Starting phenix.real_space_refine on Sun Mar 10 17:39:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5i_0140/03_2024/6h5i_0140.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5i_0140/03_2024/6h5i_0140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5i_0140/03_2024/6h5i_0140.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5i_0140/03_2024/6h5i_0140.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5i_0140/03_2024/6h5i_0140.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5i_0140/03_2024/6h5i_0140.pdb" } resolution = 3.9 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9997 atoms to isotropic. 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 196 5.16 5 C 27672 2.51 5 N 7632 2.21 5 O 8400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Ab PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ab TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac ARG 9": "NH1" <-> "NH2" Residue "Ak ARG 22": "NH1" <-> "NH2" Residue "Av ARG 63": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43900 Number of models: 1 Model: "" Number of chains: 26 Chain: "Aa" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ab" Number of atoms: 4993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 4993 Classifications: {'peptide': 632} Link IDs: {'PTRANS': 25, 'TRANS': 606} Chain breaks: 2 Chain: "Ac" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ad" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ae" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Af" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ag" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ah" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ai" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Aj" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ak" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Al" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Am" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "An" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ao" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ap" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Aq" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5004 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 25, 'TRANS': 607} Chain breaks: 1 Chain: "Ar" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "As" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "At" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1404 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "Au" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Av" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Aw" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ax" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ay" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Az" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Time building chain proxies: 16.24, per 1000 atoms: 0.37 Number of scatterers: 43900 At special positions: 0 Unit cell: (163.59, 198.17, 199.5, 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 196 16.00 O 8400 8.00 N 7632 7.00 C 27672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYSAb 353 " - pdb=" SG CYSAb 363 " distance=2.02 Simple disulfide: pdb=" SG CYSAq 353 " - pdb=" SG CYSAq 363 " distance=2.03 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: 12.41 Conformation dependent library (CDL) restraints added in 6.0 seconds 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10284 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 8 sheets defined 68.2% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'Aa' and resid 13 through 39 Processing helix chain 'Aa' and resid 48 through 76 removed outlier: 3.603A pdb=" N ALAAa 52 " --> pdb=" O LEUAa 48 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARGAa 76 " --> pdb=" O LEUAa 72 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 96 through 124 removed outlier: 3.705A pdb=" N LYSAa 124 " --> pdb=" O LEUAa 120 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 126 through 137 removed outlier: 3.546A pdb=" N TYRAa 137 " --> pdb=" O ILEAa 133 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 137 through 159 removed outlier: 3.912A pdb=" N GLYAa 159 " --> pdb=" O LEUAa 155 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 163 through 174 removed outlier: 3.969A pdb=" N GLUAa 167 " --> pdb=" O SERAa 163 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 123 through 136 Processing helix chain 'Ab' and resid 140 through 148 removed outlier: 4.119A pdb=" N ILEAb 144 " --> pdb=" O PHEAb 140 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 159 through 175 removed outlier: 3.576A pdb=" N GLUAb 163 " --> pdb=" O SERAb 159 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 239 through 244 Processing helix chain 'Ab' and resid 263 through 274 removed outlier: 3.728A pdb=" N LYSAb 267 " --> pdb=" O THRAb 263 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEUAb 274 " --> pdb=" O ASNAb 270 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 339 through 347 Processing helix chain 'Ab' and resid 421 through 439 Processing helix chain 'Ab' and resid 460 through 469 removed outlier: 3.890A pdb=" N GLYAb 469 " --> pdb=" O GLUAb 465 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 502 through 511 removed outlier: 3.569A pdb=" N GLNAb 511 " --> pdb=" O GLUAb 507 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 541 through 547 Processing helix chain 'Ab' and resid 572 through 580 removed outlier: 3.535A pdb=" N ILEAb 580 " --> pdb=" O LEUAb 576 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 582 through 604 removed outlier: 3.847A pdb=" N ASPAb 604 " --> pdb=" O LYSAb 600 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 612 through 627 removed outlier: 3.853A pdb=" N SERAb 616 " --> pdb=" O GLUAb 612 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 628 through 634 Processing helix chain 'Ab' and resid 639 through 661 Processing helix chain 'Ab' and resid 670 through 680 Processing helix chain 'Ab' and resid 681 through 686 Processing helix chain 'Ab' and resid 708 through 718 Processing helix chain 'Ab' and resid 727 through 751 removed outlier: 3.783A pdb=" N SERAb 750 " --> pdb=" O ALAAb 746 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLYAb 751 " --> pdb=" O ASNAb 747 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 13 through 41 removed outlier: 3.594A pdb=" N GLUAc 17 " --> pdb=" O HISAc 13 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHEAc 41 " --> pdb=" O METAc 37 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 48 through 77 removed outlier: 3.669A pdb=" N ALAAc 52 " --> pdb=" O LEUAc 48 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 95 through 124 removed outlier: 3.990A pdb=" N ALAAc 99 " --> pdb=" O SERAc 95 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 126 through 137 Processing helix chain 'Ac' and resid 137 through 159 Processing helix chain 'Ac' and resid 163 through 173 removed outlier: 3.814A pdb=" N GLUAc 167 " --> pdb=" O SERAc 163 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 13 through 39 Processing helix chain 'Ad' and resid 48 through 76 removed outlier: 3.691A pdb=" N ALAAd 52 " --> pdb=" O LEUAd 48 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 96 through 124 Processing helix chain 'Ad' and resid 126 through 137 Processing helix chain 'Ad' and resid 137 through 158 Processing helix chain 'Ad' and resid 163 through 173 removed outlier: 4.004A pdb=" N GLUAd 167 " --> pdb=" O SERAd 163 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 13 through 39 removed outlier: 3.713A pdb=" N GLUAe 17 " --> pdb=" O HISAe 13 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 48 through 77 removed outlier: 3.534A pdb=" N ALAAe 52 " --> pdb=" O LEUAe 48 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 95 through 123 Processing helix chain 'Ae' and resid 126 through 137 removed outlier: 3.629A pdb=" N TYRAe 137 " --> pdb=" O ILEAe 133 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 137 through 159 removed outlier: 3.527A pdb=" N GLYAe 159 " --> pdb=" O LEUAe 155 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 163 through 174 removed outlier: 3.835A pdb=" N GLUAe 167 " --> pdb=" O SERAe 163 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THRAe 174 " --> pdb=" O PHEAe 170 " (cutoff:3.500A) Processing helix chain 'Af' and resid 13 through 39 removed outlier: 3.580A pdb=" N GLUAf 17 " --> pdb=" O HISAf 13 " (cutoff:3.500A) Processing helix chain 'Af' and resid 48 through 76 removed outlier: 3.521A pdb=" N ALAAf 52 " --> pdb=" O LEUAf 48 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARGAf 76 " --> pdb=" O LEUAf 72 " (cutoff:3.500A) Processing helix chain 'Af' and resid 96 through 123 removed outlier: 3.776A pdb=" N METAf 100 " --> pdb=" O GLYAf 96 " (cutoff:3.500A) Processing helix chain 'Af' and resid 126 through 137 removed outlier: 3.792A pdb=" N CYSAf 130 " --> pdb=" O ASPAf 126 " (cutoff:3.500A) Processing helix chain 'Af' and resid 137 through 159 Processing helix chain 'Af' and resid 163 through 175 removed outlier: 3.862A pdb=" N GLUAf 167 " --> pdb=" O SERAf 163 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THRAf 174 " --> pdb=" O PHEAf 170 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEUAf 175 " --> pdb=" O ASPAf 171 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 13 through 41 removed outlier: 3.718A pdb=" N PHEAg 41 " --> pdb=" O METAg 37 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 48 through 76 removed outlier: 3.622A pdb=" N ALAAg 52 " --> pdb=" O LEUAg 48 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARGAg 76 " --> pdb=" O LEUAg 72 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 96 through 124 removed outlier: 3.798A pdb=" N METAg 100 " --> pdb=" O GLYAg 96 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 126 through 137 removed outlier: 3.545A pdb=" N TYRAg 137 " --> pdb=" O ILEAg 133 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 137 through 158 Processing helix chain 'Ag' and resid 163 through 174 removed outlier: 3.963A pdb=" N GLUAg 167 " --> pdb=" O SERAg 163 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 13 through 39 removed outlier: 3.522A pdb=" N GLUAh 17 " --> pdb=" O HISAh 13 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 48 through 76 Processing helix chain 'Ah' and resid 96 through 124 removed outlier: 3.545A pdb=" N LYSAh 124 " --> pdb=" O LEUAh 120 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 126 through 137 removed outlier: 3.572A pdb=" N CYSAh 130 " --> pdb=" O ASPAh 126 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYRAh 137 " --> pdb=" O ILEAh 133 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 137 through 159 removed outlier: 3.515A pdb=" N GLYAh 159 " --> pdb=" O LEUAh 155 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 163 through 174 removed outlier: 3.857A pdb=" N GLUAh 167 " --> pdb=" O SERAh 163 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THRAh 174 " --> pdb=" O PHEAh 170 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 13 through 41 removed outlier: 3.568A pdb=" N PHEAi 41 " --> pdb=" O METAi 37 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 48 through 76 removed outlier: 3.510A pdb=" N ALAAi 52 " --> pdb=" O LEUAi 48 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARGAi 76 " --> pdb=" O LEUAi 72 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 95 through 123 Processing helix chain 'Ai' and resid 126 through 137 removed outlier: 3.506A pdb=" N TYRAi 137 " --> pdb=" O ILEAi 133 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 137 through 159 Processing helix chain 'Ai' and resid 163 through 174 removed outlier: 3.727A pdb=" N GLUAi 167 " --> pdb=" O SERAi 163 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 13 through 39 removed outlier: 3.634A pdb=" N GLUAj 17 " --> pdb=" O HISAj 13 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 48 through 76 removed outlier: 3.547A pdb=" N ALAAj 52 " --> pdb=" O LEUAj 48 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARGAj 76 " --> pdb=" O LEUAj 72 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 95 through 124 removed outlier: 3.707A pdb=" N ALAAj 99 " --> pdb=" O SERAj 95 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 126 through 137 removed outlier: 3.538A pdb=" N TYRAj 137 " --> pdb=" O ILEAj 133 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 137 through 159 removed outlier: 3.758A pdb=" N GLYAj 159 " --> pdb=" O LEUAj 155 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 163 through 174 removed outlier: 3.805A pdb=" N GLUAj 167 " --> pdb=" O SERAj 163 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 13 through 39 removed outlier: 3.559A pdb=" N GLUAk 17 " --> pdb=" O HISAk 13 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 48 through 77 removed outlier: 3.592A pdb=" N ALAAk 52 " --> pdb=" O LEUAk 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARGAk 76 " --> pdb=" O LEUAk 72 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLYAk 77 " --> pdb=" O GLNAk 73 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 96 through 123 Processing helix chain 'Ak' and resid 126 through 137 Processing helix chain 'Ak' and resid 137 through 159 Processing helix chain 'Ak' and resid 163 through 173 removed outlier: 3.804A pdb=" N GLUAk 167 " --> pdb=" O SERAk 163 " (cutoff:3.500A) Processing helix chain 'Al' and resid 13 through 41 removed outlier: 3.511A pdb=" N PHEAl 41 " --> pdb=" O METAl 37 " (cutoff:3.500A) Processing helix chain 'Al' and resid 48 through 76 removed outlier: 3.507A pdb=" N ARGAl 76 " --> pdb=" O LEUAl 72 " (cutoff:3.500A) Processing helix chain 'Al' and resid 96 through 124 Processing helix chain 'Al' and resid 126 through 137 removed outlier: 3.648A pdb=" N TYRAl 137 " --> pdb=" O ILEAl 133 " (cutoff:3.500A) Processing helix chain 'Al' and resid 137 through 159 removed outlier: 3.707A pdb=" N GLYAl 159 " --> pdb=" O LEUAl 155 " (cutoff:3.500A) Processing helix chain 'Al' and resid 163 through 174 removed outlier: 4.261A pdb=" N GLUAl 167 " --> pdb=" O SERAl 163 " (cutoff:3.500A) Processing helix chain 'Am' and resid 13 through 41 removed outlier: 3.586A pdb=" N GLUAm 17 " --> pdb=" O HISAm 13 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHEAm 41 " --> pdb=" O METAm 37 " (cutoff:3.500A) Processing helix chain 'Am' and resid 48 through 57 Processing helix chain 'Am' and resid 59 through 77 Processing helix chain 'Am' and resid 96 through 124 Processing helix chain 'Am' and resid 126 through 137 Processing helix chain 'Am' and resid 137 through 158 Processing helix chain 'Am' and resid 164 through 174 Processing helix chain 'An' and resid 13 through 41 removed outlier: 3.686A pdb=" N GLUAn 17 " --> pdb=" O