Starting phenix.real_space_refine on Sun Mar 24 22:21:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wln_8860/03_2024/5wln_8860.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wln_8860/03_2024/5wln_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_8860/03_2024/5wln_8860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wln_8860/03_2024/5wln_8860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wln_8860/03_2024/5wln_8860.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wln_8860/03_2024/5wln_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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 21.35, 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: 13.59 Conformation dependent library (CDL) restraints added in 8.2 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: 4.91 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: 19.06 Time building geometry restraints manager: 15.11 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: 1.430 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: 9.620 Check model and map are aligned: 0.640 Set scattering table: 0.370 Process input model: 105.410 Find NCS groups from input model: 3.120 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:3.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.490 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 184 HIS 0.009 0.004 HIS K 556 PHE 0.015 0.003 PHE J 437 TYR 0.006 0.002 TYR A 584 ARG 0.007 0.001 ARG A 559 *********************** 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 : 5.172 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: G 271 MET cc_start: 0.7280 (mmm) cc_final: 0.6957 (mtm) REVERT: G 330 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6812 (tm-30) REVERT: G 355 MET cc_start: 0.5301 (tpt) cc_final: 0.5077 (tpt) REVERT: E 218 LEU cc_start: 0.8526 (tp) cc_final: 0.8296 (tp) REVERT: E 566 ARG cc_start: 0.7379 (tpt-90) cc_final: 0.6838 (mtt180) REVERT: F 271 MET cc_start: 0.7351 (mmm) cc_final: 0.6880 (mtm) REVERT: H 271 MET cc_start: 0.6982 (mmm) cc_final: 0.6684 (mtm) REVERT: I 181 ARG cc_start: 0.7297 (mtm110) cc_final: 0.7089 (mtm-85) REVERT: J 271 MET cc_start: 0.7112 (mmm) cc_final: 0.6806 (mtm) REVERT: J 511 ILE cc_start: 0.8673 (pp) cc_final: 0.8301 (mp) REVERT: K 511 ILE cc_start: 0.8522 (pp) cc_final: 0.8293 (mp) REVERT: L 271 MET cc_start: 0.7338 (mmm) cc_final: 0.6879 (mtt) REVERT: M 218 LEU cc_start: 0.8965 (tp) cc_final: 0.8645 (tt) REVERT: M 271 MET cc_start: 0.7292 (mmm) cc_final: 0.6943 (mtm) REVERT: M 355 MET cc_start: 0.5464 (tpt) cc_final: 0.5054 (tpt) REVERT: N 302 VAL cc_start: 0.9104 (t) cc_final: 0.8880 (m) outliers start: 15 outliers final: 15 residues processed: 812 average time/residue: 0.5786 time to fit residues: 749.1323 Evaluate side-chains 360 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 345 time to evaluate : 4.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain O residue 529 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain N residue 529 VAL 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: 2.9990 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: 1.4784 ------------------------------------------------------------------------------- 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 472 ASN ** 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: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2420 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= 0.230 Angle : 0.724 12.092 60750 Z= 0.366 Chirality : 0.048 0.201 7545 Planarity : 0.006 0.067 7905 Dihedral : 6.296 27.212 6255 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.65 % Favored : 91.09 % Rotamer: Outliers : 2.76 % Allowed : 10.22 % 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: -4.12 (0.09), residues: 5790 helix: -1.47 (0.13), residues: 1290 sheet: -2.35 (0.09), residues: 2715 loop : -3.97 (0.10), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 348 HIS 0.004 0.001 HIS D 556 PHE 0.021 0.002 PHE H 437 TYR 0.010 0.001 TYR J 175 ARG 0.007 0.000 ARG E 181 *********************** 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 580 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 445 time to evaluate : 5.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 271 MET cc_start: 0.7218 (mmm) cc_final: 0.6925 (mtm) REVERT: O 369 ILE cc_start: 0.8149 (mm) cc_final: 0.7905 (mt) REVERT: C 227 ARG cc_start: 0.6508 (ttm110) cc_final: 0.6053 (ttm170) REVERT: C 271 MET cc_start: 0.6096 (mtt) cc_final: 0.5750 (mtm) REVERT: D 328 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8392 (tp) REVERT: E 218 LEU cc_start: 0.8554 (tp) cc_final: 0.8294 (tp) REVERT: E 566 ARG cc_start: 0.7366 (tpt-90) cc_final: 0.6867 (mtt180) REVERT: F 271 MET cc_start: 0.7372 (mmm) cc_final: 0.6948 (mtm) REVERT: F 333 ILE cc_start: 0.9044 (mp) cc_final: 0.8802 (mt) REVERT: H 181 ARG cc_start: 0.7278 (mtm110) cc_final: 0.6976 (mtm-85) REVERT: H 271 MET cc_start: 0.6940 (mmm) cc_final: 0.6675 (mtm) REVERT: I 335 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7821 (tm-30) REVERT: J 271 MET cc_start: 0.7132 (mmm) cc_final: 0.6855 (mtm) REVERT: J 511 ILE cc_start: 0.8576 (pp) cc_final: 0.8260 (mp) REVERT: K 181 ARG cc_start: 0.7101 (mtm110) cc_final: 0.6775 (mtm-85) REVERT: K 328 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8184 (tp) REVERT: K 511 ILE cc_start: 0.8629 (pp) cc_final: 0.8385 (mp) REVERT: L 218 LEU cc_start: 0.9020 (tp) cc_final: 0.8766 (tt) REVERT: L 220 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8230 (pt) REVERT: L 271 MET cc_start: 0.7340 (mmm) cc_final: 0.6949 (mtm) REVERT: M 218 LEU cc_start: 0.9101 (tp) cc_final: 0.8783 (tt) REVERT: M 271 MET cc_start: 0.7304 (mmm) cc_final: 0.6952 (mtm) REVERT: N 214 ARG cc_start: 0.5519 (ttp80) cc_final: 0.4821 (mtt180) REVERT: N 302 VAL cc_start: 0.9183 (t) cc_final: 0.8973 (m) REVERT: N 308 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7425 (t0) REVERT: N 333 ILE cc_start: 0.8729 (mp) cc_final: 0.8515 (mt) REVERT: N 511 ILE cc_start: 0.8281 (pp) cc_final: 0.8007 (mp) outliers start: 135 outliers final: 72 residues processed: 554 average time/residue: 0.5611 time to fit residues: 507.5971 Evaluate side-chains 370 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 294 time to evaluate : 5.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 435 VAL Chi-restraints excluded: chain O residue 477 LEU Chi-restraints excluded: chain O residue 520 VAL Chi-restraints excluded: chain O residue 541 ASP Chi-restraints excluded: chain O residue 552 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 379 ASN Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 396 SER Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain L residue 390 ILE Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain M residue 241 THR Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 518 VAL Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 295 optimal weight: 0.7980 chunk 164 optimal weight: 9.9990 chunk 442 optimal weight: 8.9990 chunk 361 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 532 optimal weight: 3.9990 chunk 574 optimal weight: 1.9990 chunk 473 optimal weight: 5.9990 chunk 527 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 426 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 556 HIS ** A 326 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** ** F 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN ** F 483 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 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 472 ASN ** N 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 44805 Z= 0.258 Angle : 0.707 13.846 60750 Z= 0.354 Chirality : 0.047 0.187 7545 Planarity : 0.006 0.061 7905 Dihedral : 5.881 24.170 6254 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer: Outliers : 3.68 % Allowed : 11.53 % Favored : 84.79 % 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: -3.44 (0.10), residues: 5790 helix: -0.61 (0.14), residues: 1290 sheet: -2.06 (0.09), residues: 2715 loop : -3.59 (0.12), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 348 HIS 0.005 0.002 HIS D 556 PHE 0.018 0.002 PHE A 437 TYR 0.016 0.001 TYR E 584 ARG 0.009 0.001 ARG N 227 *********************** 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 538 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 358 time to evaluate : 5.