Starting phenix.real_space_refine on Tue Sep 24 17:40:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5i_0140/09_2024/6h5i_0140.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5i_0140/09_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_0140/09_2024/6h5i_0140.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5i_0140/09_2024/6h5i_0140.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5i_0140/09_2024/6h5i_0140.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5i_0140/09_2024/6h5i_0140.cif" } 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. Time to flip 5 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 18.44, per 1000 atoms: 0.42 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 - 3.00 Amino acid : True - 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: 7.67 Conformation dependent library (CDL) restraints added in 4.0 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: 2.76 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: 11.12 Time building geometry restraints manager: 9.21 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: 0.00 - 2.57: 59491 2.57 - 5.15: 823 5.15 - 7.72: 130 7.72 - 10.29: 14 10.29 - 12.87: 2 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 3.120 nonbonded pdb=" O GLUAb 266 " pdb=" ND2 ASNAb 270 " model vdw 2.207 3.120 nonbonded pdb=" OG1 THRAc 174 " pdb=" OH TYRAw 168 " model vdw 2.242 3.040 nonbonded pdb=" OH TYRAh 168 " pdb=" OG1 THRAu 174 " model vdw 2.246 3.040 nonbonded pdb=" OH TYRAi 168 " pdb=" OG1 THRAx 174 " model vdw 2.249 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.030 Extract box with map and model: 1.330 Check model and map are aligned: 0.250 Set scattering table: 0.320 Process input model: 68.090 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.150 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.100 ------------------------------------------------------------------------------- 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 : 3.639 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: 0.5121 time to fit residues: 559.5555 Evaluate side-chains 401 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 400 time to evaluate : 3.620 ------------------------------------------------------------------------------- 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: 0.9980 chunk 404 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 138 optimal weight: 0.5980 chunk 273 optimal weight: 1.9990 chunk 216 optimal weight: 10.0000 chunk 418 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 254 optimal weight: 0.8980 chunk 311 optimal weight: 5.9990 chunk 484 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 11 ASN Aa 118 HIS Aa 173 HIS Ab 171 ASN Ab 197 GLN Ab 348 ASN ** Ab 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 483 ASN Ab 493 ASN ** Ab 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 733 ASN Ab 747 ASN Ad 118 HIS Ad 173 HIS Ae 118 HIS ** Ae 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 136 HIS Af 11 ASN Af 21 ASN Ag 83 GLN Ag 173 HIS Ah 25 ASN Ah 136 HIS Ai 109 ASN Ai 118 HIS Ai 136 HIS Ai 154 ASN Aj 11 ASN 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 Ao 118 HIS Ao 128 HIS Ao 136 HIS Ap 11 ASN Ap 14 GLN Ap 109 ASN Ap 118 HIS Ap 136 HIS Ap 173 HIS Aq 171 ASN Aq 300 HIS ** Aq 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 154 ASN Ar 173 HIS As 7 GLN As 11 ASN As 65 HIS As 173 HIS At 11 ASN Au 11 ASN Av 118 HIS Av 136 HIS Aw 11 ASN Aw 21 ASN Aw 65 HIS Aw 109 ASN Ax 125 ASN Ax 173 HIS Ay 11 ASN Ay 65 HIS Ay 105 HIS Ay 112 GLN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0880 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 44828 Z= 0.149 Angle : 0.512 11.199 60460 Z= 0.273 Chirality : 0.037 0.223 6432 Planarity : 0.004 0.049 7916 Dihedral : 4.699 30.577 5846 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.90 % Allowed : 4.90 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 1.65 % 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: 1.16 (0.11), residues: 5332 helix: 2.07 (0.08), residues: 3621 sheet: -1.12 (0.35), residues: 193 loop : -2.36 (0.14), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPAn 93 HIS 0.010 0.001 HISAw 65 PHE 0.021 0.001 PHEAz 41 TYR 0.030 0.001 TYRAp 29 ARG 0.006 0.000 ARGAx 76 *********************** 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: 43 poor density : 439 time to evaluate : 3.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 37 MET cc_start: -0.2488 (mtt) cc_final: -0.2722 (mtt) REVERT: Aa 41 PHE cc_start: 0.3592 (m-80) cc_final: 0.3005 (m-80) REVERT: Ab 206 ASN cc_start: 0.4663 (p0) cc_final: 0.4327 (p0) REVERT: Ab 679 MET cc_start: 0.1986 (mtt) cc_final: 0.1637 (tmm) REVERT: Ad 41 PHE cc_start: 0.0340 (m-80) cc_final: -0.0028 (m-10) REVERT: Ae 20 ILE cc_start: -0.2349 (mm) cc_final: -0.2820 (mt) REVERT: Ae 37 MET cc_start: -0.0495 (mtt) cc_final: -0.2382 (tpp) REVERT: Ae 41 PHE cc_start: 0.1337 (m-80) cc_final: 0.1096 (m-80) REVERT: Ah 161 PRO cc_start: 0.5311 (Cg_endo) cc_final: 0.4835 (Cg_exo) REVERT: Ai 35 LEU cc_start: 0.2308 (tp) cc_final: 0.2048 (tp) REVERT: Ai 70 MET cc_start: 0.4600 (mmt) cc_final: 0.4342 (mmt) REVERT: Ai 80 ILE cc_start: 0.5255 (mt) cc_final: 0.5006 (mt) REVERT: Ai 158 MET cc_start: 0.4249 (tpt) cc_final: 0.3824 (tpt) REVERT: Aj 100 MET cc_start: 0.2945 (tpp) cc_final: 0.2335 (mmm) REVERT: Ap 8 VAL cc_start: 0.2480 (OUTLIER) cc_final: 0.2171 (m) REVERT: Aq 388 ASN cc_start: 0.4203 (m-40) cc_final: 0.3105 (m-40) REVERT: Aq 614 TYR cc_start: -0.1419 (m-10) cc_final: -0.1666 (m-10) REVERT: Aq 635 MET cc_start: -0.3775 (mtp) cc_final: -0.4477 (ttt) REVERT: Aq 685 PHE cc_start: -0.1072 (m-10) cc_final: -0.1784 (m-80) REVERT: Aq 694 GLU cc_start: 0.1087 (mt-10) cc_final: 0.0663 (tm-30) REVERT: At 168 TYR cc_start: -0.0655 (t80) cc_final: -0.1022 (t80) REVERT: Aw 119 LYS cc_start: 0.5617 (mmtm) cc_final: 0.4993 (mttt) REVERT: Ax 37 MET cc_start: -0.1407 (mtt) cc_final: -0.3115 (tpp) REVERT: Ax 54 TYR cc_start: 0.5664 (t80) cc_final: 0.5194 (t80) outliers start: 43 outliers final: 26 residues processed: 466 average time/residue: 0.4453 time to fit residues: 348.0938 Evaluate side-chains 380 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 353 time to evaluate : 3.638 ------------------------------------------------------------------------------- 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 494 PHE Chi-restraints excluded: chain Ab residue 604 ASP Chi-restraints excluded: chain Ab residue 670 VAL Chi-restraints excluded: chain Af residue 35 LEU Chi-restraints excluded: chain Af residue 174 THR Chi-restraints excluded: chain Ag residue 97 LEU Chi-restraints excluded: chain Ag residue 104 LEU Chi-restraints excluded: chain Aj residue 16 SER 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 Am residue 51 PHE Chi-restraints excluded: chain Am residue 82 LEU Chi-restraints excluded: chain An residue 133 ILE Chi-restraints excluded: chain Ap residue 8 VAL Chi-restraints excluded: chain Aq residue 300 HIS Chi-restraints excluded: chain Aq residue 418 LYS Chi-restraints excluded: chain Aq residue 496 VAL Chi-restraints excluded: chain At residue 90 CYS Chi-restraints excluded: chain Aw residue 109 ASN Chi-restraints excluded: chain Ax residue 65 HIS Chi-restraints excluded: chain Ay residue 104 LEU Chi-restraints excluded: chain Ay residue 105 HIS 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: 3.9990 chunk 403 optimal weight: 0.8980 chunk 330 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 485 optimal weight: 6.9990 chunk 524 optimal weight: 0.6980 chunk 432 optimal weight: 8.9990 chunk 481 optimal weight: 5.9990 chunk 165 optimal weight: 0.0270 chunk 389 optimal weight: 0.1980 overall best weight: 1.1640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ab 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 105 HIS Ad 7 GLN Ae 105 HIS Ae 173 HIS Af 128 HIS Ag 118 HIS Ah 25 ASN Ai 112 GLN Ai 151 HIS ** Aj 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 73 GLN Aj 105 HIS ** Aj 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 11 ASN ** Aq 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 300 HIS ** Aq 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 60 HIS Ar 128 HIS As 11 ASN ** As 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** At 109 ASN ** Av 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 11 