HISAn 13 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHEAn 41 " --> pdb=" O METAn 37 " (cutoff:3.500A) Processing helix chain 'An' and resid 48 through 77 removed outlier: 4.023A pdb=" N ALAAn 52 " --> pdb=" O LEUAn 48 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARGAn 76 " --> pdb=" O LEUAn 72 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLYAn 77 " --> pdb=" O GLNAn 73 " (cutoff:3.500A) Processing helix chain 'An' and resid 95 through 124 removed outlier: 3.901A pdb=" N ALAAn 99 " --> pdb=" O SERAn 95 " (cutoff:3.500A) Processing helix chain 'An' and resid 126 through 137 removed outlier: 3.642A pdb=" N CYSAn 130 " --> pdb=" O ASPAn 126 " (cutoff:3.500A) Processing helix chain 'An' and resid 137 through 159 removed outlier: 3.785A pdb=" N GLYAn 159 " --> pdb=" O LEUAn 155 " (cutoff:3.500A) Processing helix chain 'An' and resid 163 through 173 removed outlier: 4.209A pdb=" N GLUAn 167 " --> pdb=" O SERAn 163 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 13 through 39 Processing helix chain 'Ao' and resid 48 through 76 removed outlier: 3.919A pdb=" N ALAAo 52 " --> pdb=" O LEUAo 48 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARGAo 76 " --> pdb=" O LEUAo 72 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 96 through 124 Processing helix chain 'Ao' and resid 126 through 137 Processing helix chain 'Ao' and resid 137 through 159 Processing helix chain 'Ao' and resid 163 through 173 removed outlier: 4.003A pdb=" N GLUAo 167 " --> pdb=" O SERAo 163 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 13 through 39 removed outlier: 3.503A pdb=" N GLUAp 17 " --> pdb=" O HISAp 13 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 48 through 77 removed outlier: 3.710A pdb=" N ALAAp 52 " --> pdb=" O LEUAp 48 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 95 through 123 Processing helix chain 'Ap' and resid 126 through 137 removed outlier: 3.841A pdb=" N TYRAp 137 " --> pdb=" O ILEAp 133 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 137 through 158 Processing helix chain 'Ap' and resid 163 through 174 removed outlier: 4.004A pdb=" N GLUAp 167 " --> pdb=" O SERAp 163 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THRAp 174 " --> pdb=" O PHEAp 170 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 123 through 135 Processing helix chain 'Aq' and resid 140 through 148 removed outlier: 3.657A pdb=" N ILEAq 144 " --> pdb=" O PHEAq 140 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASNAq 148 " --> pdb=" O ILEAq 144 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 159 through 176 removed outlier: 4.017A pdb=" N PHEAq 176 " --> pdb=" O GLNAq 172 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 239 through 244 Processing helix chain 'Aq' and resid 263 through 274 removed outlier: 3.595A pdb=" N LYSAq 267 " --> pdb=" O THRAq 263 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEUAq 274 " --> pdb=" O ASNAq 270 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 338 through 347 Processing helix chain 'Aq' and resid 419 through 439 removed outlier: 3.660A pdb=" N LYSAq 439 " --> pdb=" O ASPAq 435 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 460 through 469 removed outlier: 4.010A pdb=" N GLYAq 469 " --> pdb=" O GLUAq 465 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 502 through 511 Processing helix chain 'Aq' and resid 528 through 532 removed outlier: 3.667A pdb=" N LYSAq 531 " --> pdb=" O TRPAq 528 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VALAq 532 " --> pdb=" O ALAAq 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aq' and resid 528 through 532' Processing helix chain 'Aq' and resid 540 through 547 removed outlier: 4.341A pdb=" N PHEAq 544 " --> pdb=" O ALAAq 540 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 572 through 580 removed outlier: 3.575A pdb=" N LEUAq 576 " --> pdb=" O THRAq 572 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 582 through 603 Processing helix chain 'Aq' and resid 612 through 627 removed outlier: 3.792A pdb=" N SERAq 616 " --> pdb=" O GLUAq 612 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 628 through 636 removed outlier: 3.557A pdb=" N ILEAq 632 " --> pdb=" O TYRAq 628 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N METAq 635 " --> pdb=" O ASPAq 631 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 639 through 661 removed outlier: 3.560A pdb=" N TYRAq 643 " --> pdb=" O LEUAq 639 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 670 through 680 Processing helix chain 'Aq' and resid 681 through 686 removed outlier: 3.659A pdb=" N HISAq 684 " --> pdb=" O VALAq 681 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHEAq 685 " --> pdb=" O GLUAq 682 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 708 through 718 Processing helix chain 'Aq' and resid 719 through 721 No H-bonds generated for 'chain 'Aq' and resid 719 through 721' Processing helix chain 'Aq' and resid 727 through 750 Processing helix chain 'Ar' and resid 13 through 41 Processing helix chain 'Ar' and resid 48 through 76 removed outlier: 3.627A pdb=" N ALAAr 52 " --> pdb=" O LEUAr 48 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARGAr 76 " --> pdb=" O LEUAr 72 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 95 through 124 removed outlier: 3.754A pdb=" N ALAAr 99 " --> pdb=" O SERAr 95 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 126 through 137 Processing helix chain 'Ar' and resid 137 through 159 Processing helix chain 'Ar' and resid 163 through 174 removed outlier: 3.982A pdb=" N GLUAr 167 " --> pdb=" O SERAr 163 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THRAr 174 " --> pdb=" O PHEAr 170 " (cutoff:3.500A) Processing helix chain 'As' and resid 13 through 39 removed outlier: 3.551A pdb=" N GLUAs 17 " --> pdb=" O HISAs 13 " (cutoff:3.500A) Processing helix chain 'As' and resid 48 through 76 removed outlier: 3.513A pdb=" N ALAAs 52 " --> pdb=" O LEUAs 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARGAs 76 " --> pdb=" O LEUAs 72 " (cutoff:3.500A) Processing helix chain 'As' and resid 96 through 124 removed outlier: 3.688A pdb=" N METAs 100 " --> pdb=" O GLYAs 96 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYSAs 124 " --> pdb=" O LEUAs 120 " (cutoff:3.500A) Processing helix chain 'As' and resid 126 through 137 removed outlier: 3.501A pdb=" N TYRAs 137 " --> pdb=" O ILEAs 133 " (cutoff:3.500A) Processing helix chain 'As' and resid 137 through 159 removed outlier: 3.887A pdb=" N GLYAs 159 " --> pdb=" O LEUAs 155 " (cutoff:3.500A) Processing helix chain 'As' and resid 163 through 174 removed outlier: 3.973A pdb=" N GLUAs 167 " --> pdb=" O SERAs 163 " (cutoff:3.500A) Processing helix chain 'At' and resid 13 through 39 removed outlier: 3.746A pdb=" N GLUAt 17 " --> pdb=" O HISAt 13 " (cutoff:3.500A) Processing helix chain 'At' and resid 48 through 76 removed outlier: 3.544A pdb=" N ALAAt 52 " --> pdb=" O LEUAt 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARGAt 76 " --> pdb=" O LEUAt 72 " (cutoff:3.500A) Processing helix chain 'At' and resid 96 through 124 removed outlier: 3.983A pdb=" N METAt 100 " --> pdb=" O GLYAt 96 " (cutoff:3.500A) Processing helix chain 'At' and resid 126 through 137 Processing helix chain 'At' and resid 137 through 158 removed outlier: 3.566A pdb=" N GLNAt 141 " --> pdb=" O TYRAt 137 " (cutoff:3.500A) Processing helix chain 'At' and resid 163 through 174 removed outlier: 4.089A pdb=" N GLUAt 167 " --> pdb=" O SERAt 163 " (cutoff:3.500A) Processing helix chain 'Au' and resid 13 through 41 removed outlier: 3.662A pdb=" N GLUAu 17 " --> pdb=" O HISAu 13 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHEAu 41 " --> pdb=" O METAu 37 " (cutoff:3.500A) Processing helix chain 'Au' and resid 48 through 77 removed outlier: 3.674A pdb=" N ALAAu 52 " --> pdb=" O LEUAu 48 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLYAu 77 " --> pdb=" O GLNAu 73 " (cutoff:3.500A) Processing helix chain 'Au' and resid 96 through 124 Processing helix chain 'Au' and resid 126 through 137 removed outlier: 3.815A pdb=" N CYSAu 130 " --> pdb=" O ASPAu 126 " (cutoff:3.500A) Processing helix chain 'Au' and resid 137 through 158 Processing helix chain 'Au' and resid 163 through 173 removed outlier: 4.006A pdb=" N GLUAu 167 " --> pdb=" O SERAu 163 " (cutoff:3.500A) Processing helix chain 'Av' and resid 13 through 41 Processing helix chain 'Av' and resid 48 through 77 removed outlier: 3.501A pdb=" N ALAAv 52 " --> pdb=" O LEUAv 48 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLYAv 77 " --> pdb=" O GLNAv 73 " (cutoff:3.500A) Processing helix chain 'Av' and resid 96 through 123 Processing helix chain 'Av' and resid 126 through 137 Processing helix chain 'Av' and resid 137 through 159 Processing helix chain 'Av' and resid 163 through 174 removed outlier: 3.956A pdb=" N GLUAv 167 " --> pdb=" O SERAv 163 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 13 through 39 removed outlier: 3.682A pdb=" N GLUAw 17 " --> pdb=" O HISAw 13 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 48 through 76 removed outlier: 3.630A pdb=" N ALAAw 52 " --> pdb=" O LEUAw 48 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARGAw 76 " --> pdb=" O LEUAw 72 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 96 through 124 Processing helix chain 'Aw' and resid 126 through 137 Processing helix chain 'Aw' and resid 137 through 158 removed outlier: 3.512A pdb=" N GLNAw 141 " --> pdb=" O TYRAw 137 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 163 through 174 removed outlier: 4.013A pdb=" N GLUAw 167 " --> pdb=" O SERAw 163 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THRAw 174 " --> pdb=" O PHEAw 170 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 13 through 39 removed outlier: 3.529A pdb=" N GLUAx 17 " --> pdb=" O HISAx 13 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 48 through 77 removed outlier: 3.568A pdb=" N ALAAx 52 " --> pdb=" O LEUAx 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLYAx 77 " --> pdb=" O GLNAx 73 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 95 through 123 removed outlier: 3.991A pdb=" N ALAAx 99 " --> pdb=" O SERAx 95 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 126 through 137 Processing helix chain 'Ax' and resid 137 through 159 removed outlier: 3.612A pdb=" N GLYAx 159 " --> pdb=" O LEUAx 155 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 163 through 174 removed outlier: 3.887A pdb=" N GLUAx 167 " --> pdb=" O SERAx 163 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 13 through 39 removed outlier: 3.662A pdb=" N GLUAy 17 " --> pdb=" O HISAy 13 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 48 through 76 removed outlier: 3.646A pdb=" N ALAAy 52 " --> pdb=" O LEUAy 48 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARGAy 76 " --> pdb=" O LEUAy 72 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 96 through 124 Processing helix chain 'Ay' and resid 126 through 137 Processing helix chain 'Ay' and resid 137 through 158 Processing helix chain 'Ay' and resid 163 through 173 removed outlier: 4.111A pdb=" N GLUAy 167 " --> pdb=" O SERAy 163 " (cutoff:3.500A) Processing helix chain 'Az' and resid 13 through 39 Processing helix chain 'Az' and resid 48 through 76 removed outlier: 3.564A pdb=" N ARGAz 76 " --> pdb=" O LEUAz 72 " (cutoff:3.500A) Processing helix chain 'Az' and resid 96 through 124 Processing helix chain 'Az' and resid 126 through 137 removed outlier: 3.502A pdb=" N TYRAz 137 " --> pdb=" O ILEAz 133 " (cutoff:3.500A) Processing helix chain 'Az' and resid 137 through 159 Processing helix chain 'Az' and resid 163 through 173 removed outlier: 4.089A pdb=" N GLUAz 167 " --> pdb=" O SERAz 163 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Ab' and resid 180 through 193 removed outlier: 5.031A pdb=" N SERAb 447 " --> pdb=" O PROAb 399 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N HISAb 401 " --> pdb=" O SERAb 447 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILEAb 449 " --> pdb=" O HISAb 401 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VALAb 403 " --> pdb=" O ILEAb 449 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALAAb 451 " --> pdb=" O VALAb 403 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VALAb 405 " --> pdb=" O ALAAb 451 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N TRPAb 453 " --> pdb=" O VALAb 405 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALAAb 407 " --> pdb=" O TRPAb 453 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ALAAb 478 " --> pdb=" O ASPAb 400 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYRAb 402 " --> pdb=" O ALAAb 478 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THRAb 480 " --> pdb=" O TYRAb 402 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLYAb 406 " --> pdb=" O ILEAb 482 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VALAb 553 " --> pdb=" O PHEAb 479 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYRAb 481 " --> pdb=" O VALAb 553 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N PHEAb 555 " --> pdb=" O TYRAb 481 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASNAb 483 " --> pdb=" O PHEAb 555 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N PHEAb 557 " --> pdb=" O ASNAb 483 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Ab' and resid 210 through 214 removed outlier: 6.801A pdb=" N VALAb 200 " --> pdb=" O VALAb 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Ab' and resid 220 through 221 Processing sheet with id=AA4, first strand: chain 'Ab' and resid 232 through 234 removed outlier: 6.321A pdb=" N VALAb 279 " --> pdb=" O GLNAb 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Ab' and resid 349 through 352 removed outlier: 6.625A pdb=" N ASPAb 352 " --> pdb=" O ARGAb 364 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARGAb 364 " --> pdb=" O ASPAb 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Aq' and resid 180 through 193 removed outlier: 7.035A pdb=" N VALAq 403 " --> pdb=" O ILEAq 449 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ALAAq 451 " --> pdb=" O VALAq 403 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VALAq 405 " --> pdb=" O ALAAq 451 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N TRPAq 453 " --> pdb=" O VALAq 405 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALAAq 407 " --> pdb=" O TRPAq 453 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYRAq 402 " --> pdb=" O ALAAq 478 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THRAq 480 " --> pdb=" O TYRAq 402 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLYAq 406 " --> pdb=" O ILEAq 482 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHEAq 555 " --> pdb=" O ASNAq 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Aq' and resid 209 through 214 removed outlier: 6.679A pdb=" N VALAq 200 " --> pdb=" O VALAq 213 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N LYSAq 371 " --> pdb=" O LEUAq 232 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEUAq 232 " --> pdb=" O LYSAq 371 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLYAq 278 " --> pdb=" O SERAq 253 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYRAq 282 " --> pdb=" O VALAq 257 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VALAq 279 " --> pdb=" O GLNAq 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Aq' and resid 349 through 352 removed outlier: 6.680A pdb=" N ASPAq 352 " --> pdb=" O ARGAq 364 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARGAq 364 " --> pdb=" O ASPAq 352 " (cutoff:3.500A) 2890 hydrogen bonds defined for protein. 