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 271 MET cc_start: 0.7252 (mmm) cc_final: 0.7011 (mtm) REVERT: G 494 GLN cc_start: 0.7352 (mm-40) cc_final: 0.7068 (mm-40) REVERT: G 547 ARG cc_start: 0.8603 (mmm160) cc_final: 0.7779 (tpm170) REVERT: O 212 ASP cc_start: 0.6709 (m-30) cc_final: 0.6380 (m-30) REVERT: A 233 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.6142 (tm) REVERT: C 227 ARG cc_start: 0.6546 (ttm110) cc_final: 0.5889 (ttm170) REVERT: C 271 MET cc_start: 0.6365 (mtt) cc_final: 0.6092 (mtm) REVERT: D 328 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8463 (tp) REVERT: E 218 LEU cc_start: 0.8656 (tp) cc_final: 0.8372 (tp) REVERT: F 271 MET cc_start: 0.7441 (mmm) cc_final: 0.6950 (mtm) REVERT: F 333 ILE cc_start: 0.9010 (mp) cc_final: 0.8765 (mt) REVERT: H 271 MET cc_start: 0.7269 (mmm) cc_final: 0.6832 (mtp) REVERT: H 428 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7735 (tm-30) REVERT: I 459 LYS cc_start: 0.6943 (ttpt) cc_final: 0.6312 (ttpt) REVERT: J 333 ILE cc_start: 0.9037 (mp) cc_final: 0.8829 (mt) REVERT: K 328 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8178 (tp) REVERT: L 218 LEU cc_start: 0.8909 (tp) cc_final: 0.8629 (tt) REVERT: L 271 MET cc_start: 0.7400 (mmm) cc_final: 0.7029 (mtm) REVERT: M 218 LEU cc_start: 0.9111 (tp) cc_final: 0.8830 (tt) REVERT: M 271 MET cc_start: 0.7403 (mmm) cc_final: 0.6977 (mtm) REVERT: M 333 ILE cc_start: 0.8904 (mp) cc_final: 0.8683 (mt) REVERT: M 584 TYR cc_start: 0.8566 (t80) cc_final: 0.8230 (t80) REVERT: N 214 ARG cc_start: 0.5788 (ttp80) cc_final: 0.5026 (mtt180) REVERT: N 218 LEU cc_start: 0.8410 (tp) cc_final: 0.8193 (tp) outliers start: 180 outliers final: 111 residues processed: 512 average time/residue: 0.5303 time to fit residues: 455.6446 Evaluate side-chains 410 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 296 time to evaluate : 4.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 186 MET Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 541 ASP Chi-restraints excluded: chain G residue 554 ASP Chi-restraints excluded: chain O residue 215 THR Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 241 THR Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 455 THR Chi-restraints excluded: chain O residue 477 LEU Chi-restraints excluded: chain O residue 520 VAL Chi-restraints excluded: chain O residue 541 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 379 ASN Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 541 ASP Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 477 LEU Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 518 VAL Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 554 ASP Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 455 THR Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain J residue 554 ASP Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 507 ILE Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 554 ASP Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain L residue 455 THR Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 186 MET Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 455 THR Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain M residue 554 ASP Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 455 THR Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 541 ASP Chi-restraints excluded: chain N residue 554 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 525 optimal weight: 5.9990 chunk 400 optimal weight: 3.9990 chunk 276 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 253 optimal weight: 7.9990 chunk 357 optimal weight: 20.0000 chunk 534 optimal weight: 2.9990 chunk 565 optimal weight: 5.9990 chunk 279 optimal weight: 20.0000 chunk 506 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 HIS ** 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** 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 326 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 ** both conformations clash, **PLEASE CHECK MANUALLY** N 472 ASN ** N 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 44805 Z= 0.398 Angle : 0.776 13.717 60750 Z= 0.389 Chirality : 0.048 0.197 7545 Planarity : 0.006 0.057 7905 Dihedral : 6.165 31.503 6254 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer: Outliers : 5.21 % Allowed : 12.21 % Favored : 82.58 % 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: -3.42 (0.10), residues: 5790 helix: -0.39 (0.14), residues: 1305 sheet: -1.99 (0.09), residues: 2625 loop : -3.83 (0.11), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 348 HIS 0.009 0.003 HIS D 556 PHE 0.034 0.002 PHE K 437 TYR 0.009 0.002 TYR N 182 ARG 0.012 0.001 ARG A 227 *********************** 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 608 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 353 time to evaluate : 4.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 547 ARG cc_start: 0.8691 (mmm160) cc_final: 0.8047 (tpm170) REVERT: O 212 ASP cc_start: 0.6699 (m-30) cc_final: 0.6440 (m-30) REVERT: C 227 ARG cc_start: 0.6465 (ttm110) cc_final: 0.5867 (ttm170) REVERT: C 258 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7078 (mptt) REVERT: C 271 MET cc_start: 0.6633 (mtt) cc_final: 0.6331 (mtm) REVERT: C 547 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.8339 (tpp-160) REVERT: D 335 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7789 (tm-30) REVERT: E 214 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7033 (ptm160) REVERT: E 218 LEU cc_start: 0.8681 (tp) cc_final: 0.8405 (tp) REVERT: E 221 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6980 (tt) REVERT: E 511 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7953 (pt) REVERT: F 271 MET cc_start: 0.7411 (mmm) cc_final: 0.6968 (mtm) REVERT: H 271 MET cc_start: 0.7278 (mmm) cc_final: 0.7008 (mtp) REVERT: J 333 ILE cc_start: 0.9065 (mp) cc_final: 0.8800 (mt) REVERT: L 218 LEU cc_start: 0.9023 (tp) cc_final: 0.8759 (tt) REVERT: L 220 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7969 (pt) REVERT: L 271 MET cc_start: 0.7438 (mmm) cc_final: 0.7091 (mtm) REVERT: L 547 ARG cc_start: 0.8588 (mmm160) cc_final: 0.8086 (tpp-160) REVERT: M 218 LEU cc_start: 0.9125 (tp) cc_final: 0.8883 (tt) REVERT: M 271 MET cc_start: 0.7385 (mmm) cc_final: 0.7031 (mtm) REVERT: M 333 ILE cc_start: 0.8977 (mp) cc_final: 0.8697 (mt) REVERT: N 214 ARG cc_start: 0.6171 (ttp80) cc_final: 0.5634 (mtt180) REVERT: N 221 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7458 (tt) REVERT: N 333 ILE cc_start: 0.8922 (mp) cc_final: 0.8699 (mt) REVERT: N 494 GLN cc_start: 0.7201 (mm-40) cc_final: 0.6912 (mm-40) REVERT: N 495 ARG cc_start: 0.7422 (mmp80) cc_final: 0.7175 (ptt180) outliers start: 255 outliers final: 171 residues processed: 579 average time/residue: 0.5132 time to fit residues: 497.5279 Evaluate side-chains 471 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 294 time to evaluate : 5.