ASN Aw 11 ASN Aw 73 GLN Aw 105 HIS Aw 112 GLN Ax 7 GLN Ay 60 HIS Ay 73 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1124 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 44828 Z= 0.143 Angle : 0.494 8.784 60460 Z= 0.262 Chirality : 0.037 0.269 6432 Planarity : 0.003 0.048 7916 Dihedral : 4.424 27.068 5845 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.43 % Allowed : 6.02 % Favored : 92.55 % 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: 2.04 (0.12), residues: 5332 helix: 2.73 (0.08), residues: 3627 sheet: -0.68 (0.37), residues: 190 loop : -2.00 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPAn 93 HIS 0.030 0.001 HISAy 105 PHE 0.025 0.001 PHEAq 442 TYR 0.017 0.001 TYRAu 32 ARG 0.009 0.000 ARGAk 63 *********************** 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 449 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 381 time to evaluate : 3.732 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 41 PHE cc_start: 0.3185 (m-80) cc_final: 0.2517 (m-80) REVERT: Ab 131 LEU cc_start: 0.4923 (tp) cc_final: 0.4552 (mm) REVERT: Ab 679 MET cc_start: 0.2147 (mtt) cc_final: 0.1759 (tmm) REVERT: Ae 98 ASN cc_start: 0.6337 (t0) cc_final: 0.6114 (p0) REVERT: Af 174 THR cc_start: 0.1194 (OUTLIER) cc_final: 0.0855 (m) REVERT: Ag 63 ARG cc_start: 0.6790 (ttp80) cc_final: 0.6547 (ptm-80) REVERT: Ah 161 PRO cc_start: 0.6347 (Cg_endo) cc_final: 0.6064 (Cg_exo) REVERT: Ai 70 MET cc_start: 0.4985 (mmt) cc_final: 0.4494 (mmt) REVERT: Ai 134 GLU cc_start: 0.2849 (mt-10) cc_final: 0.2285 (mt-10) REVERT: Ai 158 MET cc_start: 0.4322 (tpt) cc_final: 0.3996 (tpt) REVERT: Aj 100 MET cc_start: 0.3425 (tpp) cc_final: 0.2641 (mmm) REVERT: Al 51 PHE cc_start: 0.1415 (OUTLIER) cc_final: 0.0747 (m-10) REVERT: An 158 MET cc_start: -0.1292 (mtp) cc_final: -0.1873 (mtm) REVERT: Ap 8 VAL cc_start: 0.2550 (OUTLIER) cc_final: 0.2265 (m) REVERT: Aq 300 HIS cc_start: 0.1845 (OUTLIER) cc_final: 0.1543 (p-80) REVERT: Aq 388 ASN cc_start: 0.4347 (m-40) cc_final: 0.3347 (m-40) REVERT: Aq 685 PHE cc_start: -0.1178 (m-10) cc_final: -0.1961 (m-80) REVERT: Aq 694 GLU cc_start: 0.0895 (mt-10) cc_final: 0.0506 (tm-30) REVERT: Ar 74 ASN cc_start: 0.1633 (m110) cc_final: 0.1400 (t0) REVERT: Av 70 MET cc_start: -0.0357 (ttt) cc_final: -0.0876 (ttt) REVERT: Ax 12 TYR cc_start: 0.1635 (t80) cc_final: -0.0551 (t80) REVERT: Ax 37 MET cc_start: -0.1359 (mtt) cc_final: -0.3616 (tpt) REVERT: Ax 54 TYR cc_start: 0.5262 (t80) cc_final: 0.4702 (t80) outliers start: 68 outliers final: 36 residues processed: 430 average time/residue: 0.4513 time to fit residues: 323.6295 Evaluate side-chains 375 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 335 time to evaluate : 3.566 ------------------------------------------------------------------------------- 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 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 56 LEU Chi-restraints excluded: chain Ac residue 118 HIS Chi-restraints excluded: chain Ad residue 53 LYS Chi-restraints excluded: chain Ad residue 165 LEU Chi-restraints excluded: chain Af residue 13 HIS Chi-restraints excluded: chain Af residue 35 LEU Chi-restraints excluded: chain Af residue 174 THR Chi-restraints excluded: chain Ag residue 104 LEU Chi-restraints excluded: chain Ah residue 25 ASN Chi-restraints excluded: chain Ai residue 104 LEU 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 23 GLN Chi-restraints excluded: chain Ak residue 69 LEU Chi-restraints excluded: chain Al residue 51 PHE Chi-restraints excluded: chain Al residue 120 LEU Chi-restraints excluded: chain Am 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 Aq residue 213 VAL Chi-restraints excluded: chain Aq residue 300 HIS Chi-restraints excluded: chain Aq residue 496 VAL Chi-restraints excluded: chain Ar residue 71 LYS Chi-restraints excluded: chain Aw residue 46 VAL Chi-restraints excluded: chain Aw residue 72 LEU Chi-restraints excluded: chain Ax residue 65 HIS Chi-restraints excluded: chain Ay residue 60 HIS 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: 0.6980 chunk 365 optimal weight: 20.0000 chunk 252 optimal weight: 8.9990 chunk 53 optimal weight: 0.0980 chunk 231 optimal weight: 0.0980 chunk 326 optimal weight: 40.0000 chunk 487 optimal weight: 7.9990 chunk 516 optimal weight: 3.9990 chunk 254 optimal weight: 0.3980 chunk 462 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 401 HIS ** Ab 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 109 ASN Ac 173 HIS Ae 105 HIS Af 73 GLN Ag 73 GLN Ag 74 ASN Ah 25 ASN Aj 13 HIS ** Aj 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 118 HIS Ap 75 GLN Aq 234 HIS ** Aq 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 21 ASN ** As 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** At 11 ASN Au 11 ASN Au 73 GLN Av 10 GLN Av 11 ASN Aw 112 GLN Ax 11 ASN Ay 14 GLN Az 128 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1198 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 44828 Z= 0.122 Angle : 0.448 9.591 60460 Z= 0.236 Chirality : 0.035 0.155 6432 Planarity : 0.003 0.046 7916 Dihedral : 4.203 26.254 5845 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.62 % Allowed : 6.33 % Favored : 92.05 % 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: 2.59 (0.12), residues: 5332 helix: 3.17 (0.08), residues: 3605 sheet: -0.48 (0.38), residues: 190 loop : -1.81 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPAb 357 HIS 0.025 0.001 HISAy 60 PHE 0.020 0.001 PHEAe 132 TYR 0.026 0.001 TYRAq 614 ARG 0.005 0.000 ARGAk 63 *********************** 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 428 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 351 time to evaluate : 3.729 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 37 MET cc_start: -0.3138 (mtt) cc_final: -0.3342 (mtt) REVERT: Aa 41 PHE cc_start: 0.3449 (m-80) cc_final: 0.2701 (m-80) REVERT: Ab 357 TRP cc_start: -0.0902 (m-10) cc_final: -0.1368 (m-10) REVERT: Ab 436 MET cc_start: -0.0814 (mmt) cc_final: -0.1549 (mtt) REVERT: Ab 679 MET cc_start: 0.2917 (mtt) cc_final: 0.2353 (tmm) REVERT: Ae 37 MET cc_start: -0.0683 (mtt) cc_final: -0.2499 (tpp) REVERT: Ae 98 ASN cc_start: 0.6372 (t0) cc_final: 0.6159 (p0) REVERT: Af 51 PHE cc_start: 0.3462 (OUTLIER) cc_final: 0.2827 (m-10) REVERT: Af 70 MET cc_start: 0.5398 (mmt) cc_final: 0.5040 (mmm) REVERT: Ag 56 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.5698 (pp) REVERT: Ah 161 PRO cc_start: 0.6230 (Cg_endo) cc_final: 0.5841 (Cg_exo) REVERT: Ai 70 MET cc_start: 0.4829 (mmt) cc_final: 0.4375 (mmt) REVERT: Ai 134 GLU cc_start: 0.2899 (mt-10) cc_final: 0.2294 (mt-10) REVERT: Ai 158 MET cc_start: 0.3860 (tpt) cc_final: 0.1371 (ptt) REVERT: Aj 58 GLN cc_start: 0.7023 (tm-30) cc_final: 0.6623 (tm-30) REVERT: Aj 70 MET cc_start: 0.4855 (mmt) cc_final: 0.4436 (mmt) REVERT: Aj 100 MET cc_start: 0.3544 (tpp) cc_final: 0.3041 (mmm) REVERT: Aj 158 MET cc_start: 0.5016 (mmm) cc_final: 0.4776 (mmm) REVERT: Al 51 PHE cc_start: 0.1297 (OUTLIER) cc_final: 0.0789 (m-10) REVERT: Al 117 LEU cc_start: -0.3511 (OUTLIER) cc_final: -0.3881 (mp) REVERT: Am 94 GLU cc_start: 0.2925 (mt-10) cc_final: 0.1344 (mm-30) REVERT: An 117 LEU cc_start: 0.0948 (OUTLIER) cc_final: 0.0745 (tt) REVERT: Aq 300 HIS cc_start: 0.2002 (OUTLIER) cc_final: 0.1258 (p-80) REVERT: Aq 388 ASN cc_start: 0.4334 (m-40) cc_final: 0.3479 (m-40) REVERT: Aq 694 GLU cc_start: 0.0963 (mt-10) cc_final: 0.0534 (tm-30) REVERT: Ar 70 MET cc_start: -0.2748 (mtt) cc_final: -0.2984 (mtt) REVERT: Av 70 MET cc_start: -0.0889 (ttt) cc_final: -0.1105 (ttt) REVERT: Ax 12 TYR cc_start: 0.1526 (t80) cc_final: -0.0973 (t80) REVERT: Ax 37 MET cc_start: -0.1330 (mtt) cc_final: -0.3381 (tpt) outliers start: 77 outliers final: 43 residues processed: 407 average time/residue: 0.4497 time to fit residues: 308.8880 Evaluate side-chains 373 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 324 time to evaluate : 3.658 ------------------------------------------------------------------------------- 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 250 VAL 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 165 LEU Chi-restraints excluded: chain Af residue 13 HIS Chi-restraints excluded: chain Af residue 35 LEU Chi-restraints excluded: chain Af residue 51 PHE Chi-restraints excluded: chain Af residue 152 VAL Chi-restraints excluded: chain Ag residue 56 