A) removed outlier: 14.679A pdb=" N LEU E 422 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE D 521 " --> pdb=" O LEU E 420 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU E 420 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY D 523 " --> pdb=" O SER E 418 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER E 418 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER E 551 " --> pdb=" O GLU E 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU E 533 " --> pdb=" O SER E 551 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS E 553 " --> pdb=" O GLN E 531 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN E 531 " --> pdb=" O LYS E 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR E 555 " --> pdb=" O VAL E 529 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL E 529 " --> pdb=" O THR E 555 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR E 557 " --> pdb=" O ASP E 527 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP E 527 " --> pdb=" O THR E 557 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG E 559 " --> pdb=" O ILE E 525 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE E 525 " --> pdb=" O ARG E 559 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU E 561 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY E 523 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL E 563 " --> pdb=" O ILE E 521 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 519 through 535 current: chain 'F' and resid 551 through 570 removed outlier: 6.277A pdb=" N SER F 551 " --> pdb=" O GLU F 533 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU F 533 " --> pdb=" O SER F 551 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS F 553 " --> pdb=" O GLN F 531 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN F 531 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR F 555 " --> pdb=" O VAL F 529 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL F 529 " --> pdb=" O THR F 555 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR F 557 " --> pdb=" O ASP F 527 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP F 527 " --> pdb=" O THR F 557 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG F 559 " --> pdb=" O ILE F 525 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE F 525 " --> pdb=" O ARG F 559 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU F 561 " --> pdb=" O GLY F 523 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY F 523 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL F 563 " --> pdb=" O ILE F 521 " (cutoff:3.500A) removed outlier: 16.782A pdb=" N ILE F 519 " --> pdb=" O LEU G 422 " (cutoff:3.500A) removed outlier: 13.736A pdb=" N LEU G 422 " --> pdb=" O ILE F 519 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE F 521 " --> pdb=" O LEU G 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA G 407 " --> pdb=" O GLN G 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE G 350 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA G 407 " --> pdb=" O GLN G 341 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE G 398 " --> pdb=" O SER G 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE H 350 " --> pdb=" O THR H 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA H 407 " --> pdb=" O GLN H 341 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE H 398 " --> pdb=" O SER H 395 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE I 350 " --> pdb=" O THR I 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA I 407 " --> pdb=" O GLN I 341 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE I 398 " --> pdb=" O SER I 395 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE J 350 " --> pdb=" O THR J 358 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA J 407 " --> pdb=" O GLN J 341 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE J 398 " --> pdb=" O SER J 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE K 350 " --> pdb=" O THR K 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA K 407 " --> pdb=" O GLN K 341 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE K 398 " --> pdb=" O SER K 395 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 358 through 359 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 358 through 359 current: chain 'L' and resid 389 through 395 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE M 350 " --> pdb=" O THR M 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA M 407 " --> pdb=" O GLN M 341 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE M 398 " --> pdb=" O SER M 395 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 358 through 359 removed outlier: 3.888A pdb=" N ILE N 350 " --> pdb=" O THR N 358 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA N 407 " --> pdb=" O GLN N 341 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE N 398 " --> pdb=" O SER N 395 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE O 350 " --> pdb=" O THR O 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA O 407 " --> pdb=" O GLN O 341 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE O 398 " --> pdb=" O SER O 395 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 358 through 359 removed outlier: 3.888A pdb=" N ILE A 350 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A 407 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A 398 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 358 