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 186 MET Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 511 ILE Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 541 ASP Chi-restraints excluded: chain G residue 554 ASP Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 605 THR Chi-restraints excluded: chain O residue 215 THR Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 409 THR Chi-restraints excluded: chain O residue 435 VAL Chi-restraints excluded: chain O residue 455 THR Chi-restraints excluded: chain O residue 488 LEU Chi-restraints excluded: chain O residue 511 ILE Chi-restraints excluded: chain O residue 520 VAL Chi-restraints excluded: chain O residue 541 ASP Chi-restraints excluded: chain O residue 605 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 562 MET Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 379 ASN Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 511 ILE Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 541 ASP Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 554 ASP Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 605 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 409 THR Chi-restraints excluded: chain H residue 421 THR Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 477 LEU Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 605 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 421 THR Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 554 ASP Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 455 THR Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain J residue 554 ASP Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 605 THR Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 507 ILE Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 554 ASP Chi-restraints excluded: chain K residue 570 VAL Chi-restraints excluded: chain K residue 605 THR Chi-restraints excluded: chain L residue 186 MET Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 409 THR Chi-restraints excluded: chain L residue 455 THR Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 605 THR Chi-restraints excluded: chain M residue 186 MET Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 308 ASP Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 409 THR Chi-restraints excluded: chain M residue 455 THR Chi-restraints excluded: chain M residue 518 VAL Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain M residue 554 ASP Chi-restraints excluded: chain M residue 605 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 409 THR Chi-restraints excluded: chain N residue 455 THR Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 541 ASP Chi-restraints excluded: chain N residue 554 ASP Chi-restraints excluded: chain N residue 605 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 470 optimal weight: 20.0000 chunk 320 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 421 optimal weight: 0.6980 chunk 233 optimal weight: 1.9990 chunk 482 optimal weight: 4.9990 chunk 390 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 288 optimal weight: 8.9990 chunk 507 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 472 ASN ** O 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** D 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 494 GLN ** F 379 ASN ** 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 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN ** L 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 517 GLN ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 472 ASN ** N 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 44805 Z= 0.355 Angle : 0.750 12.821 60750 Z= 0.375 Chirality : 0.047 0.191 7545 Planarity : 0.006 0.059 7905 Dihedral : 6.023 28.685 6254 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 5.44 % Allowed : 13.68 % Favored : 80.88 % 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: -3.29 (0.10), residues: 5790 helix: -0.20 (0.14), residues: 1305 sheet: -1.90 (0.09), residues: 2580 loop : -3.84 (0.11), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 348 HIS 0.007 0.002 HIS E 556 PHE 0.022 0.002 PHE L 437 TYR 0.015 0.002 TYR B 175 ARG 0.015 0.001 ARG K 227 *********************** REFINEMENT MACRO_CYCLE 5 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 599 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 333 time to evaluate : 4.760 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: G 547 ARG cc_start: 0.8772 (mmm160) cc_final: 0.8130 (tpm170) REVERT: O 212 ASP cc_start: 0.6696 (m-30) cc_final: 0.6390 (m-30) REVERT: A 328 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8398 (tp) REVERT: B 218 LEU cc_start: 0.8725 (tp) cc_final: 0.8509 (tp) REVERT: B 488 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8606 (mp) REVERT: C 258 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7049 (mptt) REVERT: C 271 MET cc_start: 0.6912 (mtt) cc_final: 0.6602 (mtm) REVERT: C 547 ARG cc_start: 0.8721 (tpp-160) cc_final: 0.8336 (tpp-160) REVERT: E 214 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7141 (ptm160) REVERT: E 218 LEU cc_start: 0.8739 (tp) cc_final: 0.8464 (tp) REVERT: F 271 MET cc_start: 0.7402 (mmm) cc_final: 0.7021 (mtm) REVERT: F 488 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8512 (mp) REVERT: H 271 MET cc_start: 0.7132 (mmm) cc_final: 0.6904 (mtm) REVERT: K 480 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7467 (mp0) REVERT: K 488 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8350 (mp) REVERT: L 218 LEU cc_start: 0.9019 (tp) cc_final: 0.8811 (tt) REVERT: L 271 MET cc_start: 0.7379 (mmm) cc_final: 0.7049 (mtt) REVERT: M 218 LEU cc_start: 0.9132 (tp) cc_final: 0.8840 (tt) REVERT: M 271 MET cc_start: 0.7417 (mmm) cc_final: 0.7073 (mtm) REVERT: M 333 ILE cc_start: 0.9026 (mp) cc_final: 0.8703 (mt) REVERT: M 584 TYR cc_start: 0.8379 (t80) cc_final: 0.8145 (t80) REVERT: N 221 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7596 (tt) outliers start: 266 outliers final: 189 residues processed: 565 average time/residue: 0.5533 time to fit residues: 527.1084 Evaluate side-chains 492 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 296 time to evaluate : 4.