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 51 PHE 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 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 82 LEU Chi-restraints excluded: chain An residue 117 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 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 71 LYS Chi-restraints excluded: chain As residue 21 ASN Chi-restraints excluded: chain Aw residue 46 VAL Chi-restraints excluded: chain Aw residue 56 LEU Chi-restraints excluded: chain Aw residue 72 LEU Chi-restraints excluded: chain Ax residue 28 LEU Chi-restraints excluded: chain Ax residue 65 HIS Chi-restraints excluded: chain Ay residue 72 LEU 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: 0.9990 chunk 293 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 384 optimal weight: 10.0000 chunk 212 optimal weight: 1.9990 chunk 440 optimal weight: 3.9990 chunk 356 optimal weight: 50.0000 chunk 0 optimal weight: 30.0000 chunk 263 optimal weight: 7.9990 chunk 463 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 60 HIS Aa 73 GLN ** Ab 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 615 ASN Ab 626 ASN Ab 684 HIS Ad 73 GLN Ad 141 GLN 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 141 GLN ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 75 GLN ** Ag 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 7 GLN ** Ah 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 136 HIS Ai 10 GLN Ai 11 ASN Ai 136 HIS ** Aj 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 50 ASN Aj 112 GLN Ak 75 GLN Ak 118 HIS Ak 141 GLN Al 73 GLN Al 109 ASN ** Al 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 154 ASN Am 11 ASN ** 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 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 11 ASN Ao 50 ASN Ao 73 GLN Ap 14 GLN Ap 65 HIS Aq 300 HIS ** Aq 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 615 ASN Aq 684 HIS ** As 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 23 GLN ** As 73 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** At 11 ASN ** At 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Au 105 HIS ** Au 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Au 128 HIS Au 154 ASN Au 173 HIS Av 7 GLN Av 50 ASN Av 73 GLN ** Aw 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 136 HIS ** Aw 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 11 ASN Ax 60 HIS Ax 75 GLN ** Ax 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 14 GLN Ay 25 ASN Ay 60 HIS Ay 74 ASN Ay 75 GLN Az 128 HIS Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1882 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 44828 Z= 0.264 Angle : 0.729 10.954 60460 Z= 0.383 Chirality : 0.044 0.445 6432 Planarity : 0.005 0.073 7916 Dihedral : 5.119 31.040 5845 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.08 % Allowed : 6.90 % Favored : 91.02 % 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: 1.05 (0.11), residues: 5332 helix: 1.81 (0.08), residues: 3601 sheet: -0.43 (0.38), residues: 190 loop : -1.93 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRPAn 93 HIS 0.015 0.002 HISAl 136 PHE 0.037 0.003 PHEAe 41 TYR 0.042 0.003 TYRAl 39 ARG 0.011 0.001 ARGAz 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 489 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 390 time to evaluate : 3.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 34 TYR cc_start: 0.0738 (OUTLIER) cc_final: -0.1491 (m-80) REVERT: Aa 158 MET cc_start: 0.0927 (OUTLIER) cc_final: 0.0674 (mtp) REVERT: Ab 131 LEU cc_start: 0.4007 (tp) cc_final: 0.3530 (mt) REVERT: Ab 357 TRP cc_start: -0.0410 (m-10) cc_final: -0.1077 (m-10) REVERT: Ab 679 MET cc_start: 0.2943 (mtt) cc_final: 0.2437 (tmm) REVERT: Ad 41 PHE cc_start: 0.0983 (OUTLIER) cc_final: 0.0338 (m-10) REVERT: Ae 37 MET cc_start: -0.0065 (mtt) cc_final: -0.1618 (tpp) REVERT: Ae 98 ASN cc_start: 0.6619 (t0) cc_final: 0.5952 (p0) REVERT: Af 35 LEU cc_start: 0.2556 (OUTLIER) cc_final: 0.2178 (tp) REVERT: Af 39 TYR cc_start: 0.1292 (m-10) cc_final: 0.0497 (m-80) REVERT: Af 51 PHE cc_start: 0.4064 (OUTLIER) cc_final: 0.3508 (m-10) REVERT: Af 109 ASN cc_start: 0.5539 (m-40) cc_final: 0.5165 (m-40) REVERT: Af 134 GLU cc_start: 0.3608 (mt-10) cc_final: 0.3368 (mt-10) REVERT: Ag 34 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6120 (t80) REVERT: Ag 41 PHE cc_start: 0.7281 (m-80) cc_final: 0.7033 (m-80) REVERT: Ah 161 PRO cc_start: 0.6801 (Cg_endo) cc_final: 0.6520 (Cg_exo) REVERT: Ai 70 MET cc_start: 0.4867 (mmt) cc_final: 0.4015 (mmt) REVERT: Ai 155 LEU cc_start: 0.5113 (mt) cc_final: 0.3441 (mt) REVERT: Ai 158 MET cc_start: 0.3222 (tpt) cc_final: 0.2683 (ppp) REVERT: Aj 158 MET cc_start: 0.5344 (mmm) cc_final: 0.1615 (tmm) REVERT: Ak 75 GLN cc_start: 0.2863 (OUTLIER) cc_final: 0.0512 (mm-40) REVERT: Al 44 ASP cc_start: -0.1416 (OUTLIER) cc_final: -0.1637 (t0) REVERT: Al 70 MET cc_start: -0.0778 (tpp) cc_final: -0.1039 (tpp) REVERT: Al 117 LEU cc_start: -0.3119 (OUTLIER) cc_final: -0.3484 (mp) REVERT: Al 158 MET cc_start: -0.3110 (tpt) cc_final: -0.4642 (tpt) REVERT: An 73 GLN cc_start: 0.2056 (tp-100) cc_final: 0.1569 (tt0) REVERT: An 87 LYS cc_start: -0.0434 (OUTLIER) cc_final: -0.1571 (pttt) REVERT: Aq 173 PHE cc_start: 0.1551 (OUTLIER) cc_final: 0.1163 (t80) REVERT: Aq 388 ASN cc_start: 0.4474 (m-40) cc_final: 0.3681 (m-40) REVERT: Aq 694 GLU cc_start: 0.1175 (mt-10) cc_final: 0.0767 (tm-30) REVERT: Ar 100 MET cc_start: 0.1387 (mmt) cc_final: 0.0244 (mmt) REVERT: Ar 128 HIS cc_start: 0.2041 (t70) cc_final: 0.0644 (t-170) REVERT: At 90 CYS cc_start: 0.1129 (OUTLIER) cc_final: 0.0653 (t) REVERT: Au 37 MET cc_start: -0.1660 (mtt) cc_final: -0.2986 (mmm) REVERT: Au 70 MET cc_start: 0.1032 (mtt) cc_final: 0.0754 (mtt) REVERT: Au 89 ASP cc_start: 0.1051 (OUTLIER) cc_final: -0.0366 (p0) REVERT: Au 158 MET cc_start: -0.1124 (tpp) cc_final: -0.1445 (mmm) REVERT: Av 51 PHE cc_start: 0.3412 (OUTLIER) cc_final: 0.3090 (m-80) REVERT: Av 158 MET cc_start: 0.0665 (ttm) cc_final: 0.0268 (mtp) REVERT: Aw 60 HIS cc_start: 0.6898 (m170) cc_final: 0.6650 (m170) REVERT: Ax 12 TYR cc_start: 0.3359 (t80) cc_final: -0.0748 (t80) REVERT: Ax 37 MET cc_start: -0.2190 (mtt) cc_final: -0.3508 (tpt) REVERT: Ax 54 TYR cc_start: 0.6529 (t80) cc_final: 0.5440 (t80) REVERT: Ay 75 GLN cc_start: 0.3291 (OUTLIER) cc_final: 0.2832 (tt0) REVERT: Ay 137 TYR cc_start: 0.4972 (m-10) cc_final: 0.4540 (m-80) outliers start: 99 outliers final: 50 residues processed: 466 average time/residue: 0.4659 time to fit residues: 358.2729 Evaluate side-chains 386 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 321 time to evaluate : 3.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 34 TYR Chi-restraints excluded: chain Aa residue 53 LYS Chi-restraints excluded: chain Aa residue 158 MET Chi-restraints excluded: chain Aa residue 165 LEU Chi-restraints excluded: chain Ab residue 143 THR Chi-restraints excluded: chain Ab residue 209 LEU Chi-restraints excluded: chain Ab residue 220 VAL Chi-restraints excluded: chain Ab residue 250 VAL 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 Ad residue 165 LEU Chi-restraints excluded: chain Af residue 13 HIS Chi-restraints excluded: chain Af residue 35 LEU Chi-restraints excluded: chain Af residue 51 PHE Chi-restraints excluded: chain Ag residue 34 TYR Chi-restraints excluded: chain Ag residue 97 LEU Chi-restraints excluded: chain Ag residue 104 LEU Chi-restraints excluded: chain Ag residue 155 LEU Chi-restraints excluded: chain Ai residue 6 SER Chi-restraints excluded: chain Ai residue 104 LEU 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 65 HIS Chi-restraints excluded: chain Ak residue 75 GLN Chi-restraints excluded: chain Al residue 44 ASP 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 82 LEU Chi-restraints excluded: chain Am residue 93 TRP Chi-restraints excluded: chain An residue 13 HIS Chi-restraints excluded: chain An residue 87 LYS Chi-restraints excluded: chain An residue 133 ILE Chi-restraints excluded: chain Ao residue 51 PHE Chi-restraints excluded: chain Ao residue 72 LEU Chi-restraints excluded: chain Ap residue 8 VAL Chi-restraints excluded: chain Ap residue 65 HIS Chi-restraints excluded: chain Ap residue 104 LEU Chi-restraints excluded: chain Aq residue 173 PHE Chi-restraints excluded: chain Aq residue 213 VAL Chi-restraints excluded: chain Aq residue 300 HIS