through 359 removed outlier: 3.886A pdb=" N ILE B 350 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE B 398 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 389 through 395 removed outlier: 3.935A pdb=" N PHE C 398 " --> pdb=" O SER C 395 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 407 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE C 350 " --> pdb=" O THR C 358 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 389 through 395 removed outlier: 3.935A pdb=" N PHE C 398 " --> pdb=" O SER C 395 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 407 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE C 350 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE C 350 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 418 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 420 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE B 521 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 14.524A pdb=" N LEU C 422 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 17.506A pdb=" N ILE B 519 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP B 527 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 414 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 529 " --> pdb=" O ASN C 412 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN C 412 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 531 " --> pdb=" O LYS C 410 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 410 " --> pdb=" O GLN B 531 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 533 " --> pdb=" O ASN C 408 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN C 408 " --> pdb=" O GLU B 533 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS B 535 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER C 406 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE C 398 " --> pdb=" O SER C 395 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE D 350 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA D 407 " --> pdb=" O GLN D 341 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE D 398 " --> pdb=" O SER D 395 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 358 through 359 removed outlier: 3.887A pdb=" N ILE E 350 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN E 408 " --> pdb=" O GLU D 533 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU D 533 " --> pdb=" O ASN E 408 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS E 410 " --> pdb=" O GLN D 531 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN D 531 " --> pdb=" O LYS E 410 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN E 412 " --> pdb=" O VAL D 529 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL D 529 " --> pdb=" O ASN E 412 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 414 " --> pdb=" O ASP D 527 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP D 527 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 17.532A pdb=" N ILE D 519 " --> pdb=" O LEU E 422 " (cutoff:3.500A) removed outlier: 14.679A pdb=" N LEU E 422 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE D 521 " --> pdb=" O LEU E 420 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU E 420 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY D 523 " --> pdb=" O SER E 418 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER E 418 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE E 398 " --> pdb=" O SER E 395 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 358 through 359 removed outlier: 3.888A pdb=" N ILE F 350 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA F 407 " --> pdb=" O GLN F 341 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE F 398 " --> pdb=" O SER F 395 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 429 through 431 Processing sheet with id=AC3, first strand: chain 'G' and resid 429 through 431 Processing sheet with id=AC4, first strand: chain 'G' and resid 434 through 437 Processing sheet with id=AC5, first strand: chain 'O' and resid 175 through 178 Processing sheet with id=AC6, first strand: chain 'O' and resid 247 through 251 Processing sheet with id=AC7, first strand: chain 'O' and resid 429 through 431 Processing sheet with id=AC8, first strand: chain 'O' and resid 429 through 431 Processing sheet with id=AC9, first strand: chain 'O' and resid 434 through 437 Processing sheet with id=AD1, first strand: chain 'A' and resid 175 through 178 Processing sheet with id=AD2, first strand: chain 'A' and resid 247 through 251 Processing sheet with id=AD3, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AD4, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AD5, first strand: chain 'A' and resid 434 through 437 Processing sheet with id=AD6, first strand: chain 'B' and resid 175 through 178 Processing sheet with id=AD7, first strand: chain 'B' and resid 247 through 251 Processing sheet with id=AD8, first strand: chain 'B' and resid 429 through 431 Processing sheet with id=AD9, first strand: chain 'B' and resid 429 through 431 Processing sheet with id=AE1, first strand: chain 'B' and resid 434 through 437 Processing sheet with id=AE2, first strand: chain 'C' and resid 175 through 178 Processing sheet with id=AE3, first strand: chain 'C' and resid 247 through 251 Processing sheet with id=AE4, first strand: chain 'C' and resid 429 through 431 Processing sheet with id=AE5, first strand: chain 'C' and resid 429 through 431 Processing sheet