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 186 MET Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 421 THR Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 541 ASP Chi-restraints excluded: chain G residue 554 ASP Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 605 THR Chi-restraints excluded: chain O residue 215 THR Chi-restraints excluded: chain O residue 237 LEU Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 409 THR Chi-restraints excluded: chain O residue 455 THR Chi-restraints excluded: chain O residue 484 GLU Chi-restraints excluded: chain O residue 488 LEU Chi-restraints excluded: chain O residue 520 VAL Chi-restraints excluded: chain O residue 541 ASP Chi-restraints excluded: chain O residue 552 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 541 ASP Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 605 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 605 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 339 ASP Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 409 THR Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 477 LEU Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 605 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 267 ILE Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 518 VAL Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 541 ASP Chi-restraints excluded: chain I residue 554 ASP Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 344 VAL Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 455 THR Chi-restraints excluded: chain J residue 477 LEU Chi-restraints excluded: chain J residue 484 GLU Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain J residue 554 ASP Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 605 THR Chi-restraints excluded: chain K residue 267 ILE Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 421 THR Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 484 GLU Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain K residue 507 ILE Chi-restraints excluded: chain K residue 511 ILE Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 541 ASP Chi-restraints excluded: chain K residue 554 ASP Chi-restraints excluded: chain K residue 570 VAL Chi-restraints excluded: chain K residue 605 THR Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 421 THR Chi-restraints excluded: chain L residue 455 THR Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 605 THR Chi-restraints excluded: chain M residue 186 MET Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 409 THR Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 518 VAL Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain M residue 554 ASP Chi-restraints excluded: chain M residue 605 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 409 THR Chi-restraints excluded: chain N residue 455 THR Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 541 ASP Chi-restraints excluded: chain N residue 554 ASP Chi-restraints excluded: chain N residue 605 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 190 optimal weight: 4.9990 chunk 509 optimal weight: 40.0000 chunk 111 optimal weight: 10.0000 chunk 331 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 566 optimal weight: 7.9990 chunk 469 optimal weight: 9.9990 chunk 262 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 297 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 556 HIS A 374 GLN ** 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 364 ASN ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 ASN ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 517 GLN ** 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 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 44805 Z= 0.375 Angle : 0.770 13.589 60750 Z= 0.384 Chirality : 0.047 0.191 7545 Planarity : 0.006 0.058 7905 Dihedral : 6.048 28.870 6254 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 5.32 % Allowed : 14.81 % Favored : 79.88 % 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: -3.30 (0.10), residues: 5790 helix: -0.16 (0.14), residues: 1305 sheet: -1.89 (0.09), residues: 2580 loop : -3.90 (0.11), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 348 HIS 0.007 0.003 HIS E 556 PHE 0.028 0.002 PHE N 437 TYR 0.011 0.002 TYR C 584 ARG 0.010 0.001 ARG F 227 *********************** REFINEMENT MACRO_CYCLE 6 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 592 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 332 time to evaluate : 5.408 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: G 547 ARG cc_start: 0.8771 (mmm160) cc_final: 0.8107 (tpm170) REVERT: O 212 ASP cc_start: 0.6809 (m-30) cc_final: 0.6523 (m-30) REVERT: A 328 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8351 (tp) REVERT: A 482 GLU cc_start: 0.7005 (tt0) cc_final: 0.6764 (mt-10) REVERT: B 488 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8607 (mp) REVERT: C 271 MET cc_start: 0.7009 (mtt) cc_final: 0.6582 (mtm) REVERT: C 547 ARG cc_start: 0.8694 (tpp-160) cc_final: 0.7515 (ttm170) REVERT: E 214 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7321 (ptm160) REVERT: E 218 LEU cc_start: 0.8850 (tp) cc_final: 0.8552 (tp) REVERT: F 214 ARG cc_start: 0.5806 (ttp80) cc_final: 0.4468 (mtt180) REVERT: F 271 MET cc_start: 0.7471 (mmm) cc_final: 0.7115 (mtm) REVERT: F 488 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8506 (mp) REVERT: K 333 ILE cc_start: 0.8968 (mp) cc_final: 0.8683 (mt) REVERT: K 488 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8538 (mp) REVERT: L 271 MET cc_start: 0.7303 (mmm) cc_final: 0.7084 (mtm) REVERT: M 218 LEU cc_start: 0.8972 (tp) cc_final: 0.8729 (tt) REVERT: M 271 MET cc_start: 0.7400 (mmm) cc_final: 0.7129 (mtm) REVERT: M 333 ILE cc_start: 0.9057 (mp) cc_final: 0.8709 (mt) REVERT: N 221 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7603 (tt) outliers start: 260 outliers final: 208 residues processed: 554 average time/residue: 0.5390 time to fit residues: 507.2834 Evaluate side-chains 522 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 308 time to evaluate : 4.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 186 MET Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 421 THR Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 541 ASP Chi-restraints excluded: chain G residue 554 ASP Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 605 THR Chi-restraints excluded: chain O residue 215 THR Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 390 ILE Chi-restraints excluded: chain O residue 455 THR Chi-restraints excluded: chain O residue 484 GLU Chi-restraints excluded: chain O residue 488 LEU Chi-restraints excluded: chain O residue 520 VAL Chi-restraints excluded: chain O residue 541 ASP Chi-restraints excluded: chain O residue 552 THR Chi-restraints excluded: chain O residue 605 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain C residue 175 TYR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 541 ASP Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 605 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 484 GLU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 554 ASP Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 605 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 339 ASP Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 373 LEU Chi-restraints excluded: chain H residue 409 THR Chi-restraints excluded: chain H residue 421 THR Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 477 LEU Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 605 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 267 ILE Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 421 THR Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 518 VAL Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 541 ASP Chi-restraints excluded: chain I residue 554 ASP Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 455 THR Chi-restraints excluded: chain J residue 477 LEU Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain J residue 554 ASP Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 605 THR Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 267 ILE Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 421 THR Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain K residue 507 ILE Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 541 ASP