8634 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.81 Time building geometry restraints manager: 13.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14725 1.34 - 1.46: 10278 1.46 - 1.59: 19513 1.59 - 1.71: 0 1.71 - 1.83: 312 Bond restraints: 44828 Sorted by residual: bond pdb=" CG HISAh 57 " pdb=" CD2 HISAh 57 " ideal model delta sigma weight residual 1.354 1.394 -0.040 1.10e-02 8.26e+03 1.33e+01 bond pdb=" CG HISAk 57 " pdb=" CD2 HISAk 57 " ideal model delta sigma weight residual 1.354 1.394 -0.040 1.10e-02 8.26e+03 1.33e+01 bond pdb=" CG HISAs 57 " pdb=" CD2 HISAs 57 " ideal model delta sigma weight residual 1.354 1.394 -0.040 1.10e-02 8.26e+03 1.31e+01 bond pdb=" CG HISAe 57 " pdb=" CD2 HISAe 57 " ideal model delta sigma weight residual 1.354 1.394 -0.040 1.10e-02 8.26e+03 1.31e+01 bond pdb=" CG HISAg 57 " pdb=" CD2 HISAg 57 " ideal model delta sigma weight residual 1.354 1.394 -0.040 1.10e-02 8.26e+03 1.30e+01 ... (remaining 44823 not shown) Histogram of bond angle deviations from ideal: 97.97 - 105.36: 518 105.36 - 112.76: 23471 112.76 - 120.15: 18232 120.15 - 127.54: 17798 127.54 - 134.93: 441 Bond angle restraints: 60460 Sorted by residual: angle pdb=" N PHEAq 557 " pdb=" CA PHEAq 557 " pdb=" C PHEAq 557 " ideal model delta sigma weight residual 108.67 97.97 10.70 1.55e+00 4.16e-01 4.76e+01 angle pdb=" N PHEAb 557 " pdb=" CA PHEAb 557 " pdb=" C PHEAb 557 " ideal model delta sigma weight residual 108.96 98.89 10.07 1.59e+00 3.96e-01 4.01e+01 angle pdb=" C PHEAb 557 " pdb=" CA PHEAb 557 " pdb=" CB PHEAb 557 " ideal model delta sigma weight residual 110.22 119.06 -8.84 1.67e+00 3.59e-01 2.80e+01 angle pdb=" N ALAAb 416 " pdb=" CA ALAAb 416 " pdb=" C ALAAb 416 " ideal model delta sigma weight residual 111.28 116.79 -5.51 1.09e+00 8.42e-01 2.56e+01 angle pdb=" C LYSAq 418 " pdb=" CA LYSAq 418 " pdb=" CB LYSAq 418 " ideal model delta sigma weight residual 109.29 101.05 8.24 1.82e+00 3.02e-01 2.05e+01 ... (remaining 60455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 26029 17.38 - 34.77: 753 34.77 - 52.15: 127 52.15 - 69.54: 15 69.54 - 86.92: 71 Dihedral angle restraints: 26995 sinusoidal: 11085 harmonic: 15910 Sorted by residual: dihedral pdb=" CA THRAb 310 " pdb=" C THRAb 310 " pdb=" N PROAb 311 " pdb=" CA PROAb 311 " ideal model delta harmonic sigma weight residual 180.00 145.63 34.37 0 5.00e+00 4.00e-02 4.73e+01 dihedral pdb=" CA THRAq 310 " pdb=" C THRAq 310 " pdb=" N PROAq 311 " pdb=" CA PROAq 311 " ideal model delta harmonic sigma weight residual 180.00 146.81 33.19 0 5.00e+00 4.00e-02 4.41e+01 dihedral pdb=" CA LEUAb 209 " pdb=" C LEUAb 209 " pdb=" N VALAb 210 " pdb=" CA VALAb 210 " ideal model delta harmonic sigma weight residual -180.00 -147.96 -32.04 0 5.00e+00 4.00e-02 4.11e+01 ... (remaining 26992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4356 0.045 - 0.089: 1632 0.089 - 0.134: 373 0.134 - 0.178: 64 0.178 - 0.223: 7 Chirality restraints: 6432 Sorted by residual: chirality pdb=" CA SERAn 95 " pdb=" N SERAn 95 " pdb=" C SERAn 95 " pdb=" CB SERAn 95 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA LEUAj 148 " pdb=" N LEUAj 148 " pdb=" C LEUAj 148 " pdb=" CB LEUAj 148 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CG LEUAb 209 " pdb=" CB LEUAb 209 " pdb=" CD1 LEUAb 209 " pdb=" CD2 LEUAb 209 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 6429 not shown) Planarity restraints: 7916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLUAe 94 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" C GLUAe 94 " 0.045 2.00e-02 2.50e+03 pdb=" O GLUAe 94 " -0.017 2.00e-02 2.50e+03 pdb=" N SERAe 95 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SERAb 687 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PROAb 688 " -0.109 5.00e-02 4.00e+02 pdb=" CA PROAb 688 " 0.033 5.00e-02 4.00e+02 pdb=" CD PROAb 688 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILEAb 332 " 0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PROAb 333 " -0.105 5.00e-02 4.00e+02 pdb=" CA PROAb 333 " 0.031 5.00e-02 4.00e+02 pdb=" CD PROAb 333 " 0.034 5.00e-02 4.00e+02 ... (remaining 7913 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3234 2.74 - 3.28: 42619 3.28 - 3.82: 72837 3.82 - 4.36: 83655 4.36 - 4.90: 146757 Nonbonded interactions: 349102 Sorted by model distance: nonbonded pdb=" O GLYAb 415 " pdb=" N GLYAb 420 " model vdw 2.196 2.520 nonbonded pdb=" O GLUAb 266 " pdb=" ND2 ASNAb 270 " model vdw 2.207 2.520 nonbonded pdb=" OG1 THRAc 174 " pdb=" OH TYRAw 168 " model vdw 2.242 2.440 nonbonded pdb=" OH TYRAh 168 " pdb=" OG1 THRAu 174 " model vdw 2.246 2.440 nonbonded pdb=" OH TYRAi 168 " pdb=" OG1 THRAx 174 " model vdw 2.249 2.440 ... (remaining 349097 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 'Aa' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ac' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ad' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ae' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Af' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ag' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ah' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ai' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Aj' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ak' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Al' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Am' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'An' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ao' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ap' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ar' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'As' and (resid 5 through 86 or resid 88 through 176)) selection = chain 'At' selection = (chain 'Au' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Av' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Aw' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ax' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ay' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Az' and (resid 5 through 86 or resid 88 through 176)) } ncs_group { reference = chain 'Ab' selection = (chain 'Aq' and (resid 121 through 667 or resid 669 through 756)) } 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.320 Construct map_model_manager: 0.020 Extract box with map and model: 6.130 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 81.730 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0524 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 : 0.006 0.047 44828 Z= 0.373 Angle : 0.814 12.868 60460 Z= 0.459 Chirality : 0.048 0.223 6432 Planarity : 0.006 0.063 7916 Dihedral : 10.469 86.920 16705 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.17 % Allowed : 2.06 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 1.65 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.10), residues: 5332 helix: -0.36 (0.07), residues: 3558 sheet: -1.49 (0.36), residues: 191 loop : -2.80 (0.13), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPAg 93 HIS 0.017 0.002 HISAk 151 PHE 0.027 0.002 PHEAt 55 TYR 0.029 0.003 TYRAc 32 ARG 0.007 0.001 ARGAv 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 667 time to evaluate : 3.551 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: Ab 357 TRP cc_start: -0.1283 (m-10) cc_final: -0.2738 (m-10) REVERT: Ab 600 LYS cc_start: 0.0124 (mmmm) cc_final: -0.0148 (mmtt) REVERT: Ab 649 PHE cc_start: 0.4695 (t80) cc_final: 0.4444 (t80) REVERT: Ab 679 MET cc_start: 0.1839 (mtt) cc_final: 0.1562 (tmm) REVERT: Ae 20 ILE cc_start: -0.2714 (mm) cc_final: -0.3116 (mt) REVERT: Ae 37 MET cc_start: -0.2418 (mtt) cc_final: -0.3096 (tpp) REVERT: Ae 41 PHE cc_start: 0.0402 (m-80) cc_final: 0.0045 (m-80) REVERT: Ae 105 HIS cc_start: 0.4212 (t70) cc_final: 0.3927 (m170) REVERT: Af 80 ILE cc_start: 0.4465 (mt) cc_final: 0.4233 (mt) REVERT: Ag 36 SER cc_start: 0.6906 (t) cc_final: 0.6525 (p) REVERT: Ag 56 LEU cc_start: 0.6308 (tp) cc_final: 0.6068 (tt) REVERT: Ag 155 LEU cc_start: 0.2565 (mt) cc_final: 0.2322 (mt) REVERT: Ah 161 PRO cc_start: 0.4968 (Cg_endo) cc_final: 0.4549 (Cg_exo) REVERT: Ai 122 THR cc_start: 0.1343 (m) cc_final: 0.0851 (p) REVERT: Aj 123 ASP cc_start: 0.5487 (m-30) cc_final: 0.5135 (t70) REVERT: Aq 140 PHE cc_start: 0.0356 (m-10) cc_final: -0.0503 (m-10) REVERT: Aq 258 ARG cc_start: 0.2202 (mtm180) cc_final: 0.1392 (mtt180) REVERT: Aq 442 PHE cc_start: 0.0386 (t80) cc_final: 0.0179 (t80) REVERT: Aq 614 TYR cc_start: -0.1383 (m-10) cc_final: -0.1820 (m-10) REVERT: Aq 635 MET cc_start: -0.2218 (mtp) cc_final: -0.2905 (mtp) REVERT: Aq 685 PHE cc_start: -0.1210 (m-10) cc_final: -0.1561 (m-80) REVERT: Aq 694 GLU cc_start: 0.1166 (mt-10) cc_final: 0.0709 (tm-30) REVERT: Ar 43 ARG cc_start: 0.1426 (mtp180) cc_final: 0.0913 (mmm-85) REVERT: Av 118 HIS cc_start: 0.0983 (t-90) cc_final: -0.0231 (t70) REVERT: Av 122 THR cc_start: 0.3920 (m) cc_final: 0.3493 (p) REVERT: Ax 37 MET cc_start: -0.2251 (mtt) cc_final: -0.3780 (tpp) REVERT: Az 172 LYS cc_start: -0.2474 (mmtm) cc_final: -0.3313 (pttt) outliers start: 8 outliers final: 1 residues processed: 675 average time/residue: 0.5076 time to fit residues: 555.4926 Evaluate side-chains 401 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 400 time to evaluate : 3.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 6 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 450 optimal weight: 0.9990 chunk 404 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 273 optimal weight: 5.9990 chunk 216 optimal weight: 20.0000 chunk 418 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 254 optimal weight: 0.9990 chunk 311 optimal weight: 4.9990 chunk 484 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 11 ASN ** Aa 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 109 ASN Aa 118 HIS Aa 173 HIS Ab 171 ASN Ab 197 GLN Ab 483 ASN Ab 493 ASN ** Ab 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 733 ASN Ab 747 ASN Ac 105 HIS Ac 154 ASN Ad 21 ASN Ad 118 HIS Ad 173 HIS Ae 118 HIS Ae 136 HIS Ae 173 HIS Af 11 ASN Af 21 ASN Af 111 ASN ** Ag 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 118 HIS ** Ag 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 25 ASN Ai 109 ASN Ai 112 GLN Ai 118 HIS Ai 154 ASN Aj 11 ASN Aj 73 GLN Aj 75 GLN Aj 105 HIS Ak 73 GLN Al 11 ASN Al 60 HIS Al 98 ASN Al 109 ASN Al 118 HIS Al 128 HIS Al 136 HIS Am 25 ASN Am 57 HIS ** Am 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 118 HIS Ao 128 HIS Ao 136 HIS Ap 14 GLN Ap 109 ASN Ap 118 HIS Ap 136 HIS Ap 173 HIS Aq 171 ASN Aq 172 GLN Aq 493 ASN ** Aq 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 603 HIS Aq 733 ASN Aq 747 ASN Ar 65 HIS Ar 128 HIS Ar 141 GLN Ar 154 ASN ** Ar 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** As 7 GLN As 11 ASN ** As 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** As 136 HIS ** As 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** At 11 ASN At 109 ASN ** Au 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Au 173 HIS Av 118 HIS ** Av 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Av 136 HIS Aw 11 ASN Aw 21 ASN Aw 73 GLN Ax 75 GLN Ax 125 ASN Ax 173 HIS Ay 11 ASN ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 112 GLN Az 118 HIS Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1113 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 44828 Z= 0.185 Angle : 0.563 12.054 60460 Z= 0.298 Chirality : 0.039 0.272 6432 Planarity : 0.004 0.049 7916 Dihedral : 4.723 28.160 5846 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.14 % Allowed : 4.96 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.11), residues: 5332 helix: 1.96 (0.08), residues: 3618 sheet: -1.28 (0.35), residues: 202 loop : -2.36 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRPAn 93 HIS 0.008 0.001 HISAw 65 PHE 0.027 0.002 PHEAz 41 TYR 0.030 0.002 TYRAp 29 ARG 0.005 0.001 ARGAo 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 428 time to evaluate : 3.