Chi-restraints excluded: chain Aq residue 675 ASN Chi-restraints excluded: chain Ar residue 71 LYS Chi-restraints excluded: chain As residue 117 LEU Chi-restraints excluded: chain At residue 90 CYS Chi-restraints excluded: chain Au residue 89 ASP Chi-restraints excluded: chain Av residue 51 PHE Chi-restraints excluded: chain Aw residue 56 LEU Chi-restraints excluded: chain Aw residue 109 ASN Chi-restraints excluded: chain Aw residue 111 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 75 GLN Chi-restraints excluded: chain Az residue 70 MET Chi-restraints excluded: chain Az residue 133 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 173 optimal weight: 0.9990 chunk 464 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 303 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 516 optimal weight: 3.9990 chunk 428 optimal weight: 10.0000 chunk 239 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 271 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 136 HIS ** Ab 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 73 GLN ** Ac 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 60 HIS Ae 11 ASN ** Ae 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 141 GLN ** Af 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 151 HIS ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 118 HIS Ag 141 GLN Ag 151 HIS ** Ah 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 7 GLN Ai 57 HIS Ai 154 ASN Aj 141 GLN Ak 60 HIS Ak 118 HIS Al 136 HIS Am 25 ASN Am 125 ASN Am 141 GLN Am 173 HIS ** An 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 11 ASN ** An 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 23 GLN As 11 ASN As 21 ASN ** As 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** At 112 GLN At 173 HIS Au 23 GLN ** Au 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 21 ASN Aw 74 ASN ** Aw 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 23 GLN ** Ax 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 65 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 14 GLN Ay 65 HIS Ay 173 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2030 moved from start: 0.7245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 44828 Z= 0.237 Angle : 0.665 11.749 60460 Z= 0.348 Chirality : 0.041 0.194 6432 Planarity : 0.005 0.065 7916 Dihedral : 5.130 33.710 5845 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.21 % Allowed : 8.46 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 3595 sheet: -0.34 (0.38), residues: 192 loop : -1.91 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPAz 93 HIS 0.040 0.002 HISAp 65 PHE 0.030 0.002 PHEAr 41 TYR 0.050 0.002 TYRAf 39 ARG 0.007 0.001 ARGAy 79 *********************** 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 482 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 377 time to evaluate : 3.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 34 TYR cc_start: 0.0550 (OUTLIER) cc_final: 0.0225 (m-80) REVERT: Ab 131 LEU cc_start: 0.4207 (tp) cc_final: 0.3945 (mt) REVERT: Ab 352 ASP cc_start: 0.6581 (m-30) cc_final: 0.6338 (p0) REVERT: Ab 357 TRP cc_start: -0.0761 (m-10) cc_final: -0.0990 (m-10) REVERT: Ab 436 MET cc_start: -0.0752 (mmt) cc_final: -0.1378 (ttm) REVERT: Ab 679 MET cc_start: 0.3361 (mtt) cc_final: 0.2852 (tmm) REVERT: Ae 98 ASN cc_start: 0.6129 (t0) cc_final: 0.5582 (p0) REVERT: Ae 100 MET cc_start: -0.2704 (ptt) cc_final: -0.4915 (ttp) REVERT: Af 28 LEU cc_start: 0.3579 (OUTLIER) cc_final: 0.3294 (tp) REVERT: Af 70 MET cc_start: 0.4790 (mmt) cc_final: 0.3375 (mmt) REVERT: Ag 41 PHE cc_start: 0.7377 (m-80) cc_final: 0.7033 (m-80) REVERT: Ag 119 LYS cc_start: 0.7690 (tmtt) cc_final: 0.7052 (ptpt) REVERT: Ag 172 LYS cc_start: 0.2794 (mmtm) cc_final: 0.2518 (mmtm) REVERT: Ah 161 PRO cc_start: 0.6427 (Cg_endo) cc_final: 0.6037 (Cg_exo) REVERT: Ai 70 MET cc_start: 0.5257 (mmt) cc_final: 0.4317 (mmt) REVERT: Aj 58 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7705 (tm-30) REVERT: Aj 70 MET cc_start: 0.4750 (mmt) cc_final: 0.3358 (mmt) REVERT: Aj 158 MET cc_start: 0.4944 (mmm) cc_final: 0.1470 (tmm) REVERT: Al 43 ARG cc_start: 0.2353 (mmt180) cc_final: -0.1088 (ptp-110) REVERT: Al 117 LEU cc_start: -0.3063 (OUTLIER) cc_final: -0.3397 (mp) REVERT: Am 25 ASN cc_start: -0.3265 (OUTLIER) cc_final: -0.4136 (t0) REVERT: An 25 ASN cc_start: 0.5019 (t0) cc_final: 0.4781 (t0) REVERT: An 73 GLN cc_start: 0.2303 (tp-100) cc_final: 0.1349 (tt0) REVERT: An 87 LYS cc_start: -0.1100 (OUTLIER) cc_final: -0.2117 (pttt) REVERT: Ao 138 LEU cc_start: 0.1740 (OUTLIER) cc_final: 0.1296 (mt) REVERT: Ap 100 MET cc_start: -0.1403 (ttm) cc_final: -0.1820 (ttp) REVERT: Aq 140 PHE cc_start: 0.0638 (m-10) cc_final: -0.0572 (t80) REVERT: Aq 173 PHE cc_start: 0.1627 (OUTLIER) cc_final: 0.1142 (t80) REVERT: Aq 388 ASN cc_start: 0.5129 (m-40) cc_final: 0.4120 (m-40) REVERT: Aq 426 LEU cc_start: 0.0651 (OUTLIER) cc_final: 0.0380 (mt) REVERT: Aq 694 GLU cc_start: 0.1527 (mt-10) cc_final: 0.1073 (tm-30) REVERT: Ar 71 LYS cc_start: 0.2243 (OUTLIER) cc_final: 0.1805 (tppt) REVERT: As 60 HIS cc_start: -0.1385 (OUTLIER) cc_final: -0.1626 (t70) REVERT: As 100 MET cc_start: 0.1205 (mmt) cc_final: -0.0463 (mmt) REVERT: Au 70 MET cc_start: 0.0612 (mtt) cc_final: 0.0163 (mtt) REVERT: Au 158 MET cc_start: -0.0919 (tpp) cc_final: -0.1496 (tpt) REVERT: Aw 49 LYS cc_start: 0.6514 (mptt) cc_final: 0.6269 (mptt) REVERT: Aw 71 LYS cc_start: 0.7923 (pttt) cc_final: 0.6382 (tptp) REVERT: Aw 100 MET cc_start: 0.6826 (ttm) cc_final: 0.4479 (tmm) REVERT: Ax 54 TYR cc_start: 0.6782 (t80) cc_final: 0.5444 (t80) outliers start: 105 outliers final: 55 residues processed: 458 average time/residue: 0.4437 time to fit residues: 339.9769 Evaluate side-chains 398 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 333 time to evaluate : 3.593 ------------------------------------------------------------------------------- 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 209 LEU Chi-restraints excluded: chain Ab residue 250 VAL Chi-restraints excluded: chain Ab residue 393 ILE Chi-restraints excluded: chain Ab residue 494 PHE Chi-restraints excluded: chain Ab residue 522 LEU 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 118 HIS Chi-restraints excluded: chain Ad residue 53 LYS Chi-restraints excluded: chain Ad residue 165 LEU 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 142 VAL Chi-restraints excluded: chain Af residue 175 LEU Chi-restraints excluded: chain Ag residue 75 GLN Chi-restraints excluded: chain Ag residue 104 LEU Chi-restraints excluded: chain Ag residue 155 LEU Chi-restraints excluded: chain Ai residue 6 SER Chi-restraints excluded: chain Ai residue 68 LYS Chi-restraints excluded: chain Ai residue 104 LEU 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 80 ILE Chi-restraints excluded: chain Al residue 117 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 An residue 76 ARG Chi-restraints excluded: chain An residue 87 LYS 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 Ao residue 138 LEU Chi-restraints excluded: chain Ap residue 8 VAL Chi-restraints excluded: chain Aq residue 173 PHE Chi-restraints excluded: chain Aq residue 426 LEU Chi-restraints excluded: chain Aq residue 432 MET Chi-restraints excluded: chain Aq residue 675 ASN Chi-restraints excluded: chain Ar residue 71 LYS Chi-restraints excluded: chain As residue 60 HIS Chi-restraints excluded: chain As residue 117 LEU Chi-restraints excluded: chain Aw residue 24 ILE Chi-restraints excluded: chain Aw residue 37 MET Chi-restraints excluded: chain Aw residue 56 LEU 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 72 LEU Chi-restraints excluded: chain Ay residue 104 LEU Chi-restraints excluded: chain Ay residue 145 ILE 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: 8.9990 chunk 58 optimal weight: 3.9990 chunk 294 optimal weight: 0.9980 chunk 377 optimal weight: 30.0000 chunk 292 optimal weight: 5.9990 chunk 434 optimal weight: 7.9990 chunk 288 optimal weight: 3.9990 chunk 514 optimal weight: 5.9990 chunk 322 optimal weight: 20.0000 chunk 313 optimal weight: 3.9990 chunk 237 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 173 HIS ** Ac 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 112 GLN Ac 141 GLN ** Ad 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 151 HIS ** 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 65 HIS ** Ag 