Chi-restraints excluded: chain K residue 554 ASP Chi-restraints excluded: chain K residue 570 VAL Chi-restraints excluded: chain K residue 605 THR Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 421 THR Chi-restraints excluded: chain L residue 455 THR Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 605 THR Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 369 ILE Chi-restraints excluded: chain M residue 409 THR Chi-restraints excluded: chain M residue 518 VAL Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain M residue 554 ASP Chi-restraints excluded: chain M residue 605 THR Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 409 THR Chi-restraints excluded: chain N residue 421 THR Chi-restraints excluded: chain N residue 455 THR Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 484 GLU Chi-restraints excluded: chain N residue 511 ILE Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 541 ASP Chi-restraints excluded: chain N residue 554 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 545 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 322 optimal weight: 7.9990 chunk 413 optimal weight: 2.9990 chunk 320 optimal weight: 1.9990 chunk 476 optimal weight: 10.0000 chunk 316 optimal weight: 8.9990 chunk 563 optimal weight: 9.9990 chunk 352 optimal weight: 20.0000 chunk 343 optimal weight: 2.9990 chunk 260 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 GLN ** F 379 ASN ** 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 374 GLN I 483 GLN ** J 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 517 GLN ** L 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 44805 Z= 0.318 Angle : 0.737 13.592 60750 Z= 0.366 Chirality : 0.047 0.186 7545 Planarity : 0.006 0.059 7905 Dihedral : 5.847 25.679 6254 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 5.24 % Allowed : 15.48 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.19 (0.10), residues: 5790 helix: -0.06 (0.14), residues: 1305 sheet: -1.80 (0.09), residues: 2580 loop : -3.89 (0.11), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 348 HIS 0.005 0.002 HIS E 556 PHE 0.023 0.002 PHE N 437 TYR 0.024 0.002 TYR M 584 ARG 0.009 0.000 ARG H 547 *********************** REFINEMENT MACRO_CYCLE 7 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 582 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 326 time to evaluate : 5.019 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: O 212 ASP cc_start: 0.6876 (m-30) cc_final: 0.6587 (m-30) REVERT: B 488 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8592 (mp) REVERT: C 181 ARG cc_start: 0.7410 (mtp-110) cc_final: 0.7172 (mtm-85) REVERT: C 258 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7380 (mptt) REVERT: C 271 MET cc_start: 0.7024 (mtt) cc_final: 0.6565 (mtm) REVERT: C 547 ARG cc_start: 0.8588 (tpp-160) cc_final: 0.7568 (ttm170) REVERT: D 328 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8297 (tp) REVERT: E 214 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7439 (ptm160) REVERT: E 218 LEU cc_start: 0.8854 (tp) cc_final: 0.8567 (tp) REVERT: E 258 LYS cc_start: 0.7812 (mmtt) cc_final: 0.7430 (mmtt) REVERT: F 214 ARG cc_start: 0.5963 (ttp80) cc_final: 0.4620 (mtt180) REVERT: F 241 THR cc_start: 0.6123 (OUTLIER) cc_final: 0.5814 (p) REVERT: F 271 MET cc_start: 0.7449 (mmm) cc_final: 0.7099 (mtm) REVERT: F 488 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8517 (mp) REVERT: F 494 GLN cc_start: 0.7307 (mm-40) cc_final: 0.6994 (mm-40) REVERT: H 547 ARG cc_start: 0.8699 (mmm160) cc_final: 0.8012 (tpm170) REVERT: I 227 ARG cc_start: 0.6442 (mmp80) cc_final: 0.6202 (mmp80) REVERT: K 328 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8056 (tp) REVERT: K 488 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8537 (mp) REVERT: L 271 MET cc_start: 0.7287 (mmm) cc_final: 0.7079 (mtm) REVERT: M 218 LEU cc_start: 0.8992 (tp) cc_final: 0.8766 (tt) REVERT: M 271 MET cc_start: 0.7325 (mmm) cc_final: 0.7073 (mtm) REVERT: M 333 ILE cc_start: 0.9047 (mp) cc_final: 0.8723 (mt) REVERT: N 221 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7550 (tt) REVERT: N 330 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6875 (pp20) outliers start: 256 outliers final: 206 residues processed: 542 average time/residue: 0.5116 time to fit residues: 468.7986 Evaluate side-chains 520 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 304 time to evaluate : 4.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 186 MET Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 421 THR Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 541 ASP Chi-restraints excluded: chain G residue 554 ASP Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 605 THR Chi-restraints excluded: chain O residue 175 TYR Chi-restraints excluded: chain O residue 215 THR Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 390 ILE Chi-restraints excluded: chain O residue 409 THR Chi-restraints excluded: chain O residue 455 THR Chi-restraints excluded: chain O residue 484 GLU Chi-restraints excluded: chain O residue 488 LEU Chi-restraints excluded: chain O residue 520 VAL Chi-restraints excluded: chain O residue 541 ASP Chi-restraints excluded: chain O residue 552 THR Chi-restraints excluded: chain O residue 605 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain C residue 175 TYR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 541 ASP Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 605 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 484 GLU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 605 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 409 THR Chi-restraints excluded: chain H residue 421 THR Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 477 LEU Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 605 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 267 ILE Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 330 GLU Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 421 THR Chi-restraints excluded: chain I residue 429 ILE Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 554 ASP Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 455 THR Chi-restraints excluded: chain J residue 477 LEU Chi-restraints excluded: chain J residue 484 GLU Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain J residue 554 ASP Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 605 THR Chi-restraints excluded: chain K residue 175 TYR Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 267 ILE Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 421 THR Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain K residue 507 ILE Chi-restraints excluded: chain K residue 511 ILE Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 541 ASP Chi-restraints excluded: chain K residue 554 ASP Chi-restraints excluded: chain K residue 570 VAL Chi-restraints excluded: chain K residue 605 THR Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 421 THR Chi-restraints excluded: chain L residue 455 THR Chi-restraints excluded: chain L residue 484 GLU Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 605 THR Chi-restraints excluded: chain M residue 186 MET Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 344 VAL Chi-restraints excluded: chain M residue 369 ILE Chi-restraints excluded: chain M residue 373 LEU Chi-restraints excluded: chain M residue 409 THR Chi-restraints excluded: chain M residue 421 THR Chi-restraints excluded: chain M residue 473 ASP Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 518 VAL Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain M residue 554 ASP Chi-restraints excluded: chain M residue 605 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 330 GLU Chi-restraints excluded: chain N residue 409 THR Chi-restraints excluded: chain N residue 421 THR Chi-restraints excluded: chain N residue 455 THR Chi-restraints excluded: chain N residue 484 GLU Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 541 ASP Chi-restraints excluded: chain N residue 554 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 348 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 336 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 358 optimal weight: 0.0870 chunk 384 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 443 optimal weight: 9.