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 41 PHE cc_start: 0.3049 (m-80) cc_final: 0.2473 (m-80) REVERT: Ab 679 MET cc_start: 0.2214 (mtt) cc_final: 0.1780 (tmm) REVERT: Ad 41 PHE cc_start: 0.0620 (m-80) cc_final: 0.0185 (m-10) REVERT: Ad 158 MET cc_start: -0.1669 (mtp) cc_final: -0.2633 (mtm) REVERT: Ae 37 MET cc_start: -0.1230 (mtt) cc_final: -0.3274 (tpp) REVERT: Ae 105 HIS cc_start: 0.4715 (t70) cc_final: 0.4343 (t70) REVERT: Ah 161 PRO cc_start: 0.6563 (Cg_endo) cc_final: 0.6110 (Cg_exo) REVERT: Ai 35 LEU cc_start: 0.3165 (tp) cc_final: 0.2892 (tp) REVERT: Ai 158 MET cc_start: 0.4492 (tpt) cc_final: 0.4070 (tpt) REVERT: Aj 100 MET cc_start: 0.3408 (tpp) cc_final: 0.2542 (mmp) REVERT: Aj 123 ASP cc_start: 0.5115 (m-30) cc_final: 0.4908 (m-30) REVERT: Ao 51 PHE cc_start: 0.0977 (OUTLIER) cc_final: -0.0819 (m-10) REVERT: Ap 8 VAL cc_start: 0.2575 (OUTLIER) cc_final: 0.2262 (m) REVERT: Aq 388 ASN cc_start: 0.4530 (m-40) cc_final: 0.3187 (m-40) REVERT: Aq 635 MET cc_start: -0.3447 (mtp) cc_final: -0.4040 (ttt) REVERT: Aq 685 PHE cc_start: -0.1129 (m-10) cc_final: -0.1829 (m-80) REVERT: Aq 694 GLU cc_start: 0.1115 (mt-10) cc_final: 0.0674 (tm-30) REVERT: Aw 119 LYS cc_start: 0.5828 (mmtm) cc_final: 0.5303 (mttt) REVERT: Ax 12 TYR cc_start: 0.1499 (t80) cc_final: 0.0785 (t80) REVERT: Ax 37 MET cc_start: -0.1495 (mtt) cc_final: -0.3531 (tpt) REVERT: Ax 54 TYR cc_start: 0.5149 (t80) cc_final: 0.4726 (t80) REVERT: Ay 61 GLU cc_start: 0.5732 (mt-10) cc_final: 0.4040 (tp30) REVERT: Ay 100 MET cc_start: 0.5018 (mtt) cc_final: 0.4726 (mtm) outliers start: 54 outliers final: 25 residues processed: 461 average time/residue: 0.4557 time to fit residues: 348.0879 Evaluate side-chains 358 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 331 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 LYS Chi-restraints excluded: chain Ab residue 143 THR Chi-restraints excluded: chain Ab residue 209 LEU Chi-restraints excluded: chain Ab residue 604 ASP Chi-restraints excluded: chain Ab residue 670 VAL Chi-restraints excluded: chain Ad residue 53 LYS Chi-restraints excluded: chain Af residue 35 LEU Chi-restraints excluded: chain Ag residue 104 LEU Chi-restraints excluded: chain Ah residue 25 ASN Chi-restraints excluded: chain Ah residue 92 ASP Chi-restraints excluded: chain Ai residue 104 LEU Chi-restraints excluded: chain Aj residue 105 HIS Chi-restraints excluded: chain Aj residue 117 LEU Chi-restraints excluded: chain Aj residue 120 LEU Chi-restraints excluded: chain Ak residue 69 LEU Chi-restraints excluded: chain Al residue 120 LEU Chi-restraints excluded: chain Am residue 82 LEU Chi-restraints excluded: chain An residue 133 ILE Chi-restraints excluded: chain Ao residue 51 PHE Chi-restraints excluded: chain Ap residue 8 VAL Chi-restraints excluded: chain Aq residue 141 THR Chi-restraints excluded: chain Aq residue 210 VAL Chi-restraints excluded: chain Aq residue 418 LYS Chi-restraints excluded: chain Aq residue 496 VAL Chi-restraints excluded: chain Ax residue 65 HIS Chi-restraints excluded: chain Ay residue 104 LEU Chi-restraints excluded: chain Az residue 133 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 269 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 403 optimal weight: 3.9990 chunk 330 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 485 optimal weight: 3.9990 chunk 524 optimal weight: 0.9980 chunk 432 optimal weight: 9.9990 chunk 481 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 389 optimal weight: 0.0770 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 73 GLN ** Ab 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 109 ASN Ac 173 HIS Ad 7 GLN Af 128 HIS Ag 173 HIS Ah 25 ASN ** Ai 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 105 HIS ** Am 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 615 ASN Ar 173 HIS As 11 ASN ** As 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 173 HIS At 11 ASN At 173 HIS Au 73 GLN ** Av 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 11 ASN ** Aw 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 7 GLN Ax 11 ASN Ay 65 HIS ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 7 GLN Az 128 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1156 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 44828 Z= 0.122 Angle : 0.461 9.733 60460 Z= 0.243 Chirality : 0.036 0.185 6432 Planarity : 0.003 0.047 7916 Dihedral : 4.333 26.335 5845 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.58 % Allowed : 5.89 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % 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: 2.08 (0.12), residues: 5332 helix: 2.82 (0.08), residues: 3605 sheet: -0.65 (0.37), residues: 191 loop : -2.10 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPAn 93 HIS 0.014 0.001 HISAi 151 PHE 0.026 0.001 PHEAq 442 TYR 0.021 0.001 TYRAq 614 ARG 0.004 0.000 ARGAq 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 365 time to evaluate : 3.596 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: Aa 37 MET cc_start: -0.2765 (mtt) cc_final: -0.3019 (mtt) REVERT: Aa 41 PHE cc_start: 0.3256 (m-80) cc_final: 0.2696 (m-80) REVERT: Ab 131 LEU cc_start: 0.4323 (tp) cc_final: 0.3944 (mm) REVERT: Ab 359 THR cc_start: -0.1716 (OUTLIER) cc_final: -0.2131 (t) REVERT: Ab 679 MET cc_start: 0.2296 (mtt) cc_final: 0.1940 (tmm) REVERT: Ae 105 HIS cc_start: 0.4653 (t70) cc_final: 0.4315 (t70) REVERT: Ah 161 PRO cc_start: 0.6372 (Cg_endo) cc_final: 0.6044 (Cg_exo) REVERT: Ai 134 GLU cc_start: 0.2941 (mt-10) cc_final: 0.2597 (mt-10) REVERT: Ai 154 ASN cc_start: 0.3959 (t0) cc_final: 0.3705 (t0) REVERT: Ai 158 MET cc_start: 0.3931 (tpt) cc_final: 0.3634 (tpt) REVERT: Aj 100 MET cc_start: 0.3354 (tpp) cc_final: 0.2645 (mmm) REVERT: Aj 123 ASP cc_start: 0.5153 (m-30) cc_final: 0.4903 (m-30) REVERT: Al 51 PHE cc_start: 0.1180 (OUTLIER) cc_final: 0.0539 (m-10) REVERT: Ao 68 LYS cc_start: 0.2291 (ttmt) cc_final: 0.2034 (mmtt) REVERT: Ap 8 VAL cc_start: 0.2497 (OUTLIER) cc_final: 0.2200 (m) REVERT: Ap 100 MET cc_start: -0.2007 (OUTLIER) cc_final: -0.3150 (ptp) REVERT: Aq 250 VAL cc_start: 0.0842 (t) cc_final: 0.0580 (m) REVERT: Aq 479 PHE cc_start: -0.1498 (p90) cc_final: -0.2342 (p90) REVERT: Aq 694 GLU cc_start: 0.0927 (mt-10) cc_final: 0.0508 (tm-30) REVERT: Ar 71 LYS cc_start: 0.2147 (OUTLIER) cc_final: 0.1492 (tptp) REVERT: Ar 74 ASN cc_start: 0.1959 (m110) cc_final: 0.1657 (t0) REVERT: Av 51 PHE cc_start: 0.1815 (OUTLIER) cc_final: 0.1032 (m-80) REVERT: Av 70 MET cc_start: -0.1852 (ttt) cc_final: -0.2175 (ttt) REVERT: Aw 111 ASN cc_start: 0.5414 (t0) cc_final: 0.3971 (t0) REVERT: Ax 12 TYR cc_start: 0.1464 (t80) cc_final: -0.0902 (t80) REVERT: Ax 37 MET cc_start: -0.1284 (mtt) cc_final: -0.3593 (tpp) outliers start: 75 outliers final: 35 residues processed: 418 average time/residue: 0.4460 time to fit residues: 313.5610 Evaluate side-chains 368 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 327 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 143 THR Chi-restraints excluded: chain Ab residue 209 LEU Chi-restraints excluded: chain Ab residue 283 MET Chi-restraints excluded: chain Ab residue 359 THR Chi-restraints excluded: chain Ab residue 393 ILE Chi-restraints excluded: chain Ab residue 494 PHE Chi-restraints excluded: chain Ab residue 604 ASP Chi-restraints excluded: chain Ab residue 641 TRP Chi-restraints excluded: chain Ab residue 670 VAL Chi-restraints excluded: chain Af residue 13 HIS Chi-restraints excluded: chain Af residue 35 LEU Chi-restraints excluded: chain Ag residue 97 LEU Chi-restraints excluded: chain Ag residue 104 LEU Chi-restraints excluded: chain Ah residue 25 ASN Chi-restraints excluded: chain Ah residue 92 ASP Chi-restraints excluded: chain Ai residue 80 ILE Chi-restraints excluded: chain Aj residue 105 HIS Chi-restraints excluded: chain Aj residue 117 LEU Chi-restraints excluded: chain Aj residue 120 LEU Chi-restraints excluded: chain Ak residue 69 LEU Chi-restraints excluded: chain Al residue 51 PHE Chi-restraints excluded: chain Am residue 82 LEU Chi-restraints excluded: chain An residue 133 ILE Chi-restraints excluded: chain Ao residue 51 PHE Chi-restraints excluded: chain Ap residue 8 VAL Chi-restraints excluded: chain Ap residue 65 HIS Chi-restraints excluded: chain Ap residue 100 MET Chi-restraints excluded: chain Aq residue 141 THR Chi-restraints excluded: chain Aq residue 213 VAL Chi-restraints excluded: chain Aq residue 418 LYS Chi-restraints excluded: chain Aq residue 496 VAL Chi-restraints excluded: chain Ar residue 71 LYS Chi-restraints excluded: chain As residue 128 HIS Chi-restraints excluded: chain Av residue 51 PHE Chi-restraints excluded: chain Av residue 158 MET Chi-restraints excluded: chain Aw residue 46 VAL Chi-restraints excluded: chain Ax residue 28 LEU Chi-restraints excluded: chain Ax residue 65 HIS Chi-restraints excluded: chain Ay residue 97 LEU Chi-restraints excluded: chain Ay residue 104 LEU Chi-restraints excluded: chain Az residue 133 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 479 optimal weight: 6.9990 chunk 365 optimal weight: 20.0000 chunk 252 optimal weight: 10.0000 chunk 53 optimal weight: 30.0000 chunk 231 optimal weight: 0.0370 chunk 326 optimal weight: 40.0000 chunk 487 optimal weight: 10.0000 chunk 516 optimal weight: 5.9990 chunk 254 optimal weight: 0.0030 chunk 462 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 overall best weight: 2.8074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 109 ASN ** Ab 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 348 ASN Ab 615 ASN Ab 626 ASN Ab 684 HIS Ac 118 HIS Ad 73 GLN ** Ae 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 75 GLN ** Ae 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 60 HIS Af 73 GLN ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 141 GLN ** Ag 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 75 GLN Ag 118 HIS Ah 7 GLN Ah 128 HIS Ai 11 ASN ** Ai 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 7 GLN Aj 13 HIS ** Aj 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 105 HIS ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 141 GLN Ak 50 ASN Ak 75 GLN Al 109 ASN ** Al 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 154 ASN Am 11 ASN ** Am 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 141 GLN ** Am 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 11 ASN An 13 HIS An 128 HIS ** Ao 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 73 GLN Ap 25 ASN Ap 60 HIS Ap 75 GLN Ap 141 GLN Aq 684 HIS ** Ar 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 11 ASN ** As 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 74 ASN ** As 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** At 11 ASN ** At 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Au 154 ASN Av 7 GLN ** Av 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 128 HIS ** Aw 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 11 ASN Ax 23 GLN Ax 60 HIS ** Ax 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 74 ASN Ay 75 GLN Az 7 GLN Az 118 HIS Az 128 HIS Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1804 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 44828 Z= 0.246 Angle : 0.685 10.071 60460 Z= 0.359 Chirality : 0.042 0.219 6432 Planarity : 0.005 0.055 7916 Dihedral : 4.958 26.793 5845 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.33 % Allowed : 6.73 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.11), residues: 5332 helix: 1.87 (0.08), residues: 3604 sheet: -0.56 (0.37), residues: 192 loop : -2.00 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRPAn 93 HIS 0.049 0.002 HISAr 13 PHE 0.031 0.002 PHEAz 41 TYR 0.034 0.002 TYRAl 39 ARG 0.007 0.001 ARGAz 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 386 time to evaluate : 3.741 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: Aa 34 TYR cc_start: 0.0492 (OUTLIER) cc_final: -0.1518 (m-10) REVERT: Aa 41 PHE cc_start: 0.4365 (m-80) cc_final: 0.3924 (m-80) REVERT: Ab 131 LEU cc_start: 0.4085 (tp) cc_final: 0.3863 (mt) REVERT: Ab 209 LEU cc_start: 0.0182 (OUTLIER) cc_final: -0.1049 (mt) REVERT: Ab 436 MET cc_start: -0.0778 (mmt) cc_final: -0.1571 (ptm) REVERT: Ab 679 MET cc_start: 0.2964 (mtt) cc_final: 0.2311 (tmm) REVERT: Ad 41 PHE cc_start: 0.1289 (OUTLIER) cc_final: 0.0233 (m-10) REVERT: Ae 37 MET cc_start: -0.0886 (mtt) cc_final: -0.2735 (tpt) REVERT: Ae 98 ASN cc_start: 0.6656 (t0) cc_final: 0.5975 (p0) REVERT: Af 28 LEU cc_start: 0.2439 (OUTLIER) cc_final: 0.1794 (tp) REVERT: Af 39 TYR cc_start: 0.1065 (m-10) cc_final: 0.0324 (m-80) REVERT: Af 51 PHE cc_start: 0.3870 (OUTLIER) cc_final: 0.3316 (m-10) REVERT: Ah 161 PRO cc_start: 0.6856 (Cg_endo) cc_final: 0.6562 (Cg_exo) REVERT: Aj 158 MET cc_start: 0.5542 (mmm) cc_final: 0.1678 (tmm) REVERT: Ak 75 GLN cc_start: 0.2455 (OUTLIER) cc_final: 0.0147 (mm110) REVERT: An 40 TYR cc_start: -0.0594 (t80) cc_final: -0.0977 (t80) REVERT: An 73 GLN cc_start: 0.2171 (tp-100) cc_final: 0.1663 (tt0) REVERT: Ap 100 MET cc_start: -0.1271 (OUTLIER) cc_final: -0.2776 (ptp) REVERT: Aq 144 ILE cc_start: 0.0382 (OUTLIER) cc_final: -0.0253 (tt) REVERT: Aq 173 PHE cc_start: 0.1621 (OUTLIER) cc_final: 0.1229 (t80) REVERT: Aq 694 GLU cc_start: 0.1120 (mt-10) cc_final: 0.0672 (tm-30) REVERT: Ar 60 HIS cc_start: 0.0330 (OUTLIER) cc_final: 0.0126 (t70) REVERT: Ar 71 LYS cc_start: 0.2977 (OUTLIER) cc_final: 0.2314 (tptp) REVERT: Ar 100 MET cc_start: 0.1560 (mmt) cc_final: 0.0447 (mmt) REVERT: Ar 128 HIS cc_start: 0.2784 (t70) cc_final: 0.1574 (t-170) REVERT: As 37 MET cc_start: -0.3084 (mtt) cc_final: -0.3380 (mmt) REVERT: As 128 HIS cc_start: 0.3470 (OUTLIER) cc_final: -0.0716 (t-170) REVERT: As 158 MET cc_start: 0.0722 (tpt) cc_final: 0.0336 (tpp) REVERT: Au 37 MET cc_start: -0.1533 (mtt) cc_final: -0.3040 (mmm) REVERT: Au 70 MET cc_start: 0.1128 (mtt) cc_final: 0.0606 (mtt) REVERT: Au 89 ASP cc_start: 0.0889 (OUTLIER) cc_final: -0.0411 (p0) REVERT: Aw 71 LYS cc_start: 0.6229 (tttt) cc_final: 0.5853 (tptp) REVERT: Ax 12 TYR cc_start: 0.3031 (t80) cc_final: 0.0193 (t80) REVERT: Ax 37 MET cc_start: -0.1883 (mtt) cc_final: -0.3390 (tpp) REVERT: Ax 50 ASN cc_start: 0.2675 (m-40) cc_final: 0.2386 (m110) REVERT: Ax 54 TYR cc_start: 0.6668 (t80) cc_final: 0.5348 (t80) outliers start: 111 outliers final: 60 residues processed: 474 average time/residue: 0.4680 time to fit residues: 368.7315 Evaluate side-chains 404 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 331 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 34 TYR Chi-restraints excluded: chain Aa residue 53 LYS Chi-restraints excluded: chain Ab residue 143 THR Chi-restraints excluded: chain Ab residue 209 LEU Chi-restraints excluded: chain Ab residue 393 ILE Chi-restraints excluded: chain Ab residue 494 PHE Chi-restraints excluded: chain Ab residue 553 VAL Chi-restraints excluded: chain Ab residue 604 ASP Chi-restraints excluded: chain Ab residue 641 TRP Chi-restraints excluded: chain Ab residue 670 VAL Chi-restraints excluded: chain Ac residue 118 HIS Chi-restraints excluded: chain Ad residue 41 PHE Chi-restraints excluded: chain Ad residue 53 LYS Chi-restraints excluded: chain Af residue 13 HIS Chi-restraints excluded: chain Af residue 28 LEU Chi-restraints excluded: chain Af residue 51 PHE Chi-restraints excluded: chain Ag residue 56 LEU Chi-restraints excluded: chain Ag residue 72 LEU Chi-restraints excluded: chain Ag residue 97 LEU Chi-restraints excluded: chain Ag residue 104 LEU Chi-restraints excluded: chain Ag residue 154 ASN Chi-restraints excluded: chain Ag residue 155 LEU Chi-restraints excluded: chain Ah residue 92 ASP Chi-restraints excluded: chain Ai residue 80 ILE Chi-restraints excluded: chain Ai residue 104 LEU Chi-restraints excluded: chain Aj residue 13 HIS Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 117 LEU Chi-restraints excluded: chain Aj residue 120 LEU Chi-restraints excluded: chain Ak residue 65 HIS Chi-restraints excluded: chain Ak residue 69 LEU Chi-restraints excluded: chain Ak residue 75 GLN Chi-restraints excluded: chain Al residue 51 PHE Chi-restraints excluded: chain Al residue 120 LEU Chi-restraints excluded: chain Am residue 37 MET Chi-restraints excluded: chain Am residue 82 LEU Chi-restraints excluded: chain Am residue 93 TRP Chi-restraints excluded: chain An residue 13 HIS Chi-restraints excluded: chain An residue 133 ILE Chi-restraints excluded: chain Ao residue 51 PHE Chi-restraints excluded: chain Ap residue 8 VAL Chi-restraints excluded: chain Ap residue 65 HIS Chi-restraints excluded: chain Ap residue 100 MET Chi-restraints excluded: chain Ap residue 104 LEU Chi-restraints excluded: chain Aq residue 141 THR Chi-restraints excluded: chain Aq residue 144 ILE Chi-restraints excluded: chain Aq residue 173 PHE Chi-restraints excluded: chain Aq residue 300 HIS