with id=AE6, first strand: chain 'C' and resid 434 through 437 Processing sheet with id=AE7, first strand: chain 'D' and resid 175 through 178 Processing sheet with id=AE8, first strand: chain 'D' and resid 247 through 251 Processing sheet with id=AE9, first strand: chain 'D' and resid 429 through 431 Processing sheet with id=AF1, first strand: chain 'D' and resid 510 through 513 Processing sheet with id=AF2, first strand: chain 'D' and resid 434 through 437 Processing sheet with id=AF3, first strand: chain 'E' and resid 175 through 178 Processing sheet with id=AF4, first strand: chain 'E' and resid 247 through 251 Processing sheet with id=AF5, first strand: chain 'E' and resid 434 through 437 Processing sheet with id=AF6, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AF7, first strand: chain 'F' and resid 247 through 251 Processing sheet with id=AF8, first strand: chain 'F' and resid 429 through 431 Processing sheet with id=AF9, first strand: chain 'F' and resid 429 through 431 Processing sheet with id=AG1, first strand: chain 'F' and resid 434 through 437 Processing sheet with id=AG2, first strand: chain 'H' and resid 175 through 178 Processing sheet with id=AG3, first strand: chain 'H' and resid 247 through 251 Processing sheet with id=AG4, first strand: chain 'H' and resid 429 through 431 Processing sheet with id=AG5, first strand: chain 'H' and resid 429 through 431 Processing sheet with id=AG6, first strand: chain 'H' and resid 434 through 437 Processing sheet with id=AG7, first strand: chain 'I' and resid 175 through 178 Processing sheet with id=AG8, first strand: chain 'I' and resid 247 through 251 Processing sheet with id=AG9, first strand: chain 'I' and resid 429 through 431 Processing sheet with id=AH1, first strand: chain 'I' and resid 429 through 431 Processing sheet with id=AH2, first strand: chain 'I' and resid 434 through 437 Processing sheet with id=AH3, first strand: chain 'J' and resid 175 through 178 Processing sheet with id=AH4, first strand: chain 'J' and resid 247 through 251 Processing sheet with id=AH5, first strand: chain 'J' and resid 429 through 431 Processing sheet with id=AH6, first strand: chain 'J' and resid 429 through 431 Processing sheet with id=AH7, first strand: chain 'J' and resid 434 through 437 Processing sheet with id=AH8, first strand: chain 'K' and resid 175 through 178 Processing sheet with id=AH9, first strand: chain 'K' and resid 247 through 251 Processing sheet with id=AI1, first strand: chain 'K' and resid 429 through 431 Processing sheet with id=AI2, first strand: chain 'K' and resid 429 through 431 Processing sheet with id=AI3, first strand: chain 'K' and resid 434 through 437 Processing sheet with id=AI4, first strand: chain 'L' and resid 175 through 178 Processing sheet with id=AI5, first strand: chain 'L' and resid 247 through 251 Processing sheet with id=AI6, first strand: chain 'L' and resid 429 through 431 Processing sheet with id=AI7, first strand: chain 'L' and resid 429 through 431 Processing sheet with id=AI8, first strand: chain 'L' and resid 434 through 437 Processing sheet with id=AI9, first strand: chain 'M' and resid 175 through 178 Processing sheet with id=AJ1, first strand: chain 'M' and resid 247 through 251 Processing sheet with id=AJ2, first strand: chain 'M' and resid 429 through 431 Processing sheet with id=AJ3, first strand: chain 'M' and resid 429 through 431 Processing sheet with id=AJ4, first strand: chain 'M' and resid 434 through 437 Processing sheet with id=AJ5, first strand: chain 'N' and resid 175 through 178 Processing sheet with id=AJ6, first strand: chain 'N' and resid 247 through 251 Processing sheet with id=AJ7, first strand: chain 'N' and resid 429 through 431 Processing sheet with id=AJ8, first strand: chain 'N' and resid 429 through 431 Processing sheet with id=AJ9, first strand: chain 'N' and resid 434 through 437 2904 hydrogen bonds defined for protein. 7992 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: 19.23 Time building geometry restraints manager: 16.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13631 1.33 - 1.45: 5105 1.45 - 1.57: 25919 1.57 - 1.69: 0 1.69 - 1.80: 150 Bond restraints: 44805 Sorted by residual: bond pdb=" C ALA K 381 " pdb=" N PRO K 382 " ideal model delta sigma weight residual 1.334 1.400 -0.067 2.34e-02 1.83e+03 8.08e+00 bond pdb=" C ALA O 381 " pdb=" N PRO O 382 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 8.05e+00 bond pdb=" C ALA H 381 " pdb=" N PRO H 382 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 8.03e+00 bond pdb=" C ALA E 381 " pdb=" N PRO E 382 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 7.99e+00 bond pdb=" C ALA D 381 " pdb=" N PRO D 382 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 7.98e+00 ... (remaining 44800 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.71: 1434 106.71 - 113.55: 26380 113.55 - 120.38: 15876 120.38 - 127.21: 16820 127.21 - 134.05: 240 Bond angle restraints: 60750 Sorted by residual: angle pdb=" C SER I 395 " pdb=" N SER I 396 " pdb=" CA SER I 396 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C SER F 395 " pdb=" N SER F 396 " pdb=" CA SER F 396 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C SER E 395 " pdb=" N SER E 396 " pdb=" CA SER E 396 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C SER C 395 " pdb=" N SER C 396 " pdb=" CA SER C 396 