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 50 ASN Ai 141 GLN Ai 154 ASN Aj 74 ASN Ak 60 HIS Ak 118 HIS ** Am 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 13 HIS An 58 GLN ** An 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 128 HIS Ao 21 ASN ** Ap 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 215 ASN ** Aq 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 74 ASN ** 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 105 HIS At 109 ASN At 141 GLN Au 136 HIS Av 7 GLN Av 11 ASN ** Av 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 105 HIS ** Av 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 25 ASN ** Ax 65 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2165 moved from start: 0.8137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 44828 Z= 0.226 Angle : 0.664 11.821 60460 Z= 0.347 Chirality : 0.041 0.225 6432 Planarity : 0.005 0.073 7916 Dihedral : 5.181 33.336 5845 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.02 % Allowed : 9.93 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.80 (0.11), residues: 5332 helix: 1.55 (0.08), residues: 3602 sheet: -0.27 (0.39), residues: 186 loop : -1.86 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPAz 93 HIS 0.013 0.002 HISAv 105 PHE 0.035 0.002 PHEAb 433 TYR 0.040 0.002 TYRAf 39 ARG 0.008 0.001 ARGAr 76 *********************** 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 469 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 373 time to evaluate : 3.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 131 LEU cc_start: 0.3922 (tp) cc_final: 0.3715 (mt) REVERT: Ab 357 TRP cc_start: -0.0384 (m-10) cc_final: -0.0986 (m-10) REVERT: Ab 436 MET cc_start: -0.0517 (mmt) cc_final: -0.1040 (ttp) REVERT: Ab 679 MET cc_start: 0.3397 (mtt) cc_final: 0.2921 (tmm) REVERT: Ac 21 ASN cc_start: -0.0845 (OUTLIER) cc_final: -0.2085 (p0) REVERT: Ad 41 PHE cc_start: 0.1152 (OUTLIER) cc_final: 0.0465 (m-10) REVERT: Ad 70 MET cc_start: 0.2047 (mmm) cc_final: 0.0065 (ttt) REVERT: Ad 158 MET cc_start: 0.1066 (OUTLIER) cc_final: 0.0579 (ttp) REVERT: Ae 37 MET cc_start: -0.0320 (mmt) cc_final: -0.1423 (tpt) REVERT: Ae 57 HIS cc_start: 0.0379 (OUTLIER) cc_final: -0.1248 (m-70) REVERT: Ae 98 ASN cc_start: 0.6201 (t0) cc_final: 0.5382 (p0) REVERT: Af 28 LEU cc_start: 0.3276 (OUTLIER) cc_final: 0.3057 (tp) REVERT: Af 42 ASP cc_start: 0.6947 (t70) cc_final: 0.6745 (t0) REVERT: Af 58 GLN cc_start: 0.8086 (tm-30) cc_final: 0.6511 (tp40) REVERT: Af 70 MET cc_start: 0.5233 (mmt) cc_final: 0.4667 (mmt) REVERT: Ag 41 PHE cc_start: 0.7695 (m-80) cc_final: 0.7410 (m-80) REVERT: Ag 67 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8494 (pp20) REVERT: Ag 119 LYS cc_start: 0.7813 (tmtt) cc_final: 0.7033 (ptpt) REVERT: Ag 172 LYS cc_start: 0.2524 (mmtm) cc_final: 0.2272 (mmtp) REVERT: Ah 161 PRO cc_start: 0.7093 (Cg_endo) cc_final: 0.6764 (Cg_exo) REVERT: Ai 63 ARG cc_start: 0.6417 (tpt-90) cc_final: 0.5358 (tpt-90) REVERT: Ai 70 MET cc_start: 0.5597 (mmt) cc_final: 0.4792 (mmt) REVERT: Ai 134 GLU cc_start: 0.2444 (mt-10) cc_final: 0.2220 (mt-10) REVERT: Ai 135 THR cc_start: 0.7388 (m) cc_final: 0.7115 (t) REVERT: Aj 70 MET cc_start: 0.5223 (mmt) cc_final: 0.3549 (mmt) REVERT: Aj 74 ASN cc_start: 0.7967 (m110) cc_final: 0.7363 (m-40) REVERT: Aj 100 MET cc_start: 0.4522 (tpp) cc_final: 0.3883 (mmm) REVERT: Aj 116 GLU cc_start: 0.6009 (mt-10) cc_final: 0.5785 (mm-30) REVERT: Aj 123 ASP cc_start: 0.5702 (m-30) cc_final: 0.5400 (m-30) REVERT: Aj 137 TYR cc_start: 0.3672 (m-10) cc_final: 0.3242 (m-80) REVERT: Aj 158 MET cc_start: 0.4628 (mmm) cc_final: 0.1301 (tmm) REVERT: Ak 117 LEU cc_start: -0.3670 (OUTLIER) cc_final: -0.4036 (tp) REVERT: Al 43 ARG cc_start: 0.2546 (mmt180) cc_final: -0.0880 (ptp-110) REVERT: Al 117 LEU cc_start: -0.3122 (OUTLIER) cc_final: -0.3485 (mp) REVERT: Al 158 MET cc_start: -0.2317 (tpt) cc_final: -0.3808 (tpt) REVERT: Am 93 TRP cc_start: 0.4316 (OUTLIER) cc_final: 0.3405 (m100) REVERT: An 25 ASN cc_start: 0.5339 (t0) cc_final: 0.5129 (t0) REVERT: An 73 GLN cc_start: 0.2334 (tp-100) cc_final: 0.1603 (tt0) REVERT: Ao 138 LEU cc_start: 0.1625 (OUTLIER) cc_final: 0.1172 (mt) REVERT: Ap 12 TYR cc_start: 0.1149 (OUTLIER) cc_final: -0.2303 (t80) REVERT: Aq 173 PHE cc_start: 0.1649 (OUTLIER) cc_final: 0.1229 (t80) REVERT: Aq 388 ASN cc_start: 0.5468 (m-40) cc_final: 0.4755 (m-40) REVERT: Aq 694 GLU cc_start: 0.1497 (mt-10) cc_final: 0.1172 (tm-30) REVERT: Ar 57 HIS cc_start: 0.5594 (t-90) cc_final: 0.5053 (t70) REVERT: Ar 71 LYS cc_start: 0.2074 (OUTLIER) cc_final: 0.1196 (tppt) REVERT: As 75 GLN cc_start: 0.6619 (tt0) cc_final: 0.6406 (tt0) REVERT: As 100 MET cc_start: 0.1383 (mmt) cc_final: -0.0890 (mmt) REVERT: At 93 TRP cc_start: 0.4147 (m100) cc_final: 0.3278 (m100) REVERT: Au 37 MET cc_start: -0.2934 (mtt) cc_final: -0.3689 (mmp) REVERT: Au 70 MET cc_start: 0.0717 (mtt) cc_final: 0.0455 (mtm) REVERT: Aw 100 MET cc_start: 0.6685 (ttm) cc_final: 0.4771 (tmm) REVERT: Ax 50 ASN cc_start: 0.2751 (m-40) cc_final: 0.2410 (m-40) REVERT: Ax 54 TYR cc_start: 0.6974 (t80) cc_final: 0.5749 (t80) REVERT: Ay 137 TYR cc_start: 0.5463 (m-10) cc_final: 0.5123 (m-80) REVERT: Ay 143 LYS cc_start: 0.6524 (tmtt) cc_final: 0.6308 (mmmt) outliers start: 96 outliers final: 54 residues processed: 443 average time/residue: 0.4531 time to fit residues: 331.9682 Evaluate side-chains 400 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 333 time to evaluate : 3.598 ------------------------------------------------------------------------------- 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 250 VAL 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 Ac residue 21 ASN Chi-restraints excluded: chain Ac residue 41 PHE 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 Ad residue 158 MET 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 Ag residue 67 GLU Chi-restraints excluded: chain Ag residue 75 GLN 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 Ai residue 6 SER Chi-restraints excluded: chain Ai residue 104 LEU Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 117 LEU Chi-restraints excluded: chain Aj residue 142 VAL Chi-restraints excluded: chain Aj residue 175 LEU Chi-restraints excluded: chain Ak residue 65 HIS Chi-restraints excluded: chain Ak residue 69 LEU Chi-restraints excluded: chain Ak residue 117 LEU Chi-restraints excluded: chain Al residue 44 ASP Chi-restraints excluded: chain Al residue 80 ILE 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 Ao residue 138 LEU Chi-restraints excluded: chain Ap residue 8 VAL Chi-restraints excluded: chain Ap residue 12 TYR Chi-restraints excluded: chain Aq residue 173 PHE Chi-restraints excluded: chain Aq residue 403 VAL Chi-restraints excluded: chain Aq residue 675 ASN Chi-restraints excluded: chain Ar residue 71 LYS Chi-restraints excluded: chain As residue 117 LEU Chi-restraints excluded: chain Av residue 51 PHE Chi-restraints excluded: chain Aw residue 24 ILE Chi-restraints excluded: chain Aw residue 37 MET Chi-restraints excluded: chain Aw residue 56 LEU Chi-restraints excluded: chain Aw residue 72 LEU Chi-restraints excluded: chain Aw residue 109 ASN Chi-restraints excluded: chain Aw residue 110 VAL 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 Ay residue 104 LEU Chi-restraints excluded: chain Ay residue 145 ILE Chi-restraints excluded: chain Az residue 133 ILE 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: 4.9990 chunk 307 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 327 optimal weight: 3.9990 chunk 350 optimal weight: 40.0000 chunk 254 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 404 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ab 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 7 GLN ** Ad 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 74 ASN ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 11 ASN ** Ag 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 141 GLN ** Ah 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 60 HIS ** Aj 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 118 HIS Am 25 ASN ** An 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 74 ASN Ao 11 ASN ** Aq 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 7 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Au 136 HIS ** Av 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 65 HIS Aw 73 GLN ** Ax 