Chi-restraints excluded: chain Aq residue 496 VAL Chi-restraints excluded: chain Aq residue 675 ASN Chi-restraints excluded: chain Ar residue 45 ASP Chi-restraints excluded: chain Ar residue 60 HIS Chi-restraints excluded: chain Ar residue 71 LYS Chi-restraints excluded: chain Ar residue 72 LEU Chi-restraints excluded: chain As residue 117 LEU Chi-restraints excluded: chain As residue 128 HIS Chi-restraints excluded: chain At residue 35 LEU Chi-restraints excluded: chain At residue 90 CYS Chi-restraints excluded: chain Au residue 89 ASP Chi-restraints excluded: chain Au residue 152 VAL Chi-restraints excluded: chain Av residue 51 PHE Chi-restraints excluded: chain Aw residue 46 VAL Chi-restraints excluded: chain Aw residue 72 LEU Chi-restraints excluded: chain Aw residue 105 HIS Chi-restraints excluded: chain Ax residue 28 LEU Chi-restraints excluded: chain Ax residue 65 HIS Chi-restraints excluded: chain Ax residue 131 ASP Chi-restraints excluded: chain Ax residue 158 MET Chi-restraints excluded: chain Ay residue 97 LEU Chi-restraints excluded: chain Ay residue 104 LEU Chi-restraints excluded: chain Ay residue 145 ILE Chi-restraints excluded: chain Az residue 36 SER Chi-restraints excluded: chain Az residue 133 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 429 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 384 optimal weight: 8.9990 chunk 212 optimal weight: 0.7980 chunk 440 optimal weight: 0.2980 chunk 356 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 263 optimal weight: 6.9990 chunk 463 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 173 HIS Ac 11 ASN ** Ac 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 73 GLN ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 151 HIS ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 60 HIS ** Ag 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 151 HIS ** Ah 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 57 HIS Ai 139 ASN Ai 151 HIS Aj 21 ASN ** Aj 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 74 ASN ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 136 HIS Am 25 ASN Am 173 HIS An 7 GLN An 13 HIS Ao 50 ASN Ap 14 GLN Aq 172 GLN ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 74 ASN ** As 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** At 112 GLN ** At 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 10 GLN ** Av 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 136 HIS Ax 25 ASN ** Ax 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 14 GLN ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 75 GLN Ay 173 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1870 moved from start: 0.6375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 44828 Z= 0.186 Angle : 0.566 8.639 60460 Z= 0.300 Chirality : 0.038 0.197 6432 Planarity : 0.004 0.048 7916 Dihedral : 4.761 29.544 5845 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.36 % Allowed : 7.99 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.11), residues: 5332 helix: 2.07 (0.08), residues: 3621 sheet: -0.40 (0.39), residues: 184 loop : -1.92 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPAy 93 HIS 0.016 0.001 HISAj 13 PHE 0.030 0.002 PHEAq 685 TYR 0.024 0.002 TYRAx 34 ARG 0.005 0.001 ARGAv 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 360 time to evaluate : 3.617 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: Aa 34 TYR cc_start: 0.0248 (OUTLIER) cc_final: 0.0039 (m-80) REVERT: Ab 131 LEU cc_start: 0.4279 (tp) cc_final: 0.3878 (mt) REVERT: Ab 679 MET cc_start: 0.2944 (mtt) cc_final: 0.2281 (tmm) REVERT: Ac 21 ASN cc_start: 0.1620 (OUTLIER) cc_final: 0.0794 (p0) REVERT: Ae 57 HIS cc_start: 0.0428 (OUTLIER) cc_final: -0.0928 (m-70) REVERT: Ae 98 ASN cc_start: 0.6641 (t0) cc_final: 0.5948 (p0) REVERT: Af 28 LEU cc_start: 0.3493 (OUTLIER) cc_final: 0.3185 (tp) REVERT: Af 39 TYR cc_start: 0.1468 (m-10) cc_final: 0.0587 (m-10) REVERT: Ag 41 PHE cc_start: 0.6977 (m-80) cc_final: 0.6591 (m-80) REVERT: Ag 119 LYS cc_start: 0.7616 (tmtt) cc_final: 0.7065 (ptpt) REVERT: Ah 161 PRO cc_start: 0.7071 (Cg_endo) cc_final: 0.6719 (Cg_exo) REVERT: Ai 6 SER cc_start: 0.0124 (OUTLIER) cc_final: -0.1154 (t) REVERT: Ai 70 MET cc_start: 0.4673 (mmt) cc_final: 0.4220 (mmt) REVERT: Aj 70 MET cc_start: 0.5099 (mmm) cc_final: 0.4723 (mmt) REVERT: Aj 158 MET cc_start: 0.5618 (mmm) cc_final: 0.1919 (tmm) REVERT: Al 117 LEU cc_start: -0.3089 (OUTLIER) cc_final: -0.3477 (mp) REVERT: Am 25 ASN cc_start: -0.3364 (OUTLIER) cc_final: -0.4267 (t0) REVERT: An 25 ASN cc_start: 0.4983 (t0) cc_final: 0.4742 (t0) REVERT: Ap 37 MET cc_start: 0.0159 (ttm) cc_final: -0.0097 (mtp) REVERT: Ap 48 LEU cc_start: 0.4294 (OUTLIER) cc_final: 0.3877 (tp) REVERT: Ap 100 MET cc_start: -0.1798 (OUTLIER) cc_final: -0.2462 (ptp) REVERT: Aq 173 PHE cc_start: 0.1624 (OUTLIER) cc_final: 0.1240 (t80) REVERT: Aq 542 PHE cc_start: 0.3533 (t80) cc_final: 0.3307 (t80) REVERT: Aq 694 GLU cc_start: 0.1524 (mt-10) cc_final: 0.1063 (tm-30) REVERT: Ar 128 HIS cc_start: 0.2130 (t70) cc_final: 0.0042 (t-170) REVERT: As 100 MET cc_start: 0.1075 (mmt) cc_final: -0.0573 (mmt) REVERT: As 128 HIS cc_start: 0.3659 (OUTLIER) cc_final: -0.0359 (t-170) REVERT: As 158 MET cc_start: 0.0085 (tpt) cc_final: -0.0144 (tpp) REVERT: Au 70 MET cc_start: 0.0771 (mtt) cc_final: 0.0378 (mtt) REVERT: Aw 49 LYS cc_start: 0.6634 (mptt) cc_final: 0.6308 (mptt) REVERT: Aw 60 HIS cc_start: 0.6725 (m170) cc_final: 0.6515 (m170) REVERT: Aw 71 LYS cc_start: 0.7178 (tttt) cc_final: 0.6416 (tptp) REVERT: Ax 37 MET cc_start: -0.1828 (mtt) cc_final: -0.2045 (mmt) REVERT: Ax 50 ASN cc_start: 0.3011 (m-40) cc_final: 0.2762 (m110) REVERT: Ax 54 TYR cc_start: 0.6845 (t80) cc_final: 0.5539 (t80) outliers start: 112 outliers final: 68 residues processed: 442 average time/residue: 0.4381 time to fit residues: 321.9424 Evaluate side-chains 412 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 333 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 34 TYR Chi-restraints excluded: chain Aa residue 53 LYS Chi-restraints excluded: chain Ab residue 143 THR Chi-restraints excluded: chain Ab residue 209 LEU Chi-restraints excluded: chain Ab residue 393 ILE Chi-restraints excluded: chain Ab residue 494 PHE Chi-restraints excluded: chain Ab residue 553 VAL Chi-restraints excluded: chain Ab residue 604 ASP Chi-restraints excluded: chain Ab residue 605 VAL Chi-restraints excluded: chain Ab residue 641 TRP Chi-restraints excluded: chain Ab residue 670 VAL Chi-restraints excluded: chain Ac residue 21 ASN Chi-restraints excluded: chain Ae residue 57 HIS Chi-restraints excluded: chain Af residue 13 HIS Chi-restraints excluded: chain Af residue 28 LEU Chi-restraints excluded: chain Af residue 114 LEU Chi-restraints excluded: chain Af residue 118 HIS Chi-restraints excluded: chain Af residue 142 VAL Chi-restraints excluded: chain Af residue 175 LEU Chi-restraints excluded: chain Ag residue 56 LEU Chi-restraints excluded: chain Ag residue 60 HIS Chi-restraints excluded: chain Ag residue 97 LEU Chi-restraints excluded: chain Ag residue 104 LEU Chi-restraints excluded: chain Ag residue 154 ASN Chi-restraints excluded: chain Ag residue 155 LEU Chi-restraints excluded: chain Ah residue 44 ASP Chi-restraints excluded: chain Ah residue 51 PHE Chi-restraints excluded: chain Ah residue 92 ASP Chi-restraints excluded: chain Ai residue 6 SER Chi-restraints excluded: chain Ai residue 80 ILE Chi-restraints excluded: chain Ai residue 104 LEU Chi-restraints excluded: chain Ai residue 122 THR Chi-restraints excluded: chain Aj residue 21 ASN Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 117 LEU Chi-restraints excluded: chain Aj residue 120 LEU Chi-restraints excluded: chain Aj residue 175 LEU Chi-restraints excluded: chain Ak residue 69 LEU Chi-restraints excluded: chain Al residue 51 PHE Chi-restraints excluded: chain Al residue 117 LEU Chi-restraints excluded: chain Al residue 120 LEU Chi-restraints excluded: chain Am residue 25 ASN Chi-restraints excluded: chain Am residue 41 PHE Chi-restraints excluded: chain Am residue 82 LEU Chi-restraints excluded: chain Am residue 93 TRP Chi-restraints excluded: chain An residue 117 LEU Chi-restraints excluded: chain An residue 133 ILE Chi-restraints excluded: chain Ao residue 6 SER Chi-restraints excluded: chain Ao residue 51 PHE Chi-restraints excluded: chain Ap residue 8 VAL Chi-restraints excluded: chain Ap residue 48 LEU Chi-restraints excluded: chain Ap residue 65 HIS Chi-restraints excluded: chain Ap residue 100 MET Chi-restraints excluded: chain Aq residue 141 THR Chi-restraints excluded: chain Aq residue 173 PHE Chi-restraints excluded: chain Aq residue 300 HIS Chi-restraints excluded: chain Aq residue 332 ILE Chi-restraints excluded: chain Aq residue 418 LYS Chi-restraints excluded: chain Aq residue 496 VAL Chi-restraints excluded: chain Aq residue 675 ASN Chi-restraints excluded: chain Ar residue 45 ASP Chi-restraints excluded: chain Ar residue 71 LYS Chi-restraints excluded: chain As residue 117 LEU Chi-restraints excluded: chain As residue 128 HIS Chi-restraints excluded: chain Au residue 71 LYS Chi-restraints excluded: chain Av residue 51 PHE Chi-restraints excluded: chain Av residue 158 MET Chi-restraints excluded: chain Aw residue 37 MET Chi-restraints excluded: chain Aw residue 105 HIS Chi-restraints excluded: chain Aw residue 109 ASN Chi-restraints excluded: chain Ax residue 28 LEU Chi-restraints excluded: chain Ax residue 51 PHE Chi-restraints excluded: chain Ax residue 131 ASP Chi-restraints excluded: chain Ax residue 158 MET Chi-restraints excluded: chain Ay residue 97 LEU Chi-restraints excluded: chain Ay residue 104 LEU Chi-restraints excluded: chain Az residue 36 SER Chi-restraints excluded: chain Az residue 133 ILE Chi-restraints excluded: chain Az residue 158 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 173 optimal weight: 10.0000 chunk 464 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 303 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 516 optimal weight: 7.9990 chunk 428 optimal weight: 9.9990 chunk 239 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 170 optimal weight: 7.9990 chunk 271 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 75 GLN Aa 136 HIS Ab 164 ASN ** Ac 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 105 HIS Ac 112 GLN Ac 141 GLN ** Ad 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 60 HIS ** Ad 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 65 HIS ** Ae 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 141 GLN ** Ae 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 11 ASN ** Ag 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 65 HIS Ag 73 GLN ** Ag 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 151 HIS Ah 25 ASN ** Ai 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 57 HIS Ai 141 GLN Ai 154 ASN ** Aj 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 60 HIS ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 151 HIS ** Ao 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 73 GLN Ap 105 HIS Ap 109 ASN ** Ap 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 234 HIS ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 75 GLN ** As 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** At 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 136 HIS At 141 GLN ** Au 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Au 23 GLN ** Au 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Au 136 HIS Av 105 HIS ** Av 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 141 GLN ** Aw 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 60 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2414 moved from start: 0.8620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 44828 Z= 0.350 Angle : 0.899 19.340 60460 Z= 0.470 Chirality : 0.049 0.327 6432 Planarity : 0.006 0.100 7916 Dihedral : 6.056 35.964 5845 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.88 % Allowed : 9.70 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.11), residues: 5332 helix: 0.57 (0.08), residues: 3591 sheet: -0.51 (0.38), residues: 182 loop : -2.14 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPAz 93 HIS 0.044 0.002 HISAg 60 PHE 0.038 0.003 PHEAu 41 TYR 0.048 0.003 TYRAf 39 ARG 0.011 0.001 ARGAr 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 396 time to evaluate : 3.644 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: Aa 34 TYR cc_start: 0.0400 (OUTLIER) cc_final: -0.0256 (m-80) REVERT: Aa 53 LYS cc_start: -0.0558 (OUTLIER) cc_final: -0.1249 (ttpt) REVERT: Ab 131 LEU cc_start: 0.4307 (tp) cc_final: 0.4066 (mm) REVERT: Ab 234 HIS cc_start: -0.1375 (t-90) cc_final: -0.2520 (t70) REVERT: Ab 243 PHE cc_start: 0.2148 (m-80) cc_final: 0.1901 (m-80) REVERT: Ab 282 TYR cc_start: 0.3777 (OUTLIER) cc_final: 0.2314 (p90) REVERT: Ab 436 MET cc_start: -0.1369 (mmt) cc_final: -0.2056 (mtp) REVERT: Ab 669 PHE cc_start: 0.1891 (t80) cc_final: 0.1526 (t80) REVERT: Ab 679 MET cc_start: 0.3842 (mtt) cc_final: 0.3326 (tmm) REVERT: Ad 41 PHE cc_start: 0.1171 (OUTLIER) cc_final: 0.0519 (m-10) REVERT: Ae 37 MET cc_start: -0.0823 (mtt) cc_final: -0.2381 (tpt) REVERT: Ae 57 HIS cc_start: 0.0924 (OUTLIER) cc_final: -0.0340 (t70) REVERT: Ae 98 ASN cc_start: 0.6313 (t0) cc_final: 0.5275 (p0) REVERT: Af 70 MET cc_start: 0.5429 (mmt) cc_final: 0.5018 (mmt) REVERT: Af 100 MET cc_start: 0.5165 (OUTLIER) cc_final: 0.4886 (tmm) REVERT: Ag 75 GLN cc_start: 0.3442 (OUTLIER) cc_final: 0.2668 (tt0) REVERT: Ag 119 LYS cc_start: 0.7947 (tmtt) cc_final: 0.7303 (ptpt) REVERT: Ai 58 GLN cc_start: 0.5749 (tp40) cc_final: 0.3615 (tp40) REVERT: Ai 61 GLU cc_start: 0.4721 (mt-10) cc_final: 0.4464 (tt0) REVERT: Ai 118 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.7099 (t70) REVERT: Ai 155 LEU cc_start: 0.5924 (mt) cc_final: 0.5600 (mt) REVERT: Aj 58 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7628 (tm-30) REVERT: Aj 116 GLU cc_start: 0.6441 (mt-10) cc_final: 0.6049 (mm-30) REVERT: Aj 123 ASP cc_start: 0.6459 (m-30) cc_final: 0.5909 (m-30) REVERT: Aj 158 MET cc_start: 0.4754 (mmm) cc_final: 0.1313 (tmm) REVERT: Ak 34 TYR cc_start: 0.0602 (OUTLIER) cc_final: -0.1161 (m-80) REVERT: Al 60 HIS cc_start: -0.1086 (OUTLIER) cc_final: -0.2315 (m170) REVERT: Al 117 LEU cc_start: -0.3310 (OUTLIER) cc_final: -0.3727 (mp) REVERT: Am 93 TRP cc_start: 0.4722 (OUTLIER) cc_final: 0.3379 (m100) REVERT: An 9 ARG cc_start: 0.3834 (ptt-90) cc_final: 0.3458 (ptt180) REVERT: An 25 ASN cc_start: 0.5333 (t0) cc_final: 0.5107 (t0) REVERT: Ap 12 TYR cc_start: 0.1464 (t80) cc_final: 0.0669 (t80) REVERT: Ap 37 MET cc_start: 0.0181 (ttm) cc_final: -0.0240 (mtm) REVERT: Ap 48 LEU cc_start: 0.4847 (OUTLIER) cc_final: 0.4259 (tp) REVERT: Ap 75 GLN cc_start: -0.0541 (OUTLIER) cc_final: -0.1460 (mt0) REVERT: Aq 173 PHE cc_start: 0.1543 (OUTLIER) cc_final: 0.1211 (t80) REVERT: Aq 208 ARG cc_start: 0.0961 (mtm-85) cc_final: 0.0755 (tpt170) REVERT: Aq 694 GLU cc_start: 0.1618 (mt-10) cc_final: 0.1186 (tm-30) REVERT: Ar 45 ASP cc_start: 0.3973 (OUTLIER) cc_final: 0.3620 (p0) REVERT: Ar 71 LYS cc_start: 0.2967 (OUTLIER) cc_final: 0.1245 (tppt) REVERT: Ar 75 GLN cc_start: 0.7607 (mt0) cc_final: 0.7057 (mt0) REVERT: As 21 ASN cc_start: 0.6301 (OUTLIER) cc_final: 0.6022 (p0) REVERT: As 45 ASP cc_start: 0.2946 (OUTLIER) cc_final: 0.1614 (p0) REVERT: As 100 MET cc_start: 0.1066 (mmt) cc_final: -0.1226 (mmt) REVERT: As 128 HIS cc_start: 0.3644 (OUTLIER) cc_final: -0.0254 (t-170) REVERT: As 158 MET cc_start: 0.0983 (tpt) cc_final: 0.0676 (tpp) REVERT: Au 37 MET cc_start: -0.2713 (mtt) cc_final: -0.3150 (mmp) REVERT: Au 45 ASP cc_start: 0.0423 (OUTLIER) cc_final: -0.0142 (p0) REVERT: Au 70 MET cc_start: 0.1113 (mtt) cc_final: 0.0708 (mtt) REVERT: Au 89 ASP cc_start: 0.0702 (OUTLIER) cc_final: -0.0839 (p0) REVERT: Aw 60 HIS cc_start: 0.6602 (m170) cc_final: 0.6310 (m170) REVERT: Aw 100 MET cc_start: 0.7308 (mtt) cc_final: 0.5144 (tmm) REVERT: Ax 50 ASN cc_start: 0.3611 (m-40) cc_final: 0.3240 (m-40) REVERT: Ay 137 TYR cc_start: 0.6119 (m-10) cc_final: 0.5887 (m-80) REVERT: Ay 143 LYS cc_start: 0.6560 (tmtt) cc_final: 0.6348 (mmmt) REVERT: Az 83 GLN cc_start: 0.1477 (mm-40) cc_final: 0.1195 (mm-40) outliers start: 137 outliers final: 68 residues processed: 494 average time/residue: 0.4431 time to fit residues: 364.2646 Evaluate side-chains 424 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 334 time to evaluate : 3.