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C SER K 395 " pdb=" N SER K 396 " pdb=" CA SER K 396 " ideal model delta sigma weight residual 121.54 129.39 -7.85 1.91e+00 2.74e-01 1.69e+01 ... (remaining 60745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.18: 25885 14.18 - 28.37: 1461 28.37 - 42.55: 269 42.55 - 56.73: 30 56.73 - 70.91: 30 Dihedral angle restraints: 27675 sinusoidal: 10785 harmonic: 16890 Sorted by residual: dihedral pdb=" CA ALA M 242 " pdb=" C ALA M 242 " pdb=" N ARG M 243 " pdb=" CA ARG M 243 " ideal model delta harmonic sigma weight residual -180.00 -155.43 -24.57 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA ALA I 242 " pdb=" C ALA I 242 " pdb=" N ARG I 243 " pdb=" CA ARG I 243 " ideal model delta harmonic sigma weight residual -180.00 -155.44 -24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ALA B 242 " pdb=" C ALA B 242 " pdb=" N ARG B 243 " pdb=" CA ARG B 243 " ideal model delta harmonic sigma weight residual -180.00 -155.45 -24.55 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 27672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 5533 0.060 - 0.120: 1501 0.120 - 0.181: 391 0.181 - 0.241: 64 0.241 - 0.301: 56 Chirality restraints: 7545 Sorted by residual: chirality pdb=" CB ILE C 507 " pdb=" CA ILE C 507 " pdb=" CG1 ILE C 507 " pdb=" CG2 ILE C 507 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE I 507 " pdb=" CA ILE I 507 " pdb=" CG1 ILE I 507 " pdb=" CG2 ILE I 507 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB ILE H 507 " pdb=" CA ILE H 507 " pdb=" CG1 ILE H 507 " pdb=" CG2 ILE H 507 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 7542 not shown) Planarity restraints: 7905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 468 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.45e+00 pdb=" N PRO I 469 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO I 469 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 469 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 468 " 0.048 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO B 469 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 469 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 469 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR K 468 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO K 469 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO K 469 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO K 469 " 0.040 5.00e-02 4.00e+02 ... (remaining 7902 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5244 2.75 - 3.28: 41261 3.28 - 3.82: 67688 3.82 - 4.36: 78319 4.36 - 4.90: 141300 Nonbonded interactions: 333812 Sorted by model distance: nonbonded pdb=" NH2 ARG O 458 " pdb=" O THR N 498 " model vdw 2.206 2.520 nonbonded pdb=" O THR C 498 " pdb=" NH2 ARG D 458 " model vdw 2.214 2.520 nonbonded pdb=" OD1 ASP M 339 " pdb=" OG1 THR M 409 " model vdw 2.219 2.440 nonbonded pdb=" OD1 ASP O 339 " pdb=" OG1 THR O 409 " model vdw 2.219 2.440 nonbonded pdb=" OD1 ASP F 339 " pdb=" OG1 THR F 409 " model vdw 2.219 2.440 ... (remaining 333807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.890 Check model and map are aligned: 0.680 Set scattering table: 0.400 Process input model: 106.850 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.300 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 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 : 0.010 0.067 44805 Z= 0.630 Angle : 1.135 8.013 60750 Z= 0.603 Chirality : 0.064 0.301 7545 Planarity : 0.008 0.073 7905 Dihedral : 10.118 70.914 16695 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 0.31 % Allowed : 4.29 % Favored : 95.40 % 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: -5.04 (0.09), residues: 5790 helix: -2.68 (0.10), residues: 1245 sheet: -2.88 (0.09), residues: 2610 loop : -4.09 (0.09), residues: 1935 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 797 time to evaluate : 5.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 15 residues processed: 812 average time/residue: 0.6099 time to fit residues: 786.1220 Evaluate side-chains 356 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 341 time to evaluate : 5.831 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3762 time to fit residues: 17.8519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 493 optimal weight: 0.7980 chunk 443 optimal weight: 0.5980 chunk 246 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 236 optimal weight: 7.9990 chunk 458 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 278 optimal weight: 6.9990 chunk 341 optimal weight: 4.9990 chunk 531 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 608 ASN ** O 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 517 GLN O 560 ASN O 608 ASN ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 560 ASN A 608 ASN B 179 ASN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN C 208 GLN ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN C 608 ASN ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 ASN E 472 ASN ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 608 ASN ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN ** F 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 517 GLN F 556 HIS F 608 ASN ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 608 ASN I 179 ASN ** I 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 472 ASN ** I 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 