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- 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 ** O 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 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 364 ASN ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 44805 Z= 0.252 Angle : 0.705 12.598 60750 Z= 0.348 Chirality : 0.046 0.205 7545 Planarity : 0.006 0.059 7905 Dihedral : 5.567 24.886 6254 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 4.56 % Allowed : 16.44 % Favored : 79.00 % 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: -3.04 (0.10), residues: 5790 helix: 0.08 (0.14), residues: 1305 sheet: -1.79 (0.09), residues: 2685 loop : -3.75 (0.11), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 348 HIS 0.004 0.001 HIS O 556 PHE 0.041 0.002 PHE E 437 TYR 0.017 0.001 TYR M 584 ARG 0.009 0.000 ARG H 547 *********************** REFINEMENT MACRO_CYCLE 8 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 555 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 332 time to evaluate : 5.107 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: O 212 ASP cc_start: 0.6827 (m-30) cc_final: 0.6546 (m-30) REVERT: A 482 GLU cc_start: 0.6941 (tt0) cc_final: 0.6679 (mt-10) REVERT: B 488 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8661 (mp) REVERT: C 181 ARG cc_start: 0.7340 (mtp-110) cc_final: 0.7122 (mtm-85) REVERT: C 258 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7389 (mptt) REVERT: C 271 MET cc_start: 0.7091 (mtt) cc_final: 0.6740 (mtm) REVERT: C 547 ARG cc_start: 0.8585 (tpp-160) cc_final: 0.7585 (ttm170) REVERT: D 328 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8340 (tp) REVERT: E 218 LEU cc_start: 0.8862 (tp) cc_final: 0.8567 (tp) REVERT: E 258 LYS cc_start: 0.7890 (mmtt) cc_final: 0.7661 (mmtt) REVERT: F 214 ARG cc_start: 0.5892 (ttp80) cc_final: 0.4512 (mtt180) REVERT: F 241 THR cc_start: 0.6115 (OUTLIER) cc_final: 0.5824 (p) REVERT: F 271 MET cc_start: 0.7456 (mmm) cc_final: 0.7132 (mtm) REVERT: F 488 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8565 (mp) REVERT: J 547 ARG cc_start: 0.8406 (mmm160) cc_final: 0.7916 (tpp-160) REVERT: K 328 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8075 (tp) REVERT: K 488 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8505 (mp) REVERT: M 218 LEU cc_start: 0.8894 (tp) cc_final: 0.8655 (tt) REVERT: M 271 MET cc_start: 0.7298 (mmm) cc_final: 0.7065 (mtm) REVERT: N 221 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7628 (tt) outliers start: 223 outliers final: 172 residues processed: 519 average time/residue: 0.4764 time to fit residues: 420.2324 Evaluate side-chains 489 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 309 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 421 THR Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 541 ASP Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 605 THR Chi-restraints excluded: chain O residue 175 TYR Chi-restraints excluded: chain O residue 215 THR Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 390 ILE Chi-restraints excluded: chain O residue 409 THR Chi-restraints excluded: chain O residue 455 THR Chi-restraints excluded: chain O residue 520 VAL Chi-restraints excluded: chain O residue 541 ASP Chi-restraints excluded: chain O residue 552 THR Chi-restraints excluded: chain O residue 605 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 175 TYR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 541 ASP Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 484 GLU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 554 ASP Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 421 THR Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 477 LEU Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 267 ILE Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 421 THR Chi-restraints excluded: chain I residue 429 ILE Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 518 VAL Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 477 LEU Chi-restraints excluded: chain J residue 484 GLU Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain K residue 175 TYR Chi-restraints excluded: chain K residue 267 ILE Chi-restraints excluded: chain K residue 308 ASP Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 421 THR Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain K residue 507 ILE Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 570 VAL Chi-restraints excluded: chain K residue 605 THR Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 421 THR Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain L residue 605 THR Chi-restraints excluded: chain M residue 186 MET Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 369 ILE Chi-restraints excluded: chain M residue 409 THR Chi-restraints excluded: chain M residue 421 THR Chi-restraints excluded: chain M residue 473 ASP Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 518 VAL Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain M residue 605 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 409 THR Chi-restraints excluded: chain N residue 421 THR Chi-restraints excluded: chain N residue 455 THR Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 541 ASP Chi-restraints excluded: chain N residue 605 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 512 optimal weight: 1.9990 chunk 540 optimal weight: 8.9990 chunk 492 optimal weight: 4.9990 chunk 525 optimal weight: 8.9990 chunk 316 optimal weight: 0.0570 chunk 228 optimal weight: 6.9990 chunk 412 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 474 optimal weight: 4.9990 chunk 496 optimal weight: 4.9990 chunk 523 optimal weight: 0.9980 overall best weight: 2.6104 ------------------------------------------------------------------------------- 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** ** O 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 364 ASN ** N 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 44805 Z= 0.279 Angle : 0.716 12.060 60750 Z= 0.353 Chirality : 0.046 0.180 7545 Planarity : 0.006 0.058 7905 Dihedral : 5.557 24.645 6254 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 4.68 % Allowed : 16.38 % Favored : 78.94 % 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: -2.98 (0.10), residues: 5790 helix: 0.13 (0.14), residues: 1305 sheet: -1.75 (0.09), residues: 2685 loop : -3.74 (0.11), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 348 HIS 0.005 0.002 HIS E 556 PHE 0.028 0.002 PHE E 437 TYR 0.014 0.001 TYR H 175 ARG 0.006 0.000 ARG H 547 *********************** REFINEMENT MACRO_CYCLE 9 