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 34 TYR Chi-restraints excluded: chain Aa residue 53 LYS Chi-restraints excluded: chain Ab residue 143 THR Chi-restraints excluded: chain Ab residue 146 LEU Chi-restraints excluded: chain Ab residue 206 ASN Chi-restraints excluded: chain Ab residue 209 LEU Chi-restraints excluded: chain Ab residue 282 TYR Chi-restraints excluded: chain Ab residue 393 ILE Chi-restraints excluded: chain Ab residue 553 VAL Chi-restraints excluded: chain Ab residue 604 ASP Chi-restraints excluded: chain Ab residue 641 TRP Chi-restraints excluded: chain Ab residue 670 VAL Chi-restraints excluded: chain Ac residue 21 ASN Chi-restraints excluded: chain Ac residue 41 PHE Chi-restraints excluded: chain Ad residue 41 PHE Chi-restraints excluded: chain Ad residue 53 LYS Chi-restraints excluded: chain Ae residue 57 HIS Chi-restraints excluded: chain Af residue 13 HIS Chi-restraints excluded: chain Af residue 100 MET Chi-restraints excluded: chain Af residue 114 LEU Chi-restraints excluded: chain Af residue 118 HIS Chi-restraints excluded: chain Af residue 142 VAL Chi-restraints excluded: chain Af residue 175 LEU Chi-restraints excluded: chain Ag residue 56 LEU Chi-restraints excluded: chain Ag residue 75 GLN Chi-restraints excluded: chain Ag residue 97 LEU Chi-restraints excluded: chain Ag residue 154 ASN Chi-restraints excluded: chain Ag residue 155 LEU Chi-restraints excluded: chain Ah residue 25 ASN Chi-restraints excluded: chain Ah residue 44 ASP Chi-restraints excluded: chain Ah residue 51 PHE Chi-restraints excluded: chain Ai residue 54 TYR Chi-restraints excluded: chain Ai residue 104 LEU Chi-restraints excluded: chain Ai residue 118 HIS Chi-restraints excluded: chain Ai residue 122 THR Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 117 LEU Chi-restraints excluded: chain Aj residue 139 ASN Chi-restraints excluded: chain Aj residue 142 VAL Chi-restraints excluded: chain Ak residue 34 TYR Chi-restraints excluded: chain Ak residue 65 HIS Chi-restraints excluded: chain Ak residue 69 LEU Chi-restraints excluded: chain Al residue 51 PHE Chi-restraints excluded: chain Al residue 60 HIS Chi-restraints excluded: chain Al residue 117 LEU Chi-restraints excluded: chain Al residue 120 LEU Chi-restraints excluded: chain Am residue 41 PHE Chi-restraints excluded: chain Am residue 82 LEU Chi-restraints excluded: chain Am residue 93 TRP Chi-restraints excluded: chain An residue 33 VAL Chi-restraints excluded: chain An residue 133 ILE Chi-restraints excluded: chain Ao residue 6 SER Chi-restraints excluded: chain Ao residue 51 PHE Chi-restraints excluded: chain Ap residue 8 VAL Chi-restraints excluded: chain Ap residue 48 LEU Chi-restraints excluded: chain Ap residue 65 HIS Chi-restraints excluded: chain Ap residue 75 GLN Chi-restraints excluded: chain Aq residue 141 THR Chi-restraints excluded: chain Aq residue 173 PHE Chi-restraints excluded: chain Aq residue 300 HIS Chi-restraints excluded: chain Aq residue 332 ILE Chi-restraints excluded: chain Aq residue 418 LYS Chi-restraints excluded: chain Aq residue 675 ASN Chi-restraints excluded: chain Ar residue 45 ASP Chi-restraints excluded: chain Ar residue 70 MET Chi-restraints excluded: chain Ar residue 71 LYS Chi-restraints excluded: chain Ar residue 72 LEU Chi-restraints excluded: chain As residue 21 ASN Chi-restraints excluded: chain As residue 45 ASP Chi-restraints excluded: chain As residue 117 LEU Chi-restraints excluded: chain As residue 128 HIS Chi-restraints excluded: chain At residue 80 ILE Chi-restraints excluded: chain Au residue 45 ASP Chi-restraints excluded: chain Au residue 71 LYS Chi-restraints excluded: chain Au residue 89 ASP Chi-restraints excluded: chain Av residue 51 PHE Chi-restraints excluded: chain Aw residue 37 MET Chi-restraints excluded: chain Aw residue 109 ASN Chi-restraints excluded: chain Aw residue 110 VAL Chi-restraints excluded: chain Ax residue 25 ASN Chi-restraints excluded: chain Ax residue 28 LEU Chi-restraints excluded: chain Ax residue 48 LEU Chi-restraints excluded: chain Ax residue 51 PHE Chi-restraints excluded: chain Ax residue 158 MET Chi-restraints excluded: chain Ay residue 97 LEU Chi-restraints excluded: chain Ay residue 104 LEU Chi-restraints excluded: chain Ay residue 109 ASN Chi-restraints excluded: chain Ay residue 145 ILE Chi-restraints excluded: chain Az residue 36 SER Chi-restraints excluded: chain Az residue 133 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 498 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 294 optimal weight: 0.9990 chunk 377 optimal weight: 20.0000 chunk 292 optimal weight: 0.9990 chunk 434 optimal weight: 4.9990 chunk 288 optimal weight: 0.9980 chunk 514 optimal weight: 3.9990 chunk 322 optimal weight: 6.9990 chunk 313 optimal weight: 0.9990 chunk 237 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 65 HIS Aa 75 GLN Ac 105 HIS Ac 109 ASN Ad 7 GLN ** Ad 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 11 ASN ** Ae 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 7 GLN ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 58 GLN ** Ag 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 65 HIS ** Ah 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 154 ASN Aj 11 ASN ** Aj 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 141 GLN An 151 HIS ** Ao 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 109 ASN ** Ap 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 215 ASN Aq 300 HIS ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 128 HIS ** As 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Au 136 HIS Av 7 GLN Aw 65 HIS Aw 141 GLN ** Ax 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 7 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2121 moved from start: 0.8360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 44828 Z= 0.159 Angle : 0.568 12.630 60460 Z= 0.295 Chirality : 0.038 0.179 6432 Planarity : 0.004 0.085 7916 Dihedral : 4.973 32.161 5845 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.89 % Allowed : 11.88 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.11), residues: 5332 helix: 1.70 (0.08), residues: 3600 sheet: -0.21 (0.40), residues: 177 loop : -1.95 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPAp 93 HIS 0.011 0.001 HISAy 60 PHE 0.026 0.001 PHEAb 433 TYR 0.044 0.002 TYRAx 29 ARG 0.007 0.000 ARGAn 9 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 362 time to evaluate : 3.754 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: Ab 131 LEU cc_start: 0.4409 (tp) cc_final: 0.4081 (mm) REVERT: Ab 234 HIS cc_start: -0.1479 (t-90) cc_final: -0.3043 (t-90) REVERT: Ab 243 PHE cc_start: 0.2024 (m-80) cc_final: 0.1785 (m-80) REVERT: Ab 282 TYR cc_start: 0.3621 (OUTLIER) cc_final: 0.2187 (p90) REVERT: Ab 679 MET cc_start: 0.3838 (mtt) cc_final: 0.3308 (tmm) REVERT: Ad 41 PHE cc_start: 0.1201 (OUTLIER) cc_final: 0.0313 (m-10) REVERT: Ae 57 HIS cc_start: 0.0262 (OUTLIER) cc_final: -0.1009 (m-70) REVERT: Ae 98 ASN cc_start: 0.6144 (t0) cc_final: 0.5390 (p0) REVERT: Af 158 MET cc_start: 0.0410 (ptt) cc_final: 0.0012 (ptt) REVERT: Ag 73 GLN cc_start: 0.5414 (tp40) cc_final: 0.5096 (tt0) REVERT: Ag 119 LYS cc_start: 0.8062 (tmtt) cc_final: 0.7396 (ptpt) REVERT: Aj 70 MET cc_start: 0.4841 (mmt) cc_final: 0.3741 (mmt) REVERT: Aj 116 GLU cc_start: 0.6127 (mt-10) cc_final: 0.5812 (mm-30) REVERT: Aj 158 MET cc_start: 0.4422 (mmm) cc_final: 0.1099 (tmm) REVERT: Al 117 LEU cc_start: -0.3288 (OUTLIER) cc_final: -0.3614 (mp) REVERT: Al 158 MET cc_start: -0.3249 (tpt) cc_final: -0.3465 (tpt) REVERT: Am 168 TYR cc_start: -0.0363 (t80) cc_final: -0.1209 (t80) REVERT: Ap 12 TYR cc_start: 0.1749 (t80) cc_final: 0.0874 (t80) REVERT: Ap 37 MET cc_start: -0.0145 (ttm) cc_final: -0.0486 (mtm) REVERT: Aq 173 PHE cc_start: 0.2308 (OUTLIER) cc_final: 0.2019 (t80) REVERT: Aq 208 ARG cc_start: 0.1059 (mtm-85) cc_final: 0.0781 (tpt170) REVERT: Aq 694 GLU cc_start: 0.1514 (mt-10) cc_final: 0.1140 (tm-30) REVERT: Ar 71 LYS cc_start: 0.2178 (OUTLIER) cc_final: 0.1270 (tppt) REVERT: Ar 100 MET cc_start: 0.1715 (mmt) cc_final: 0.0610 (mmt) REVERT: As 158 MET cc_start: 0.0589 (tpt) cc_final: -0.0052 (tpp) REVERT: At 70 MET cc_start: -0.2479 (mmm) cc_final: -0.3819 (mmm) REVERT: Au 70 MET cc_start: 0.0494 (mtt) cc_final: 0.0255 (mtm) REVERT: Aw 60 HIS cc_start: 0.6379 (m170) cc_final: 0.6074 (m170) REVERT: Aw 100 MET cc_start: 0.6983 (mtt) cc_final: 0.5193 (tmm) REVERT: Aw 116 GLU cc_start: 0.7632 (pp20) cc_final: 0.7191 (mm-30) REVERT: Aw 132 PHE cc_start: 0.7342 (t80) cc_final: 0.6502 (t80) REVERT: Ax 48 LEU cc_start: 0.2691 (OUTLIER) cc_final: 0.2065 (tp) REVERT: Ax 50 ASN cc_start: 0.3606 (m-40) cc_final: 0.2678 (m-40) REVERT: Ax 54 TYR cc_start: 0.6911 (t80) cc_final: 0.5531 (t80) REVERT: Ay 65 HIS cc_start: 0.6588 (m170) cc_final: 0.5954 (m-70) REVERT: Ay 137 TYR cc_start: 0.5367 (m-10) cc_final: 0.5041 (m-80) REVERT: Az 83 GLN cc_start: 0.1110 (mm-40) cc_final: 0.0783 (mm-40) outliers start: 90 outliers final: 60 residues processed: 426 average time/residue: 0.4451 time to fit residues: 314.8445 Evaluate side-chains 402 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 335 time to evaluate : 4.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 LYS Chi-restraints excluded: chain Ab residue 143 THR Chi-restraints excluded: chain Ab residue 146 LEU Chi-restraints excluded: chain Ab residue 206 ASN Chi-restraints excluded: chain Ab residue 209 LEU Chi-restraints excluded: chain Ab residue 282 TYR Chi-restraints excluded: chain Ab residue 494 PHE Chi-restraints excluded: chain Ab residue 553 VAL Chi-restraints excluded: chain Ab residue 605 VAL Chi-restraints excluded: chain Ab residue 641 TRP Chi-restraints excluded: chain Ab residue 670 VAL Chi-restraints excluded: chain Ac residue 21 ASN Chi-restraints excluded: chain Ac residue 41 PHE Chi-restraints excluded: chain Ad residue 41 PHE Chi-restraints excluded: chain Ae residue 57 HIS Chi-restraints excluded: chain Af residue 13 HIS Chi-restraints excluded: chain Af residue 114 LEU Chi-restraints excluded: chain Af residue 142 VAL Chi-restraints excluded: chain Ag residue 75 GLN Chi-restraints excluded: chain Ag residue 97 LEU Chi-restraints excluded: chain Ag residue 145 ILE Chi-restraints excluded: chain Ai residue 13 HIS Chi-restraints excluded: chain Ai residue 54 TYR Chi-restraints excluded: chain Ai residue 76 ARG Chi-restraints excluded: chain Ai residue 104 LEU Chi-restraints excluded: chain Ai residue 122 THR Chi-restraints excluded: chain Ai residue 137 TYR Chi-restraints excluded: chain Ai residue 168 TYR Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 117 LEU Chi-restraints excluded: chain Ak residue 65 HIS Chi-restraints excluded: chain Ak residue 69 LEU Chi-restraints excluded: chain Al residue 117 LEU Chi-restraints excluded: chain Al residue 120 LEU Chi-restraints excluded: chain Am residue 41 PHE Chi-restraints excluded: chain Am residue 42 ASP Chi-restraints excluded: chain Am residue 82 LEU Chi-restraints excluded: chain Ao residue 51 PHE Chi-restraints excluded: chain Ap residue 8 VAL Chi-restraints excluded: chain Ap residue 65 HIS Chi-restraints excluded: chain Aq residue 141 THR Chi-restraints excluded: chain Aq residue 173 PHE Chi-restraints excluded: chain Aq residue 300 HIS Chi-restraints excluded: chain Aq residue 332 ILE Chi-restraints excluded: chain Aq residue 403 VAL Chi-restraints excluded: chain Aq residue 418 LYS Chi-restraints excluded: chain Aq residue 488 VAL Chi-restraints excluded: chain Aq residue 675 ASN Chi-restraints excluded: chain Ar residue 45 ASP Chi-restraints excluded: chain Ar residue 71 LYS Chi-restraints excluded: chain As residue 117 LEU Chi-restraints excluded: chain As residue 128 HIS Chi-restraints excluded: chain At residue 80 ILE Chi-restraints excluded: chain Av residue 51 PHE Chi-restraints excluded: chain Aw residue 37 MET Chi-restraints excluded: chain Aw residue 64 GLU Chi-restraints excluded: chain Aw residue 109 ASN Chi-restraints excluded: chain Ax residue 25 ASN Chi-restraints excluded: chain Ax residue 28 LEU Chi-restraints excluded: chain Ax residue 48 LEU Chi-restraints excluded: chain Ax residue 51 PHE Chi-restraints excluded: chain Ay residue 72 LEU Chi-restraints excluded: chain Ay residue 104 LEU Chi-restraints excluded: chain Ay residue 109 ASN Chi-restraints excluded: chain Ay residue 145 ILE Chi-restraints excluded: chain Az residue 72 LEU Chi-restraints excluded: chain Az residue 158 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 318 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 307 optimal weight: 0.8980 chunk 155 optimal weight: 0.0770 chunk 101 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 327 optimal weight: 7.9990 chunk 350 optimal weight: 30.0000 chunk 254 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 404 optimal weight: 9.