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 111 ASN ** 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 154 ASN ** Az 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2180 moved from start: 0.8611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 44828 Z= 0.204 Angle : 0.630 12.229 60460 Z= 0.326 Chirality : 0.040 0.253 6432 Planarity : 0.004 0.072 7916 Dihedral : 5.070 33.342 5845 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.81 % Allowed : 10.96 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.11), residues: 5332 helix: 1.65 (0.08), residues: 3592 sheet: -0.18 (0.40), residues: 186 loop : -1.90 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAq 412 HIS 0.014 0.001 HISAy 60 PHE 0.023 0.002 PHEAr 41 TYR 0.046 0.002 TYRAx 29 ARG 0.010 0.001 ARGAr 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 460 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 374 time to evaluate : 3.683 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: 0.3964 (tp) cc_final: 0.3692 (mt) REVERT: Ab 243 PHE cc_start: 0.2259 (m-80) cc_final: 0.1998 (m-80) REVERT: Ab 352 ASP cc_start: 0.5376 (t0) cc_final: 0.5140 (p0) REVERT: Ab 353 CYS cc_start: -0.1766 (OUTLIER) cc_final: -0.1984 (p) REVERT: Ab 357 TRP cc_start: -0.0848 (m-10) cc_final: -0.1195 (m-10) REVERT: Ab 436 MET cc_start: -0.0640 (mmt) cc_final: -0.1120 (ttt) REVERT: Ab 679 MET cc_start: 0.3412 (mtt) cc_final: 0.2927 (tmm) REVERT: Ac 21 ASN cc_start: -0.0819 (OUTLIER) cc_final: -0.2047 (p0) REVERT: Ad 41 PHE cc_start: 0.1102 (OUTLIER) cc_final: 0.0492 (m-10) REVERT: Ae 57 HIS cc_start: 0.0208 (OUTLIER) cc_final: -0.1034 (t70) REVERT: Ae 98 ASN cc_start: 0.6313 (m-40) cc_final: 0.6099 (p0) REVERT: Af 42 ASP cc_start: 0.7186 (t70) cc_final: 0.6870 (t0) REVERT: Af 70 MET cc_start: 0.5243 (mmt) cc_final: 0.4034 (mmt) REVERT: Ag 40 TYR cc_start: 0.5974 (t80) cc_final: 0.5349 (t80) REVERT: Ag 41 PHE cc_start: 0.7579 (m-80) cc_final: 0.7217 (m-80) REVERT: Ag 63 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7423 (tmt-80) REVERT: Ag 74 ASN cc_start: 0.4584 (OUTLIER) cc_final: 0.4077 (m110) REVERT: Ag 119 LYS cc_start: 0.8050 (tmtt) cc_final: 0.7357 (ptpt) REVERT: Ag 172 LYS cc_start: 0.2354 (mmtm) cc_final: 0.1987 (mmtp) REVERT: Ah 93 TRP cc_start: 0.1668 (m100) cc_final: 0.0268 (m100) REVERT: Ai 61 GLU cc_start: 0.3646 (mt-10) cc_final: 0.2439 (tt0) REVERT: Ai 70 MET cc_start: 0.5011 (mmt) cc_final: 0.4618 (mmt) REVERT: Ai 114 LEU cc_start: 0.5063 (mt) cc_final: 0.4809 (mt) REVERT: Ai 155 LEU cc_start: 0.4045 (mt) cc_final: 0.3771 (tp) REVERT: Aj 58 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7894 (tm-30) REVERT: Aj 70 MET cc_start: 0.5136 (mmt) cc_final: 0.3825 (mmt) REVERT: Aj 100 MET cc_start: 0.4529 (tpp) cc_final: 0.4027 (mmm) REVERT: Aj 116 GLU cc_start: 0.6255 (mt-10) cc_final: 0.6026 (mm-30) REVERT: Aj 123 ASP cc_start: 0.6001 (m-30) cc_final: 0.5600 (m-30) REVERT: Aj 134 GLU cc_start: 0.4915 (mt-10) cc_final: 0.4309 (mt-10) REVERT: Aj 137 TYR cc_start: 0.4022 (m-10) cc_final: 0.3525 (m-80) REVERT: Aj 158 MET cc_start: 0.4190 (mmm) cc_final: 0.1032 (tmm) REVERT: Ak 117 LEU cc_start: -0.3700 (OUTLIER) cc_final: -0.4039 (tp) REVERT: Al 43 ARG cc_start: 0.3177 (mmt180) cc_final: -0.0413 (ptp-110) REVERT: Al 117 LEU cc_start: -0.3152 (OUTLIER) cc_final: -0.3503 (mp) REVERT: Al 158 MET cc_start: -0.1992 (tpt) cc_final: -0.3778 (tpt) REVERT: Am 25 ASN cc_start: -0.2914 (OUTLIER) cc_final: -0.3708 (t0) REVERT: Am 93 TRP cc_start: 0.4412 (OUTLIER) cc_final: 0.3883 (m100) REVERT: Am 126 ASP cc_start: -0.0734 (OUTLIER) cc_final: -0.1274 (p0) REVERT: Am 168 TYR cc_start: -0.0635 (t80) cc_final: -0.1598 (t80) REVERT: An 73 GLN cc_start: 0.1832 (tp-100) cc_final: 0.1251 (tt0) REVERT: Ao 138 LEU cc_start: 0.1686 (OUTLIER) cc_final: 0.1208 (mt) REVERT: Ap 12 TYR cc_start: 0.1452 (OUTLIER) cc_final: -0.2571 (t80) REVERT: Ap 158 MET cc_start: 0.2654 (mmt) cc_final: 0.2405 (mmt) REVERT: Aq 140 PHE cc_start: 0.0384 (m-10) cc_final: -0.0875 (t80) REVERT: Aq 173 PHE cc_start: 0.2281 (OUTLIER) cc_final: 0.2007 (t80) REVERT: Aq 388 ASN cc_start: 0.5359 (m-40) cc_final: 0.4519 (m-40) REVERT: Aq 635 MET cc_start: -0.4356 (mtm) cc_final: -0.4649 (ttt) REVERT: Aq 694 GLU cc_start: 0.1511 (mt-10) cc_final: 0.1144 (tm-30) REVERT: Ar 57 HIS cc_start: 0.5397 (t-90) cc_final: 0.4976 (t70) REVERT: As 48 LEU cc_start: 0.1537 (mp) cc_final: 0.1227 (mp) REVERT: As 100 MET cc_start: 0.1156 (mmt) cc_final: -0.1239 (mmt) REVERT: At 37 MET cc_start: 0.6314 (tpp) cc_final: 0.6008 (tpp) REVERT: Au 70 MET cc_start: 0.0478 (mtt) cc_final: 0.0196 (mtm) REVERT: Aw 100 MET cc_start: 0.6795 (ttm) cc_final: 0.4780 (tmm) REVERT: Ax 100 MET cc_start: -0.3280 (ttm) cc_final: -0.3744 (ttp) REVERT: Ay 137 TYR cc_start: 0.5332 (m-10) cc_final: 0.4991 (m-80) outliers start: 86 outliers final: 56 residues processed: 439 average time/residue: 0.4451 time to fit residues: 325.3271 Evaluate side-chains 406 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 337 time to evaluate : 3.631 ------------------------------------------------------------------------------- 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 209 LEU Chi-restraints excluded: chain Ab residue 353 CYS Chi-restraints excluded: chain Ab residue 476 LEU Chi-restraints excluded: chain Ab residue 484 LEU 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 118 HIS Chi-restraints excluded: chain Ad residue 41 PHE Chi-restraints excluded: chain Ad residue 53 LYS Chi-restraints excluded: chain Ae residue 51 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 Ag residue 64 GLU Chi-restraints excluded: chain Ag residue 74 ASN Chi-restraints excluded: chain Ag residue 145 ILE Chi-restraints excluded: chain Ag residue 155 LEU Chi-restraints excluded: chain Ah residue 44 ASP Chi-restraints excluded: chain Ai residue 6 SER Chi-restraints excluded: chain Ai residue 104 LEU Chi-restraints excluded: chain Ai residue 122 THR Chi-restraints excluded: chain Aj residue 11 ASN Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 114 LEU Chi-restraints excluded: chain Aj residue 117 LEU Chi-restraints excluded: chain Aj residue 143 LYS Chi-restraints excluded: chain Aj residue 175 LEU Chi-restraints excluded: chain Ak residue 65 HIS Chi-restraints excluded: chain Ak residue 69 LEU Chi-restraints excluded: chain Ak residue 117 LEU Chi-restraints excluded: chain Al residue 80 ILE 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 Am residue 126 ASP 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 Ao residue 138 LEU Chi-restraints excluded: chain Ap residue 8 VAL Chi-restraints excluded: chain Ap residue 12 TYR 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 675 ASN Chi-restraints excluded: chain As residue 117 LEU Chi-restraints excluded: chain Aw residue 24 ILE Chi-restraints excluded: chain Aw residue 37 MET Chi-restraints excluded: chain Aw residue 56 LEU Chi-restraints excluded: chain Aw residue 60 HIS Chi-restraints excluded: chain Aw residue 73 GLN Chi-restraints excluded: chain Aw residue 109 ASN Chi-restraints excluded: chain Aw residue 110 VAL 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 Ay residue 104 LEU Chi-restraints excluded: chain Az residue 133 ILE 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: 3.9990 chunk 493 optimal weight: 6.9990 chunk 449 optimal weight: 0.2980 chunk 479 optimal weight: 0.8980 chunk 492 optimal weight: 2.9990 chunk 288 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 376 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 433 optimal weight: 5.9990 chunk 453 optimal weight: 7.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ab 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 75 GLN Af 11 ASN ** Af 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 23 GLN ** Ag 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 60 HIS Aj 75 GLN Ak 118 HIS Am 25 ASN ** An 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 73 GLN Ap 105 HIS Ap 109 ASN ** Aq 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 300 HIS ** Ar 7 GLN ** 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 112 GLN ** As 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** At 13 HIS Au 136 HIS ** Av 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 21 ASN Aw 65 HIS Aw 73 GLN ** Ax 65 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 11 ASN Ay 74 ASN ** Az 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2162 moved from start: 0.8801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 44828 Z= 0.180 Angle : 0.602 13.452 60460 Z= 0.309 Chirality : 0.039 0.234 6432 Planarity : 0.004 0.089 7916 Dihedral : 4.930 32.816 5845 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.70 % Allowed : 11.51 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.12 (0.11), residues: 5332 helix: 1.80 (0.08), residues: 3621 sheet: -0.13 (0.40), residues: 186 loop : -1.84 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAp 93 HIS 0.015 0.001 HISAy 60 PHE 0.019 0.002 PHEAr 41 TYR 0.036 0.002 TYRAw 34 ARG 0.015 0.001 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 444 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 363 time to evaluate : 3.