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 545 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 316 time to evaluate : 4.912 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: O 212 ASP cc_start: 0.6918 (m-30) cc_final: 0.6603 (m-30) REVERT: O 227 ARG cc_start: 0.6571 (mmp80) cc_final: 0.5983 (mmp80) REVERT: A 362 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.6714 (t80) REVERT: B 488 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8686 (mp) REVERT: C 258 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7397 (mptt) REVERT: C 547 ARG cc_start: 0.8576 (tpp-160) cc_final: 0.7681 (ttm170) REVERT: D 227 ARG cc_start: 0.6747 (mmp80) cc_final: 0.6157 (mmp80) REVERT: D 328 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8338 (tp) REVERT: E 218 LEU cc_start: 0.8838 (tp) cc_final: 0.8529 (tp) REVERT: E 230 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7135 (pp) REVERT: F 214 ARG cc_start: 0.5979 (ttp80) cc_final: 0.4532 (mtt180) REVERT: F 227 ARG cc_start: 0.6320 (mmp80) cc_final: 0.5952 (mmm160) REVERT: F 241 THR cc_start: 0.6085 (OUTLIER) cc_final: 0.5800 (p) REVERT: F 271 MET cc_start: 0.7475 (mmm) cc_final: 0.7157 (mtm) REVERT: F 488 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8605 (mp) REVERT: F 494 GLN cc_start: 0.7256 (mm-40) cc_final: 0.6984 (mm-40) REVERT: F 495 ARG cc_start: 0.7483 (mmp80) cc_final: 0.7131 (ptt180) REVERT: J 271 MET cc_start: 0.7042 (mtm) cc_final: 0.6627 (mtm) REVERT: J 547 ARG cc_start: 0.8263 (mmm160) cc_final: 0.7831 (tpp-160) REVERT: K 271 MET cc_start: 0.6940 (mtm) cc_final: 0.6476 (mtm) REVERT: K 328 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8045 (tp) REVERT: K 488 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8558 (mp) REVERT: M 218 LEU cc_start: 0.8894 (tp) cc_final: 0.8666 (tt) REVERT: M 271 MET cc_start: 0.7295 (mmm) cc_final: 0.7088 (mtm) REVERT: N 221 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7470 (tt) outliers start: 229 outliers final: 192 residues processed: 511 average time/residue: 0.4827 time to fit residues: 420.6644 Evaluate side-chains 502 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 300 time to evaluate : 5.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 421 THR Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 541 ASP Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 605 THR Chi-restraints excluded: chain O residue 175 TYR Chi-restraints excluded: chain O residue 215 THR Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 390 ILE Chi-restraints excluded: chain O residue 409 THR Chi-restraints excluded: chain O residue 455 THR Chi-restraints excluded: chain O residue 520 VAL Chi-restraints excluded: chain O residue 541 ASP Chi-restraints excluded: chain O residue 552 THR Chi-restraints excluded: chain O residue 605 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 549 PHE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain C residue 175 TYR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 541 ASP Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 605 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 484 GLU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 605 THR Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 421 THR Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 477 LEU Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain H residue 605 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 267 ILE Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 421 THR Chi-restraints excluded: chain I residue 429 ILE Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 518 VAL Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 477 LEU Chi-restraints excluded: chain J residue 484 GLU Chi-restraints excluded: chain J residue 488 LEU Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain J residue 554 ASP Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 605 THR Chi-restraints excluded: chain K residue 175 TYR Chi-restraints excluded: chain K residue 267 ILE Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 334 VAL Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 421 THR Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain K residue 507 ILE Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 570 VAL Chi-restraints excluded: chain K residue 605 THR Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 421 THR Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 605 THR Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 369 ILE Chi-restraints excluded: chain M residue 421 THR Chi-restraints excluded: chain M residue 473 ASP Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 518 VAL Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain M residue 554 ASP Chi-restraints excluded: chain M residue 605 THR Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 421 THR Chi-restraints excluded: chain N residue 455 THR Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 541 ASP Chi-restraints excluded: chain N residue 554 ASP Chi-restraints excluded: chain N residue 605 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 345 optimal weight: 9.9990 chunk 555 optimal weight: 9.9990 chunk 339 optimal weight: 3.9990 chunk 263 optimal weight: 0.9990 chunk 386 optimal weight: 2.9990 chunk 582 optimal weight: 6.9990 chunk 536 optimal weight: 0.0470 chunk 464 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 358 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- 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** ** O 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 483 GLN ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 364 ASN ** N 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 44805 Z= 0.264 Angle : 0.706 11.835 60750 Z= 0.346 Chirality : 0.046 0.178 7545 Planarity : 0.006 0.059 7905 Dihedral : 5.459 24.109 6254 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 4.31 % Allowed : 16.65 % Favored : 79.04 % 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: -2.90 (0.10), residues: 5790 helix: 0.20 (0.14), residues: 1305 sheet: -1.69 (0.09), residues: 2685 loop : -3.71 (0.11), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 348 HIS 0.005 0.002 HIS M 556 PHE 0.027 0.002 PHE E 437 TYR 0.015 0.001 TYR H 175 ARG 0.008 0.000 ARG C 181 ********************** REFINEMENT MACRO_CYCLE 10 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 518 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 307 time to evaluate : 4.907 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: O 212 ASP cc_start: 0.6919 (m-30) cc_final: 0.6661 (m-30) REVERT: O 227 ARG cc_start: 0.6980 (mmp80) cc_final: 0.6341 (mmp80) REVERT: A 362 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6751 (t80) REVERT: B 488 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8680 (mp) REVERT: C 181 ARG cc_start: 0.7345 (mtp-110) cc_final: 0.7127 (mtm-85) REVERT: C 258 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7399 (mptt) REVERT: C 547 ARG cc_start: 0.8558 (tpp-160) cc_final: 0.7690 (ttm170) REVERT: D 328 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8467 (tp) REVERT: E 214 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7519 (ptm160) REVERT: E 218 LEU cc_start: 0.8845 (tp) cc_final: 0.8539 (tp) REVERT: E 230 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7150 (pp) REVERT: F 214 ARG cc_start: 0.5994 (ttp80) cc_final: 0.4502 (mtt180) REVERT: F 227 ARG cc_start: 0.6452 (mmp80) cc_final: 0.5897 (mmm160) REVERT: F 241 THR cc_start: 0.6188 (OUTLIER) cc_final: 0.5927 (p) REVERT: F 271 MET cc_start: 0.7478 (mmm) cc_final: 0.7162 (mtm) REVERT: F 488 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8612 (mp) REVERT: J 271 MET cc_start: 0.7044 (mtm) cc_final: 0.6733 (mtm) REVERT: J 547 ARG cc_start: 0.8200 (mmm160) cc_final: 0.7869 (tpp-160) REVERT: K 271 MET cc_start: 0.6991 (mtm) cc_final: 0.6081 (mtm) REVERT: K 328 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8030 (tp) REVERT: K 488 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8571 (mp) REVERT: M 218 LEU cc_start: 0.8878 (tp) cc_final: 0.8658 (tt) REVERT: M 271 MET cc_start: 0.7341 (mmm) cc_final: 0.7115 (mtm) REVERT: N 330 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6687 (pp20) REVERT: N 362 PHE cc_start: 0.7131 (m-80) cc_final: 0.6889 (m-80) outliers start: 211 outliers final: 186 residues processed: 488 average time/residue: 0.5173 time to fit residues: 428.2402 Evaluate side-chains 496 residues out of total 4890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 299 time to evaluate : 4.