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 75 GLN ** Ae 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 58 GLN ** Ag 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 98 ASN Ah 25 ASN ** Ah 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 65 HIS Aj 21 ASN ** Aj 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 74 ASN ** Ao 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 57 HIS ** Ar 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 74 ASN ** As 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** At 25 ASN ** Au 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 21 ASN Aw 65 HIS ** Ax 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 11 ASN ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2077 moved from start: 0.8417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 44828 Z= 0.144 Angle : 0.533 11.277 60460 Z= 0.274 Chirality : 0.037 0.174 6432 Planarity : 0.004 0.072 7916 Dihedral : 4.609 31.371 5845 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.85 % Allowed : 12.39 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.12), residues: 5332 helix: 2.23 (0.08), residues: 3621 sheet: -0.13 (0.40), residues: 183 loop : -1.84 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAq 453 HIS 0.013 0.001 HISAy 60 PHE 0.040 0.001 PHEAb 433 TYR 0.034 0.001 TYRAw 34 ARG 0.003 0.000 ARGAv 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 355 time to evaluate : 3.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 131 LEU cc_start: 0.4206 (tp) cc_final: 0.3945 (mp) REVERT: Ab 234 HIS cc_start: -0.1595 (t-90) cc_final: -0.2431 (t70) REVERT: Ab 282 TYR cc_start: 0.3517 (OUTLIER) cc_final: 0.2252 (p90) REVERT: Ab 436 MET cc_start: -0.0654 (mmm) cc_final: -0.1391 (ttt) REVERT: Ab 679 MET cc_start: 0.4008 (mtt) cc_final: 0.3400 (tmm) REVERT: Ac 100 MET cc_start: -0.0518 (mmm) cc_final: -0.0748 (mmm) REVERT: Ad 41 PHE cc_start: 0.0880 (OUTLIER) cc_final: 0.0113 (m-10) REVERT: Ad 70 MET cc_start: 0.3296 (mmm) cc_final: 0.1207 (tpp) REVERT: Ae 98 ASN cc_start: 0.6685 (t0) cc_final: 0.5803 (p0) REVERT: Ae 100 MET cc_start: -0.2768 (ttp) cc_final: -0.3065 (ttp) REVERT: Af 39 TYR cc_start: 0.2984 (m-10) cc_final: 0.2306 (m-80) REVERT: Af 117 LEU cc_start: 0.6341 (pp) cc_final: 0.5953 (tt) REVERT: Af 158 MET cc_start: 0.0402 (ptt) cc_final: 0.0112 (ptt) REVERT: Ag 41 PHE cc_start: 0.7540 (m-80) cc_final: 0.7270 (m-80) REVERT: Ag 73 GLN cc_start: 0.5430 (tp40) cc_final: 0.5095 (tt0) REVERT: Ag 119 LYS cc_start: 0.8042 (tmtt) cc_final: 0.7397 (ptpt) REVERT: Ai 134 GLU cc_start: 0.3440 (mt-10) cc_final: 0.3208 (mt-10) REVERT: Aj 58 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7968 (tm-30) REVERT: Aj 70 MET cc_start: 0.4784 (mmt) cc_final: 0.3878 (mmt) REVERT: Aj 76 ARG cc_start: 0.5228 (mmp80) cc_final: 0.2660 (ttp80) REVERT: Aj 116 GLU cc_start: 0.6168 (mt-10) cc_final: 0.5909 (mm-30) REVERT: Aj 158 MET cc_start: 0.4329 (mmm) cc_final: 0.1022 (tmm) REVERT: Al 117 LEU cc_start: -0.3273 (OUTLIER) cc_final: -0.3650 (mp) REVERT: Am 168 TYR cc_start: -0.0381 (t80) cc_final: -0.1172 (t80) REVERT: Ao 51 PHE cc_start: 0.1512 (OUTLIER) cc_final: 0.0829 (m-10) REVERT: Ap 12 TYR cc_start: 0.1751 (t80) cc_final: 0.0759 (t80) REVERT: Ap 37 MET cc_start: -0.0245 (ttm) cc_final: -0.0501 (mtp) REVERT: Aq 173 PHE cc_start: 0.2315 (OUTLIER) cc_final: 0.2043 (t80) REVERT: Aq 208 ARG cc_start: 0.0992 (mtm-85) cc_final: 0.0595 (tpt170) REVERT: Aq 300 HIS cc_start: 0.1068 (OUTLIER) cc_final: 0.0516 (p-80) REVERT: Aq 396 PHE cc_start: 0.2365 (p90) cc_final: 0.1656 (m-80) REVERT: Aq 694 GLU cc_start: 0.1774 (mt-10) cc_final: 0.1215 (tm-30) REVERT: Ar 71 LYS cc_start: 0.2031 (OUTLIER) cc_final: 0.1187 (tppt) REVERT: Ar 100 MET cc_start: 0.1571 (mmt) cc_final: 0.0480 (mmt) REVERT: Ar 128 HIS cc_start: 0.3292 (OUTLIER) cc_final: 0.0176 (t-170) REVERT: As 45 ASP cc_start: 0.2088 (OUTLIER) cc_final: 0.0675 (p0) REVERT: As 158 MET cc_start: 0.0695 (tpt) cc_final: 0.0405 (tpp) REVERT: Au 70 MET cc_start: 0.0284 (mtt) cc_final: -0.0259 (mtt) REVERT: Aw 60 HIS cc_start: 0.6071 (m170) cc_final: 0.5661 (m170) REVERT: Aw 100 MET cc_start: 0.6745 (mtt) cc_final: 0.5085 (tmm) REVERT: Ax 37 MET cc_start: 0.0794 (mmt) cc_final: -0.1923 (tpp) REVERT: Ax 48 LEU cc_start: 0.2552 (mt) cc_final: 0.2129 (tp) REVERT: Ax 50 ASN cc_start: 0.3535 (m-40) cc_final: 0.3143 (m-40) REVERT: Ax 54 TYR cc_start: 0.6888 (t80) cc_final: 0.5591 (t80) REVERT: Ay 65 HIS cc_start: 0.6683 (m170) cc_final: 0.6224 (m170) REVERT: Ay 137 TYR cc_start: 0.5316 (m-10) cc_final: 0.4989 (m-80) outliers start: 88 outliers final: 58 residues processed: 418 average time/residue: 0.4400 time to fit residues: 306.3920 Evaluate side-chains 404 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 337 time to evaluate : 4.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 LYS Chi-restraints excluded: chain Ab residue 143 THR Chi-restraints excluded: chain Ab residue 146 LEU Chi-restraints excluded: chain Ab residue 206 ASN Chi-restraints excluded: chain Ab residue 209 LEU Chi-restraints excluded: chain Ab residue 250 VAL Chi-restraints excluded: chain Ab residue 282 TYR Chi-restraints excluded: chain Ab residue 365 MET Chi-restraints excluded: chain Ab residue 372 ASN Chi-restraints excluded: chain Ab residue 494 PHE Chi-restraints excluded: chain Ab residue 553 VAL Chi-restraints excluded: chain Ab residue 605 VAL Chi-restraints excluded: chain Ab residue 641 TRP Chi-restraints excluded: chain Ab residue 670 VAL Chi-restraints excluded: chain Ac residue 21 ASN Chi-restraints excluded: chain Ad residue 41 PHE Chi-restraints excluded: chain Ad residue 53 LYS Chi-restraints excluded: chain Af residue 13 HIS Chi-restraints excluded: chain Af residue 114 LEU Chi-restraints excluded: chain Af residue 142 VAL Chi-restraints excluded: chain Ag residue 97 LEU Chi-restraints excluded: chain Ag residue 145 ILE Chi-restraints excluded: chain Ag residue 154 ASN Chi-restraints excluded: chain Ag residue 155 LEU Chi-restraints excluded: chain Ah residue 25 ASN Chi-restraints excluded: chain Ai residue 54 TYR Chi-restraints excluded: chain Ai residue 104 LEU Chi-restraints excluded: chain Ai residue 114 LEU Chi-restraints excluded: chain Ai residue 168 TYR Chi-restraints excluded: chain Aj residue 21 ASN Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 104 LEU Chi-restraints excluded: chain Ak residue 65 HIS Chi-restraints excluded: chain Ak residue 69 LEU Chi-restraints excluded: chain Al residue 117 LEU Chi-restraints excluded: chain Al residue 120 LEU Chi-restraints excluded: chain Am residue 41 PHE Chi-restraints excluded: chain Am residue 42 ASP Chi-restraints excluded: chain Ao residue 51 PHE Chi-restraints excluded: chain Ap residue 8 VAL Chi-restraints excluded: chain Ap residue 65 HIS Chi-restraints excluded: chain Aq residue 173 PHE Chi-restraints excluded: chain Aq residue 300 HIS Chi-restraints excluded: chain Aq residue 332 ILE Chi-restraints excluded: chain Aq residue 403 VAL Chi-restraints excluded: chain Aq residue 418 LYS Chi-restraints excluded: chain Aq residue 488 VAL Chi-restraints excluded: chain Aq residue 675 ASN Chi-restraints excluded: chain Ar residue 45 ASP Chi-restraints excluded: chain Ar residue 71 LYS Chi-restraints excluded: chain Ar residue 128 HIS Chi-restraints excluded: chain As residue 13 HIS Chi-restraints excluded: chain As residue 45 ASP Chi-restraints excluded: chain As residue 117 LEU Chi-restraints excluded: chain As residue 128 HIS Chi-restraints excluded: chain At residue 80 ILE Chi-restraints excluded: chain Av residue 51 PHE Chi-restraints excluded: chain Aw residue 37 MET Chi-restraints excluded: chain Aw residue 109 ASN Chi-restraints excluded: chain Aw residue 155 LEU Chi-restraints excluded: chain Ax residue 28 LEU Chi-restraints excluded: chain Ay residue 104 LEU Chi-restraints excluded: chain Ay residue 109 ASN Chi-restraints excluded: chain Ay residue 155 LEU Chi-restraints excluded: chain Az residue 51 PHE Chi-restraints excluded: chain Az residue 72 LEU Chi-restraints excluded: chain Az residue 158 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 468 optimal weight: 7.9990 chunk 493 optimal weight: 5.9990 chunk 449 optimal weight: 7.9990 chunk 479 optimal weight: 10.0000 chunk 492 optimal weight: 0.9980 chunk 288 optimal weight: 0.9990 chunk 208 optimal weight: 10.0000 chunk 376 optimal weight: 6.9990 chunk 147 optimal weight: 0.3980 chunk 433 optimal weight: 7.9990 chunk 453 optimal weight: 0.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 626 ASN ** Ac 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 11 ASN ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 65 HIS Ag 141 GLN Ah 25 ASN ** Ah 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 300 HIS ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 57 HIS ** Ar 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 112 GLN ** As 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Av 7 GLN Av 11 ASN ** Aw 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 154 ASN ** Ax 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 11 ASN Ay 65 HIS ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2207 moved from start: 0.8867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 44828 Z= 0.181 Angle : 0.594 14.693 60460 Z= 0.304 Chirality : 0.038 0.197 6432 Planarity : 0.004 0.067 7916 Dihedral : 4.771 32.558 5845 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.91 % Allowed : 12.60 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.11), residues: 5332 helix: 2.05 (0.08), residues: 3621 sheet: -0.10 (0.40), residues: 183 loop : -1.84 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAy 93 HIS 0.014 0.001 HISAy 60 PHE 0.021 0.002 PHEAw 55 TYR 0.041 0.002 TYRAy 34 ARG 0.006 0.000 ARGAi 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 366 time to evaluate : 3.585 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: Ab 131 LEU cc_start: 0.4223 (tp) cc_final: 0.3904 (mp) REVERT: Ab 234 HIS cc_start: -0.1669 (t-90) cc_final: -0.2952 (t-90) REVERT: Ab 243 PHE cc_start: 0.2119 (m-80) cc_final: 0.1849 (m-80) REVERT: Ab 282 TYR cc_start: 0.3818 (OUTLIER) cc_final: 0.2271 (p90) REVERT: Ab 353 CYS cc_start: -0.1516 (p) cc_final: -0.1823 (t) REVERT: Ab 433 PHE cc_start: 0.3374 (t80) cc_final: 0.2831 (m-80) REVERT: Ab 436 MET cc_start: -0.0772 (mmm) cc_final: -0.1476 (ttt) REVERT: Ab 679 MET cc_start: 0.4043 (mtt) cc_final: 0.3414 (tmm) REVERT: Ad 41 PHE cc_start: 0.0850 (OUTLIER) cc_final: 0.0260 (m-10) REVERT: Ad 70 MET cc_start: 0.3370 (mmm) cc_final: 0.1475 (tpt) REVERT: Ae 37 MET cc_start: 0.1107 (mmt) cc_final: 0.0320 (mmt) REVERT: Ae 65 HIS cc_start: 0.2767 (m-70) cc_final: 0.2481 (m-70) REVERT: Ae 98 ASN cc_start: 0.6593 (t0) cc_final: 0.5720 (p0) REVERT: Ae 100 MET cc_start: -0.2638 (ttp) cc_final: -0.2991 (ttp) REVERT: Af 117 LEU cc_start: 0.6446 (pp) cc_final: 0.6096 (tt) REVERT: Af 137 TYR cc_start: 0.5069 (m-80) cc_final: 0.4727 (m-80) REVERT: Af 158 MET cc_start: 0.0260 (ptt) cc_final: -0.0016 (ptt) REVERT: Ag 67 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7903 (pp20) REVERT: Ag 73 GLN cc_start: 0.4960 (tp40) cc_final: 0.4703 (tt0) REVERT: Ag 119 LYS cc_start: 0.8056 (tmtt) cc_final: 0.7368 (ptpt) REVERT: Ai 134 GLU cc_start: 0.3431 (mt-10) cc_final: 0.3155 (mt-10) REVERT: Aj 58 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7535 (tm-30) REVERT: Aj 63 ARG cc_start: 0.6291 (ttp80) cc_final: 0.5525 (ptt90) REVERT: Aj 70 MET cc_start: 0.5116 (mmt) cc_final: 0.3863 (mmt) REVERT: Aj 76 ARG cc_start: 0.5303 (mmp80) cc_final: 0.2704 (ttp80) REVERT: Aj 123 ASP cc_start: 0.6655 (m-30) cc_final: 0.6053 (m-30) REVERT: Aj 137 TYR cc_start: 0.4592 (m-80) cc_final: 0.4152 (m-80) REVERT: Aj 158 MET cc_start: 0.4468 (mmm) cc_final: 0.1088 (tmm) REVERT: Al 43 ARG cc_start: 0.3611 (mmt180) cc_final: -0.0162 (ptp-110) REVERT: Al 117 LEU cc_start: -0.3234 (OUTLIER) cc_final: -0.3594 (mp) REVERT: Al 158 MET cc_start: -0.3309 (tpt) cc_final: -0.3570 (tpt) REVERT: Am 22 ARG cc_start: -0.2156 (OUTLIER) cc_final: -0.2521 (ptt180) REVERT: Am 168 TYR cc_start: -0.0724 (t80) cc_final: -0.1174 (t80) REVERT: Ao 51 PHE cc_start: 0.1580 (OUTLIER) cc_final: 0.0864 (m-10) REVERT: Ap 37 MET cc_start: -0.0199 (ttm) cc_final: -0.0449 (mtp) REVERT: Ap 48 LEU cc_start: 0.4618 (OUTLIER) cc_final: 0.3919 (tp) REVERT: Ap 100 MET cc_start: -0.1864 (ttm) cc_final: -0.2296 (ptm) REVERT: Ap 131 ASP cc_start: 0.0701 (OUTLIER) cc_final: 0.0409 (p0) REVERT: Aq 173 PHE cc_start: 0.2303 (OUTLIER) cc_final: 0.2046 (t80) REVERT: Aq 208 ARG cc_start: 0.1087 (mtm-85) cc_final: 0.0736 (tpt170) REVERT: Aq 349 MET cc_start: 0.2472 (ptm) cc_final: 0.2258 (tmm) REVERT: Aq 396 PHE cc_start: 0.2682 (p90) cc_final: 0.1746 (m-80) REVERT: Aq 694 GLU cc_start: 0.1757 (mt-10) cc_final: 0.1432 (tm-30) REVERT: Ar 45 ASP cc_start: 0.3371 (OUTLIER) cc_final: 0.3022 (p0) REVERT: Ar 71 LYS cc_start: 0.2449 (OUTLIER) cc_final: 0.1310 (tppt) REVERT: Ar 100 MET cc_start: 0.1605 (mmt) cc_final: 0.0504 (mmt) REVERT: Ar 128 HIS cc_start: 0.3304 (OUTLIER) cc_final: 0.0336 (t-170) REVERT: As 45 ASP cc_start: 0.2115 (OUTLIER) cc_final: 0.0654 (p0) REVERT: As 158 MET cc_start: 0.0740 (tpt) cc_final: 0.0106 (tpp) REVERT: At 70 MET cc_start: -0.2392 (mmm) cc_final: -0.3384 (mmm) REVERT: Au 70 MET cc_start: 0.0471 (mtt) cc_final: 0.0237 (mtm) REVERT: Aw 49 LYS cc_start: 0.6723 (mptt) cc_final: 0.6501 (mptt) REVERT: Ax 37 MET cc_start: 0.1021 (mmt) cc_final: -0.1737 (tpp) REVERT: Ax 48 LEU cc_start: 0.2569 (mt) cc_final: 0.2162 (tp) REVERT: Ax 50 ASN cc_start: 0.3715 (m-40) cc_final: 0.3307 (m-40) REVERT: Ax 54 TYR cc_start: 0.6992 (t80) cc_final: 0.5617 (t80) REVERT: Ax 70 MET cc_start: -0.1985 (mmp) cc_final: -0.2200 (mmt) REVERT: Ay 137 TYR cc_start: 0.5523 (m-10) cc_final: 0.5290 (m-80) REVERT: Az 44 ASP cc_start: -0.0424 (t0) cc_final: -0.0644 (t0) outliers start: 91 outliers final: 64 residues processed: 426 average time/residue: 0.4525 time to fit residues: 321.2636 Evaluate side-chains 418 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 341 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 LYS Chi-restraints excluded: chain Ab residue 143 THR Chi-restraints excluded: chain Ab residue 146 LEU Chi-restraints excluded: chain Ab residue 206 ASN Chi-restraints excluded: chain Ab residue 209 LEU Chi-restraints excluded: chain Ab residue 282 TYR Chi-restraints excluded: chain Ab residue 365 MET Chi-restraints excluded: chain Ab residue 372 ASN Chi-restraints excluded: chain Ab residue 553 VAL Chi-restraints excluded: chain Ab residue 605 VAL Chi-restraints excluded: chain Ab residue 641 TRP Chi-restraints excluded: chain Ab residue 670 VAL Chi-restraints excluded: chain Ac residue 21 ASN Chi-restraints excluded: chain Ad residue 41 PHE Chi-restraints excluded: chain Ad residue 53 LYS Chi-restraints excluded: chain Ad residue 69 LEU Chi-restraints excluded: chain Af residue 13 HIS Chi-restraints excluded: chain Af residue 114 LEU Chi-restraints