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 131 LEU cc_start: 0.4016 (tp) cc_final: 0.3758 (mt) REVERT: Ab 243 PHE cc_start: 0.2237 (m-80) cc_final: 0.1982 (m-80) REVERT: Ab 357 TRP cc_start: -0.1117 (m-10) cc_final: -0.1443 (m-10) REVERT: Ab 436 MET cc_start: -0.0621 (mmt) cc_final: -0.1184 (ttp) REVERT: Ab 679 MET cc_start: 0.3854 (mtt) cc_final: 0.3270 (tmm) REVERT: Ac 21 ASN cc_start: -0.0652 (OUTLIER) cc_final: -0.1902 (p0) REVERT: Ad 41 PHE cc_start: 0.1007 (OUTLIER) cc_final: 0.0406 (m-10) REVERT: Ae 37 MET cc_start: -0.0189 (mmt) cc_final: -0.0435 (tpp) REVERT: Ae 57 HIS cc_start: 0.0062 (OUTLIER) cc_final: -0.1359 (m-70) REVERT: Ae 98 ASN cc_start: 0.6751 (t0) cc_final: 0.5591 (p0) REVERT: Af 58 GLN cc_start: 0.7936 (tm-30) cc_final: 0.4969 (tp40) REVERT: Af 70 MET cc_start: 0.5186 (mmt) cc_final: 0.4057 (mmt) REVERT: Af 117 LEU cc_start: 0.6650 (pp) cc_final: 0.6322 (tt) REVERT: Ag 26 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7315 (mp) REVERT: Ag 40 TYR cc_start: 0.5988 (t80) cc_final: 0.5331 (t80) REVERT: Ag 41 PHE cc_start: 0.7540 (m-80) cc_final: 0.7210 (m-80) REVERT: Ag 63 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7367 (tmt-80) REVERT: Ag 119 LYS cc_start: 0.7978 (tmtt) cc_final: 0.7336 (ptpt) REVERT: Ah 93 TRP cc_start: 0.1690 (m100) cc_final: 0.0425 (m100) REVERT: Ai 70 MET cc_start: 0.5087 (mmt) cc_final: 0.4621 (mmt) REVERT: Aj 58 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7780 (tm-30) REVERT: Aj 70 MET cc_start: 0.5082 (mmt) cc_final: 0.3765 (mmt) REVERT: Aj 134 GLU cc_start: 0.4872 (mt-10) cc_final: 0.4204 (mt-10) REVERT: Aj 137 TYR cc_start: 0.3845 (m-10) cc_final: 0.3416 (m-80) REVERT: Aj 158 MET cc_start: 0.4381 (mmm) cc_final: 0.1230 (tmm) REVERT: Ak 34 TYR cc_start: 0.0216 (OUTLIER) cc_final: -0.2219 (m-80) REVERT: Al 43 ARG cc_start: 0.3183 (mmt180) cc_final: -0.0352 (ptp-110) REVERT: Al 117 LEU cc_start: -0.3211 (OUTLIER) cc_final: -0.3550 (mp) REVERT: Al 158 MET cc_start: -0.2045 (tpt) cc_final: -0.3672 (tpt) REVERT: Am 25 ASN cc_start: -0.3019 (OUTLIER) cc_final: -0.3717 (t0) REVERT: Am 93 TRP cc_start: 0.4525 (OUTLIER) cc_final: 0.4055 (m100) REVERT: Am 168 TYR cc_start: -0.0355 (t80) cc_final: -0.1383 (t80) REVERT: Ao 138 LEU cc_start: 0.1684 (OUTLIER) cc_final: 0.1247 (mt) REVERT: Ap 12 TYR cc_start: 0.1046 (OUTLIER) cc_final: -0.0318 (t80) REVERT: Ap 158 MET cc_start: 0.2708 (mmt) cc_final: 0.2498 (mmt) REVERT: Aq 173 PHE cc_start: 0.2304 (OUTLIER) cc_final: 0.2023 (t80) REVERT: Aq 349 MET cc_start: 0.2445 (ptm) cc_final: 0.2129 (ppp) REVERT: Aq 388 ASN cc_start: 0.5323 (m-40) cc_final: 0.4913 (m-40) REVERT: Aq 635 MET cc_start: -0.4335 (mtm) cc_final: -0.4691 (ttt) REVERT: Aq 694 GLU cc_start: 0.1643 (mt-10) cc_final: 0.1257 (tm-30) REVERT: Ar 57 HIS cc_start: 0.5335 (t-90) cc_final: 0.4942 (t70) REVERT: As 48 LEU cc_start: 0.1636 (mp) cc_final: 0.1302 (mp) REVERT: As 75 GLN cc_start: 0.6555 (tm-30) cc_final: 0.6278 (tm-30) REVERT: As 100 MET cc_start: 0.1133 (mmt) cc_final: -0.0645 (mmt) REVERT: Au 70 MET cc_start: 0.0608 (mtt) cc_final: 0.0322 (mtp) REVERT: Au 89 ASP cc_start: 0.0418 (OUTLIER) cc_final: -0.1364 (p0) REVERT: Au 158 MET cc_start: -0.0672 (tpp) cc_final: -0.1297 (tpt) REVERT: Aw 22 ARG cc_start: 0.7541 (ptt-90) cc_final: 0.6207 (ttp80) REVERT: Aw 100 MET cc_start: 0.6869 (ttm) cc_final: 0.4846 (tmm) REVERT: Aw 116 GLU cc_start: 0.7449 (pp20) cc_final: 0.7171 (mm-30) REVERT: Ax 100 MET cc_start: -0.3027 (ttm) cc_final: -0.3983 (ttp) REVERT: Ay 137 TYR cc_start: 0.5476 (m-10) cc_final: 0.5141 (m-80) outliers start: 81 outliers final: 57 residues processed: 418 average time/residue: 0.4473 time to fit residues: 310.9045 Evaluate side-chains 415 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 346 time to evaluate : 3.615 ------------------------------------------------------------------------------- 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 209 LEU Chi-restraints excluded: chain Ab residue 393 ILE Chi-restraints excluded: chain Ab residue 484 LEU 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 Ac residue 21 ASN 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 Ae residue 51 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 140 GLU Chi-restraints excluded: chain Ag residue 23 GLN Chi-restraints excluded: chain Ag residue 26 LEU Chi-restraints excluded: chain Ag residue 64 GLU Chi-restraints excluded: chain Ag residue 145 ILE Chi-restraints excluded: chain Ag residue 155 LEU Chi-restraints excluded: chain Ah residue 44 ASP Chi-restraints excluded: chain Ai residue 6 SER Chi-restraints excluded: chain Ai residue 104 LEU Chi-restraints excluded: chain Aj residue 11 ASN Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 114 LEU Chi-restraints excluded: chain Aj residue 143 LYS Chi-restraints excluded: chain Aj residue 175 LEU 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 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 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 Ao residue 138 LEU Chi-restraints excluded: chain Ap residue 8 VAL Chi-restraints excluded: chain Ap residue 12 TYR 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 675 ASN Chi-restraints excluded: chain As residue 117 LEU Chi-restraints excluded: chain At residue 13 HIS Chi-restraints excluded: chain Au residue 89 ASP Chi-restraints excluded: chain Aw residue 37 MET Chi-restraints excluded: chain Aw residue 56 LEU Chi-restraints excluded: chain Aw residue 60 HIS Chi-restraints excluded: chain Aw residue 73 GLN Chi-restraints excluded: chain Aw residue 109 ASN Chi-restraints excluded: chain Aw residue 115 LEU Chi-restraints excluded: chain Aw residue 155 LEU Chi-restraints excluded: chain Ax residue 28 LEU Chi-restraints excluded: chain Ax residue 51 PHE Chi-restraints excluded: chain Ay residue 56 LEU Chi-restraints excluded: chain Ay residue 104 LEU Chi-restraints excluded: chain Az residue 51 PHE 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: 3.9990 chunk 314 optimal weight: 0.9980 chunk 507 optimal weight: 3.9990 chunk 309 optimal weight: 0.0020 chunk 240 optimal weight: 0.6980 chunk 352 optimal weight: 8.9990 chunk 532 optimal weight: 1.9990 chunk 489 optimal weight: 0.6980 chunk 423 optimal weight: 0.0040 chunk 43 optimal weight: 20.0000 chunk 327 optimal weight: 20.0000 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ab 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 675 ASN Ac 21 ASN Ad 105 HIS Ae 11 ASN ** Ae 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 128 HIS ** 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 ** Ag 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 105 HIS Ai 109 ASN Aj 11 ASN Ak 118 HIS ** An 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 11 ASN An 25 ASN Ao 112 GLN Ap 109 ASN ** Ap 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 300 HIS ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 21 ASN ** As 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 118 HIS At 13 HIS ** At 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 136 HIS ** Av 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 111 ASN Aw 65 HIS Ax 11 ASN ** Ax 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 111 ASN ** 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 154 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1974 moved from start: 0.8669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 44828 Z= 0.139 Angle : 0.551 13.604 60460 Z= 0.281 Chirality : 0.037 0.234 6432 Planarity : 0.004 0.075 7916 Dihedral : 4.558 29.763 5845 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.16 % Allowed : 12.26 % Favored : 86.58 % 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: 1.77 (0.12), residues: 5332 helix: 2.37 (0.08), residues: 3605 sheet: 0.06 (0.39), residues: 188 loop : -1.74 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRPAw 93 HIS 0.023 0.001 HISAt 13 PHE 0.021 0.001 PHEAo 170 TYR 0.037 0.001 TYRAy 34 ARG 0.008 0.000 ARGAw 22 ********************** 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 415 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 360 time to evaluate : 3.701 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: Ab 131 LEU cc_start: 0.3812 (tp) cc_final: 0.3530 (mt) REVERT: Ab 243 PHE cc_start: 0.2189 (m-80) cc_final: 0.1942 (m-80) REVERT: Ab 352 ASP cc_start: 0.6245 (t0) cc_final: 0.5524 (p0) REVERT: Ab 357 TRP cc_start: -0.1110 (m-10) cc_final: -0.1483 (m-10) REVERT: Ab 436 MET cc_start: -0.0710 (mmt) cc_final: -0.1247 (ttp) REVERT: Ab 679 MET cc_start: 0.3867 (mtt) cc_final: 0.3250 (tmm) REVERT: Ac 21 ASN cc_start: -0.1071 (OUTLIER) cc_final: -0.2337 (p0) REVERT: Ae 98 ASN cc_start: 0.6586 (t0) cc_final: 0.5671 (p0) REVERT: Af 58 GLN cc_start: 0.7743 (tm-30) cc_final: 0.5291 (tp40) REVERT: Af 70 MET cc_start: 0.4426 (mmt) cc_final: 0.3222 (mmt) REVERT: Af 117 LEU cc_start: 0.6506 (pp) cc_final: 0.6130 (tt) REVERT: Ag 23 GLN cc_start: 0.6580 (OUTLIER) cc_final: 0.5883 (tp-100) REVERT: Ag 40 TYR cc_start: 0.5638 (t80) cc_final: 0.4999 (t80) REVERT: Ag 63 ARG cc_start: 0.7557 (ttp80) cc_final: 0.7077 (tmt-80) REVERT: Ag 67 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8621 (pp20) REVERT: Ag 100 MET cc_start: 0.5590 (ttt) cc_final: 0.4956 (tmm) REVERT: Ah 93 TRP cc_start: 0.1382 (m100) cc_final: 0.0055 (m100) REVERT: Ai 61 GLU cc_start: 0.2895 (mt-10) cc_final: 0.1877 (pt0) REVERT: Ai 70 MET cc_start: 0.5664 (mmt) cc_final: 0.5338 (mmt) REVERT: Ai 124 LYS cc_start: 0.6081 (pttt) cc_final: 0.5606 (tttp) REVERT: Aj 70 MET cc_start: 0.4776 (mmt) cc_final: 0.4225 (mmt) REVERT: Aj 74 ASN cc_start: 0.7934 (m110) cc_final: 0.7393 (m-40) REVERT: Aj 134 GLU cc_start: 0.4798 (mt-10) cc_final: 0.4064 (mt-10) REVERT: Aj 137 TYR cc_start: 0.3956 (m-10) cc_final: 0.3453 (m-80) REVERT: Aj 158 MET cc_start: 0.4117 (mmm) cc_final: 0.1126 (tmm) REVERT: Al 43 ARG cc_start: 0.3355 (mmt180) cc_final: -0.0238 (ptp-110) REVERT: Al 158 MET cc_start: -0.2209 (tpt) cc_final: -0.3793 (tpt) REVERT: Am 168 TYR cc_start: -0.0489 (t80) cc_final: -0.1411 (t80) REVERT: An 73 GLN cc_start: 0.2087 (tp40) cc_final: 0.1767 (tt0) REVERT: An 100 MET cc_start: 0.1517 (mpp) cc_final: 0.1076 (mpp) REVERT: Ao 51 PHE cc_start: 0.1395 (OUTLIER) cc_final: 0.0709 (m-10) REVERT: Ap 12 TYR cc_start: 0.0633 (OUTLIER) cc_final: -0.0604 (t80) REVERT: Ap 158 MET cc_start: 0.2666 (mmt) cc_final: 0.2462 (mmt) REVERT: Aq 173 PHE cc_start: 0.2334 (OUTLIER) cc_final: 0.1842 (t80) REVERT: Aq 388 ASN cc_start: 0.5303 (m-40) cc_final: 0.4532 (m-40) REVERT: Aq 635 MET cc_start: -0.3963 (mtm) cc_final: -0.4314 (ttt) REVERT: Aq 694 GLU cc_start: 0.1739 (mt-10) cc_final: 0.1249 (tm-30) REVERT: Ar 57 HIS cc_start: 0.5316 (t-90) cc_final: 0.4938 (t70) REVERT: Ar 158 MET cc_start: 0.0014 (tpp) cc_final: -0.0237 (tpp) REVERT: As 70 MET cc_start: -0.0301 (mtt) cc_final: -0.0786 (ttm) REVERT: As 75 GLN cc_start: 0.6552 (tm-30) cc_final: 0.6248 (tm-30) REVERT: Au 70 MET cc_start: 0.0276 (mtt) cc_final: -0.0037 (mtp) REVERT: Aw 64 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7623 (pt0) REVERT: Aw 100 MET cc_start: 0.6614 (ttm) cc_final: 0.4800 (tmm) REVERT: Aw 116 GLU cc_start: 0.7494 (pp20) cc_final: 0.7155 (mm-30) REVERT: Aw 132 PHE cc_start: 0.7354 (t80) cc_final: 0.5694 (t80) REVERT: Ay 137 TYR cc_start: 0.5329 (m-10) cc_final: 0.4949 (m-80) outliers start: 55 outliers final: 42 residues processed: 398 average time/residue: 0.4434 time to fit residues: 294.8856 Evaluate side-chains 391 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 343 time to evaluate : 3.488 ------------------------------------------------------------------------------- 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 209 LEU Chi-restraints excluded: chain Ab residue 494 PHE Chi-restraints excluded: chain Ab residue 553 VAL Chi-restraints excluded: chain Ab residue 641 TRP Chi-restraints excluded: chain Ac residue 21 ASN Chi-restraints excluded: chain Ac residue 118 HIS Chi-restraints excluded: chain Ae residue 51 PHE Chi-restraints excluded: chain Af residue 13 HIS Chi-restraints excluded: chain Af residue 114 LEU Chi-restraints excluded: chain Ag residue 23 GLN Chi-restraints excluded: chain Ag residue 56 LEU Chi-restraints excluded: chain Ai residue 6 SER Chi-restraints excluded: chain Ai residue 114 LEU Chi-restraints excluded: chain Aj residue 63 ARG Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 114 LEU Chi-restraints excluded: chain Aj residue 143 LYS Chi-restraints excluded: chain Am residue 41 PHE Chi-restraints excluded: chain Am residue 82 LEU Chi-restraints excluded: chain An residue 25 ASN 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 12 TYR 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 675 ASN Chi-restraints excluded: chain As residue 21 ASN Chi-restraints excluded: chain As residue 117 LEU Chi-restraints excluded: chain At residue 13 HIS Chi-restraints excluded: chain Aw residue 37 MET Chi-restraints excluded: chain Aw residue 60 HIS 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 28 LEU Chi-restraints excluded: chain Ax residue 51 PHE Chi-restraints excluded: chain Ax residue 131 ASP Chi-restraints excluded: chain Ay residue 56 LEU Chi-restraints excluded: chain Ay residue 154 ASN Chi-restraints excluded: chain Az residue 51 PHE 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: 0.6980 chunk 336 optimal weight: 0.8980 chunk 451 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 424 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 435 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 118 HIS ** Ab 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 608 ASN ** Ac 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 173 HIS ** 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 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 74 ASN ** Ah 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 109 ASN Ak 118 HIS ** Al 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 25 ASN ** An 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 25 ASN ** Ap 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 65 HIS ** Aq 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 7 GLN ** 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** At 13 HIS ** At 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** At 83 GLN At 105 HIS At 109 ASN At 136 HIS ** Au 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 83 GLN Au 136 HIS Av 7 GLN Av 128 HIS ** Aw 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 73 GLN Ax 11 ASN ** Ax 65 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 11 ASN ** Ay 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 154 ASN ** Az 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 60 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.244576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.217954 restraints weight = 100041.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.221031 restraints weight = 60003.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.222978 restraints weight = 38749.527| |-----------------------------------------------------------------------------| r_work (final): 0.4664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2415 moved from start: 0.9265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 44828 Z= 0.239 Angle : 0.692 13.751 60460 Z= 0.356 Chirality : 0.042 0.231 6432 Planarity : 0.005 0.088 7916 Dihedral : 5.013 34.193 5845 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.43 % Allowed : 12.07 % Favored : 86.50 % 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: 1.09 (0.11), residues: 5332 helix: 1.80 (0.08), residues: 3593 sheet: 0.01 (0.41), residues: 182 loop : -1.85 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAo 93 HIS 0.025 0.002 HISAq 300 PHE 0.027 0.002 PHEAr 41 TYR 0.026 0.002 TYRAl 39 ARG 0.011 0.001 ARGAs 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7230.80 seconds wall clock time: 128 minutes 6.19 seconds (7686.19 seconds total)