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 344 VAL Chi-restraints excluded: chain G residue 421 THR Chi-restraints excluded: chain G residue 477 LEU Chi-restraints excluded: chain G residue 484 GLU Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain G residue 520 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain G residue 541 ASP Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 605 THR Chi-restraints excluded: chain O residue 175 TYR Chi-restraints excluded: chain O residue 267 ILE Chi-restraints excluded: chain O residue 344 VAL Chi-restraints excluded: chain O residue 390 ILE Chi-restraints excluded: chain O residue 409 THR Chi-restraints excluded: chain O residue 455 THR Chi-restraints excluded: chain O residue 520 VAL Chi-restraints excluded: chain O residue 541 ASP Chi-restraints excluded: chain O residue 552 THR Chi-restraints excluded: chain O residue 605 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 541 ASP Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 541 ASP Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain E residue 186 MET Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain E residue 541 ASP Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 605 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 484 GLU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 520 VAL Chi-restraints excluded: chain F residue 529 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 605 THR Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 421 THR Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 477 LEU Chi-restraints excluded: chain H residue 484 GLU Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain H residue 520 VAL Chi-restraints excluded: chain H residue 529 VAL Chi-restraints excluded: chain H residue 605 THR Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 267 ILE Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 421 THR Chi-restraints excluded: chain I residue 429 ILE Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 484 GLU Chi-restraints excluded: chain I residue 518 VAL Chi-restraints excluded: chain I residue 520 VAL Chi-restraints excluded: chain I residue 529 VAL Chi-restraints excluded: chain I residue 605 THR Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 477 LEU Chi-restraints excluded: chain J residue 484 GLU Chi-restraints excluded: chain J residue 488 LEU Chi-restraints excluded: chain J residue 511 ILE Chi-restraints excluded: chain J residue 520 VAL Chi-restraints excluded: chain J residue 529 VAL Chi-restraints excluded: chain J residue 554 ASP Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 605 THR Chi-restraints excluded: chain K residue 175 TYR Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 267 ILE Chi-restraints excluded: chain K residue 328 LEU Chi-restraints excluded: chain K residue 344 VAL Chi-restraints excluded: chain K residue 421 THR Chi-restraints excluded: chain K residue 477 LEU Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain K residue 507 ILE Chi-restraints excluded: chain K residue 520 VAL Chi-restraints excluded: chain K residue 529 VAL Chi-restraints excluded: chain K residue 554 ASP Chi-restraints excluded: chain K residue 570 VAL Chi-restraints excluded: chain K residue 605 THR Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 241 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 421 THR Chi-restraints excluded: chain L residue 520 VAL Chi-restraints excluded: chain L residue 529 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 605 THR Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 340 ILE Chi-restraints excluded: chain M residue 369 ILE Chi-restraints excluded: chain M residue 421 THR Chi-restraints excluded: chain M residue 473 ASP Chi-restraints excluded: chain M residue 484 GLU Chi-restraints excluded: chain M residue 518 VAL Chi-restraints excluded: chain M residue 520 VAL Chi-restraints excluded: chain M residue 529 VAL Chi-restraints excluded: chain M residue 554 ASP Chi-restraints excluded: chain M residue 605 THR Chi-restraints excluded: chain N residue 308 ASP Chi-restraints excluded: chain N residue 330 GLU Chi-restraints excluded: chain N residue 421 THR Chi-restraints excluded: chain N residue 455 THR Chi-restraints excluded: chain N residue 456 VAL Chi-restraints excluded: chain N residue 518 VAL Chi-restraints excluded: chain N residue 520 VAL Chi-restraints excluded: chain N residue 529 VAL Chi-restraints excluded: chain N residue 541 ASP Chi-restraints excluded: chain N residue 554 ASP Chi-restraints excluded: chain N residue 605 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 368 optimal weight: 5.9990 chunk 494 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 427 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 464 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 477 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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** ** O 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** 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** D 472 ASN ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 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 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.164217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.101537 restraints weight = 55833.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.105280 restraints weight = 29940.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.107482 restraints weight = 21648.975| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 44805 Z= 0.348 Angle : 0.749 11.951 60750 Z= 0.369 Chirality : 0.047 0.183 7545 Planarity : 0.006 0.058 7905 Dihedral : 5.713 27.432 6254 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.47 % Favored : 87.53 % Rotamer: Outliers : 4.66 % Allowed : 16.42 % Favored : 78.92 % 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: -2.98 (0.10), residues: 5790 helix: 0.11 (0.14), residues: 1305 sheet: -1.66 (0.09), residues: 2595 loop : -3.80 (0.11), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 348 HIS 0.007 0.002 HIS E 556 PHE 0.029 0.002 PHE E 437 TYR 0.015 0.002 TYR C 584 ARG 0.008 0.000 ARG N 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9102.59 seconds wall clock time: 165 minutes 21.80 seconds (9921.80 seconds total)