excluded: chain Af residue 142 VAL Chi-restraints excluded: chain Ag residue 67 GLU Chi-restraints excluded: chain Ag residue 72 LEU Chi-restraints excluded: chain Ag residue 97 LEU Chi-restraints excluded: chain Ag residue 145 ILE Chi-restraints excluded: chain Ag residue 154 ASN Chi-restraints excluded: chain Ag residue 155 LEU Chi-restraints excluded: chain Ah residue 25 ASN Chi-restraints excluded: chain Ai residue 54 TYR Chi-restraints excluded: chain Ai residue 76 ARG Chi-restraints excluded: chain Ai residue 104 LEU Chi-restraints excluded: chain Ai residue 114 LEU Chi-restraints excluded: chain Ai residue 168 TYR Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 104 LEU Chi-restraints excluded: chain Ak residue 56 LEU Chi-restraints excluded: chain Ak residue 65 HIS Chi-restraints excluded: chain Ak residue 69 LEU Chi-restraints excluded: chain Al residue 117 LEU Chi-restraints excluded: chain Al residue 120 LEU Chi-restraints excluded: chain Am residue 22 ARG Chi-restraints excluded: chain Am residue 37 MET Chi-restraints excluded: chain Am residue 41 PHE Chi-restraints excluded: chain Am residue 42 ASP Chi-restraints excluded: chain Ao residue 51 PHE Chi-restraints excluded: chain Ap residue 8 VAL Chi-restraints excluded: chain Ap residue 48 LEU Chi-restraints excluded: chain Ap residue 65 HIS Chi-restraints excluded: chain Ap residue 131 ASP Chi-restraints excluded: chain Aq residue 173 PHE Chi-restraints excluded: chain Aq residue 300 HIS Chi-restraints excluded: chain Aq residue 403 VAL Chi-restraints excluded: chain Aq residue 418 LYS Chi-restraints excluded: chain Aq residue 488 VAL Chi-restraints excluded: chain Aq residue 675 ASN Chi-restraints excluded: chain Ar residue 45 ASP Chi-restraints excluded: chain Ar residue 71 LYS Chi-restraints excluded: chain Ar residue 128 HIS Chi-restraints excluded: chain As residue 13 HIS Chi-restraints excluded: chain As residue 21 ASN Chi-restraints excluded: chain As residue 45 ASP Chi-restraints excluded: chain As residue 117 LEU Chi-restraints excluded: chain At residue 80 ILE Chi-restraints excluded: chain Au residue 71 LYS Chi-restraints excluded: chain Av residue 51 PHE Chi-restraints excluded: chain Aw residue 37 MET Chi-restraints excluded: chain Aw residue 40 TYR Chi-restraints excluded: chain Aw residue 64 GLU Chi-restraints excluded: chain Aw residue 109 ASN Chi-restraints excluded: chain Aw residue 155 LEU Chi-restraints excluded: chain Ax residue 25 ASN Chi-restraints excluded: chain Ax residue 28 LEU Chi-restraints excluded: chain Ax residue 51 PHE Chi-restraints excluded: chain Ay residue 104 LEU Chi-restraints excluded: chain Ay residue 109 ASN Chi-restraints excluded: chain Ay residue 155 LEU Chi-restraints excluded: chain Az residue 72 LEU Chi-restraints excluded: chain Az residue 133 ILE Chi-restraints excluded: chain Az residue 158 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 477 optimal weight: 2.9990 chunk 314 optimal weight: 8.9990 chunk 507 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 352 optimal weight: 50.0000 chunk 532 optimal weight: 0.0470 chunk 489 optimal weight: 5.9990 chunk 423 optimal weight: 6.9990 chunk 43 optimal weight: 30.0000 chunk 327 optimal weight: 40.0000 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 23 GLN ** Ad 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 65 HIS Ai 154 ASN ** Aj 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 11 ASN An 151 HIS ** Ao 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 300 HIS ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 57 HIS ** Ar 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 136 HIS ** As 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 11 ASN Ay 65 HIS ** Ay 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2429 moved from start: 0.9733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 44828 Z= 0.257 Angle : 0.730 14.575 60460 Z= 0.375 Chirality : 0.042 0.203 6432 Planarity : 0.005 0.068 7916 Dihedral : 5.375 34.931 5845 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.04 % Allowed : 12.71 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.11), residues: 5332 helix: 1.36 (0.08), residues: 3561 sheet: -0.23 (0.40), residues: 185 loop : -1.98 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPAr 93 HIS 0.020 0.002 HISAq 300 PHE 0.030 0.002 PHEAq 298 TYR 0.035 0.003 TYRAu 34 ARG 0.011 0.001 ARGAi 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10664 Ramachandran restraints generated. 5332 Oldfield, 0 Emsley, 5332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 355 time to evaluate : 3.684 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: Aa 132 PHE cc_start: 0.0830 (OUTLIER) cc_final: -0.1695 (t80) REVERT: Ab 131 LEU cc_start: 0.3933 (tp) cc_final: 0.3614 (mp) REVERT: Ab 234 HIS cc_start: -0.1719 (t-90) cc_final: -0.2893 (t-90) REVERT: Ab 243 PHE cc_start: 0.2492 (m-80) cc_final: 0.2199 (m-80) REVERT: Ab 282 TYR cc_start: 0.3810 (OUTLIER) cc_final: 0.2434 (p90) REVERT: Ab 679 MET cc_start: 0.4217 (mtt) cc_final: 0.3573 (tmm) REVERT: Ac 39 TYR cc_start: 0.6732 (m-10) cc_final: 0.6470 (m-80) REVERT: Ad 41 PHE cc_start: 0.1131 (OUTLIER) cc_final: 0.0404 (m-10) REVERT: Ad 70 MET cc_start: 0.3288 (mmm) cc_final: 0.1311 (tpt) REVERT: Ae 57 HIS cc_start: 0.0589 (OUTLIER) cc_final: -0.0477 (t70) REVERT: Ae 98 ASN cc_start: 0.6155 (t0) cc_final: 0.5189 (p0) REVERT: Ae 100 MET cc_start: -0.2489 (ttp) cc_final: -0.2814 (ttp) REVERT: Af 117 LEU cc_start: 0.6679 (pp) cc_final: 0.6475 (tt) REVERT: Af 137 TYR cc_start: 0.4885 (m-80) cc_final: 0.4592 (m-80) REVERT: Af 158 MET cc_start: -0.0459 (ptt) cc_final: -0.0667 (ptt) REVERT: Ag 62 GLU cc_start: 0.5846 (mm-30) cc_final: 0.5616 (mt-10) REVERT: Ag 67 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8036 (pp20) REVERT: Ag 70 MET cc_start: 0.6974 (tmm) cc_final: 0.6434 (tmm) REVERT: Ag 73 GLN cc_start: 0.5628 (tp40) cc_final: 0.5157 (tt0) REVERT: Ai 134 GLU cc_start: 0.2933 (mt-10) cc_final: 0.2641 (tt0) REVERT: Aj 58 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7545 (tm-30) REVERT: Aj 70 MET cc_start: 0.5391 (mmt) cc_final: 0.4293 (mmt) REVERT: Aj 76 ARG cc_start: 0.5339 (mmp80) cc_final: 0.2949 (ttp80) REVERT: Aj 123 ASP cc_start: 0.6835 (m-30) cc_final: 0.6419 (m-30) REVERT: Al 43 ARG cc_start: 0.4015 (mmt180) cc_final: 0.0311 (ptp-110) REVERT: Al 117 LEU cc_start: -0.3172 (OUTLIER) cc_final: -0.3504 (mp) REVERT: Am 22 ARG cc_start: -0.1816 (OUTLIER) cc_final: -0.2086 (ptt180) REVERT: Am 168 TYR cc_start: -0.0106 (t80) cc_final: -0.0876 (t80) REVERT: Ap 12 TYR cc_start: 0.0678 (OUTLIER) cc_final: -0.2974 (t80) REVERT: Ap 37 MET cc_start: -0.0061 (ttm) cc_final: -0.0410 (mtm) REVERT: Ap 70 MET cc_start: -0.1748 (mmm) cc_final: -0.2078 (mmp) REVERT: Aq 173 PHE cc_start: 0.2303 (OUTLIER) cc_final: 0.1854 (t80) REVERT: Aq 208 ARG cc_start: 0.1396 (mtm-85) cc_final: 0.0946 (tmm-80) REVERT: Aq 349 MET cc_start: 0.2520 (ptm) cc_final: 0.2309 (ptm) REVERT: Aq 396 PHE cc_start: 0.3285 (p90) cc_final: 0.1854 (m-80) REVERT: Ar 71 LYS cc_start: 0.2472 (OUTLIER) cc_final: 0.1512 (tppt) REVERT: Ar 100 MET cc_start: 0.1369 (mmt) cc_final: 0.0361 (mmt) REVERT: Ar 128 HIS cc_start: 0.4123 (OUTLIER) cc_final: 0.0999 (t-170) REVERT: As 45 ASP cc_start: 0.2755 (OUTLIER) cc_final: 0.1563 (p0) REVERT: As 100 MET cc_start: 0.0991 (mmt) cc_final: -0.1151 (mmt) REVERT: As 158 MET cc_start: 0.0863 (tpt) cc_final: 0.0596 (tpp) REVERT: Au 70 MET cc_start: 0.0984 (mtt) cc_final: 0.0689 (mtm) REVERT: Av 12 TYR cc_start: 0.4713 (t80) cc_final: 0.2899 (t80) REVERT: Aw 40 TYR cc_start: 0.5831 (OUTLIER) cc_final: 0.3526 (t80) REVERT: Aw 55 PHE cc_start: 0.5126 (OUTLIER) cc_final: 0.4129 (t80) REVERT: Aw 100 MET cc_start: 0.7127 (mtt) cc_final: 0.5048 (tmm) REVERT: Aw 158 MET cc_start: 0.6833 (mmm) cc_final: 0.6434 (mmm) REVERT: Ax 50 ASN cc_start: 0.3681 (m-40) cc_final: 0.3148 (m-40) REVERT: Ay 63 ARG cc_start: 0.7305 (tmt-80) cc_final: 0.6921 (tmt-80) REVERT: Ay 137 TYR cc_start: 0.6124 (m-10) cc_final: 0.5899 (m-80) REVERT: Az 44 ASP cc_start: 0.1172 (t0) cc_final: -0.0676 (t70) outliers start: 97 outliers final: 67 residues processed: 417 average time/residue: 0.4582 time to fit residues: 315.2604 Evaluate side-chains 409 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 328 time to evaluate : 4.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 132 PHE Chi-restraints excluded: chain Ab residue 143 THR Chi-restraints excluded: chain Ab residue 146 LEU Chi-restraints excluded: chain Ab residue 206 ASN Chi-restraints excluded: chain Ab residue 209 LEU Chi-restraints excluded: chain Ab residue 282 TYR Chi-restraints excluded: chain Ab residue 372 ASN Chi-restraints excluded: chain Ab residue 553 VAL Chi-restraints excluded: chain Ab residue 605 VAL Chi-restraints excluded: chain Ab residue 641 TRP Chi-restraints excluded: chain Ab residue 670 VAL Chi-restraints excluded: chain Ab residue 717 LYS Chi-restraints excluded: chain Ac residue 21 ASN Chi-restraints excluded: chain Ad residue 41 PHE Chi-restraints excluded: chain Ad residue 53 LYS Chi-restraints excluded: chain Ad residue 69 LEU Chi-restraints excluded: chain Ae residue 57 HIS Chi-restraints excluded: chain Af residue 13 HIS Chi-restraints excluded: chain Af residue 114 LEU Chi-restraints excluded: chain Af residue 140 GLU Chi-restraints excluded: chain Af residue 142 VAL Chi-restraints excluded: chain Ag residue 60 HIS Chi-restraints excluded: chain Ag residue 67 GLU Chi-restraints excluded: chain Ag residue 72 LEU Chi-restraints excluded: chain Ag residue 97 LEU Chi-restraints excluded: chain Ag residue 145 ILE Chi-restraints excluded: chain Ag residue 154 ASN Chi-restraints excluded: chain Ag residue 155 LEU Chi-restraints excluded: chain Ag residue 158 MET Chi-restraints excluded: chain Ai residue 13 HIS Chi-restraints excluded: chain Ai residue 54 TYR Chi-restraints excluded: chain Ai residue 76 ARG Chi-restraints excluded: chain Ai residue 104 LEU Chi-restraints excluded: chain Ai residue 114 LEU Chi-restraints excluded: chain Ai residue 168 TYR Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 104 LEU Chi-restraints excluded: chain Aj residue 118 HIS Chi-restraints excluded: chain Ak residue 56 LEU Chi-restraints excluded: chain Ak residue 65 HIS Chi-restraints excluded: chain Ak residue 69 LEU Chi-restraints excluded: chain Al residue 117 LEU Chi-restraints excluded: chain Al residue 120 LEU Chi-restraints excluded: chain Am residue 22 ARG Chi-restraints excluded: chain Am residue 37 MET Chi-restraints excluded: chain Am residue 41 PHE Chi-restraints excluded: chain Am residue 42 ASP Chi-restraints excluded: chain Ao residue 51 PHE Chi-restraints excluded: chain Ap residue 8 VAL Chi-restraints excluded: chain Ap residue 12 TYR Chi-restraints excluded: chain Ap residue 45 ASP Chi-restraints excluded: chain Ap residue 65 HIS Chi-restraints excluded: chain Aq residue 173 PHE Chi-restraints excluded: chain Aq residue 403 VAL Chi-restraints excluded: chain Aq residue 418 LYS Chi-restraints excluded: chain Aq residue 488 VAL Chi-restraints excluded: chain Aq residue 675 ASN Chi-restraints excluded: chain Ar residue 71 LYS Chi-restraints excluded: chain Ar residue 72 LEU Chi-restraints excluded: chain Ar residue 128 HIS Chi-restraints excluded: chain As residue 13 HIS Chi-restraints excluded: chain As residue 45 ASP Chi-restraints excluded: chain As residue 117 LEU Chi-restraints excluded: chain At residue 80 ILE Chi-restraints excluded: chain Au residue 71 LYS Chi-restraints excluded: chain Av residue 51 PHE Chi-restraints excluded: chain Aw residue 37 MET Chi-restraints excluded: chain Aw residue 40 TYR Chi-restraints excluded: chain Aw residue 55 PHE Chi-restraints excluded: chain Aw residue 106 LEU Chi-restraints excluded: chain Aw residue 109 ASN Chi-restraints excluded: chain Aw residue 155 LEU Chi-restraints excluded: chain Ax residue 25 ASN Chi-restraints excluded: chain Ax residue 28 LEU Chi-restraints excluded: chain Ax residue 51 PHE Chi-restraints excluded: chain Ay residue 97 LEU Chi-restraints excluded: chain Ay residue 104 LEU Chi-restraints excluded: chain Ay residue 109 ASN Chi-restraints excluded: chain Az residue 72 LEU Chi-restraints excluded: chain Az residue 133 ILE Chi-restraints excluded: chain Az residue 158 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 259 optimal weight: 7.9990 chunk 336 optimal weight: 3.9990 chunk 451 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 390 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 424 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 435 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 408 GLN Ab 626 ASN Ab 675 ASN ** Ac 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 73 GLN ** Ae 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 21 ASN ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 25 ASN ** Ah 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 7 GLN ** Aj 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 151 HIS ** Al 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 50 ASN An 74 ASN Ao 21 ASN ** Ao 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 11 ASN ** Aq 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 7 GLN Ar 11 ASN ** Ar 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 57 HIS ** Ar 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 136 HIS ** As 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 75 GLN Au 98 ASN ** Au 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 65 HIS Aw 141 GLN ** Ax 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.246274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.219630 restraints weight = 101113.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.223070 restraints weight = 62468.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.224999 restraints weight = 39517.751| |-----------------------------------------------------------------------------| r_work (final): 0.4679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2447 moved from start: 0.9680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 44828 Z= 0.163 Angle : 0.584 13.745 60460 Z= 0.298 Chirality : 0.038 0.176 6432 Planarity : 0.004 0.070 7916 Dihedral : 4.869 31.992 5845 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.77 % Allowed : 13.34 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.11), residues: 5332 helix: 1.86 (0.08), residues: 3605 sheet: -0.02 (0.39), residues: 191 loop : -1.84 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPAw 93 HIS 0.019 0.001 HISAy 60 PHE 0.018 0.001 PHEAz 55 TYR 0.026 0.002 TYRAu 34 ARG 0.006 0.000 ARGAi 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7095.48 seconds wall clock time: 128 minutes 7.36 seconds (7687.36 seconds total)