608 ASN ** J 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 517 GLN J 608 ASN ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 472 ASN ** K 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 608 ASN L 472 ASN ** L 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 494 GLN L 608 ASN ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 472 ASN M 483 GLN M 517 GLN M 608 ASN ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 608 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44805 Z= 0.224 Angle : 0.722 12.072 60750 Z= 0.367 Chirality : 0.047 0.201 7545 Planarity : 0.006 0.067 7905 Dihedral : 6.172 27.255 6240 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.43 % Favored : 91.31 % Rotamer: Outliers : 2.49 % Allowed : 10.49 % Favored : 87.01 % 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: -4.09 (0.09), residues: 5790 helix: -1.44 (0.13), residues: 1290 sheet: -2.32 (0.09), residues: 2715 loop : -3.96 (0.10), residues: 1785 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 448 time to evaluate : 5.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 58 residues processed: 543 average time/residue: 0.5728 time to fit residues: 505.8679 Evaluate side-chains 353 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 295 time to evaluate : 5.159 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.3658 time to fit residues: 47.8221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 295 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 442 optimal weight: 7.9990 chunk 361 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 532 optimal weight: 1.9990 chunk 574 optimal weight: 0.0270 chunk 473 optimal weight: 8.9990 chunk 527 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 426 optimal weight: 7.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 472 ASN ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 374 GLN O 472 ASN ** O 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 434 ASN ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 472 ASN ** H 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 472 ASN ** J 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 434 ASN N 472 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 44805 Z= 0.337 Angle : 0.758 14.169 60750 Z= 0.380 Chirality : 0.048 0.190 7545 Planarity : 0.006 0.061 7905 Dihedral : 6.016 23.621 6240 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.02 % Favored : 87.98 % Rotamer: Outliers : 2.97 % Allowed : 12.27 % Favored : 84.76 % 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: -3.52 (0.10), residues: 5790 helix: -0.69 (0.13), residues: 1290 sheet: -2.10 (0.09), residues: 2625 loop : -3.61 (0.12), residues: 1875 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 345 time to evaluate : 5.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 84 residues processed: 468 average time/residue: 0.5411 time to fit residues: 424.9223 Evaluate side-chains 370 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 286 time to evaluate : 5.600 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 0 residues processed: 84 average time/residue: 0.3829 time to fit residues: 68.8503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 525 optimal weight: 10.0000 chunk 400 optimal weight: 4.9990 chunk 276 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 357 optimal weight: 0.0030 chunk 534 optimal weight: 0.9980 chunk 565 optimal weight: 20.0000 chunk 279 optimal weight: 0.8980 chunk 506 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 overall best weight: 1.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 254 HIS ** O 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 HIS ** H 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 44805 Z= 0.242 Angle : 0.687 11.948 60750 Z= 0.343 Chirality : 0.046 0.188 7545 Planarity : 0.006 0.062 7905 Dihedral : 5.652 22.550 6240 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 3.03 % Allowed : 12.78 % Favored : 84.19 % 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: -3.20 (0.10), residues: 5790 helix: -0.29 (0.14), residues: 1305 sheet: -1.88 (0.09), residues: 2625 loop : -3.62 (0.11), residues: 1860 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 354 time to evaluate : 5.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 148 outliers final: 80 residues processed: 483 average time/residue: 0.5362 time to fit residues: 433.4597 Evaluate side-chains 359 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 279 time to evaluate : 5.093 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 0.3785 time to fit residues: 65.8668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 470 optimal weight: 30.0000 chunk 320 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 421 optimal weight: 3.9990 chunk 233 optimal weight: 9.9990 chunk 482 optimal weight: 8.9990 chunk 390 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 288 optimal weight: 9.9990 chunk 507 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN A 379 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 ASN F 556 HIS F 560 ASN ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN ** L 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 374 GLN ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 472 ASN N 496 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4300 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: