Starting phenix.real_space_refine on Thu Dec 7 19:05:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5i_0140/12_2023/6h5i_0140.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5i_0140/12_2023/6h5i_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_0140/12_2023/6h5i_0140.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5i_0140/12_2023/6h5i_0140.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5i_0140/12_2023/6h5i_0140.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5i_0140/12_2023/6h5i_0140.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9997 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 196 5.16 5 C 27672 2.51 5 N 7632 2.21 5 O 8400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Ab PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ab TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac ARG 9": "NH1" <-> "NH2" Residue "Ak ARG 22": "NH1" <-> "NH2" Residue "Av ARG 63": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 43900 Number of models: 1 Model: "" Number of chains: 26 Chain: "Aa" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ab" Number of atoms: 4993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 4993 Classifications: {'peptide': 632} Link IDs: {'PTRANS': 25, 'TRANS': 606} Chain breaks: 2 Chain: "Ac" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ad" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ae" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Af" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ag" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ah" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ai" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Aj" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ak" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Al" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Am" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "An" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ao" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ap" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Aq" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5004 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 25, 'TRANS': 607} Chain breaks: 1 Chain: "Ar" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "As" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "At" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1404 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "Au" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Av" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Aw" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ax" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Ay" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Az" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Time building chain proxies: 16.37, per 1000 atoms: 0.37 Number of scatterers: 43900 At special positions: 0 Unit cell: (163.59, 198.17, 199.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 196 16.00 O 8400 8.00 N 7632 7.00 C 27672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYSAb 353 " - pdb=" SG CYSAb 363 " distance=2.02 Simple disulfide: pdb=" SG CYSAq 353 " - pdb=" SG CYSAq 363 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.14 Conformation dependent library (CDL) restraints added in 5.8 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: 2.53 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: 11.54 Time building geometry restraints manager: 13.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14725 1.34 - 1.46: 10278 1.46 - 1.59: 19513 1.59 - 1.71: 0 1.71 - 1.83: 312 Bond restraints: 44828 Sorted by residual: bond pdb=" CG HISAh 57 " pdb=" CD2 HISAh 57 " ideal model delta sigma weight residual 1.354 1.394 -0.040 1.10e-02 8.26e+03 1.33e+01 bond pdb=" CG HISAk 57 " pdb=" CD2 HISAk 57 " ideal model delta sigma weight residual 1.354 1.394 -0.040 1.10e-02 8.26e+03 1.33e+01 bond pdb=" CG HISAs 57 " pdb=" CD2 HISAs 57 " ideal model delta sigma weight residual 1.354 1.394 -0.040 1.10e-02 8.26e+03 1.31e+01 bond pdb=" CG HISAe 57 " pdb=" CD2 HISAe 57 " ideal model delta sigma weight residual 1.354 1.394 -0.040 1.10e-02 8.26e+03 1.31e+01 bond pdb=" CG HISAg 57 " pdb=" CD2 HISAg 57 " ideal model delta sigma weight residual 1.354 1.394 -0.040 1.10e-02 8.26e+03 1.30e+01 ... (remaining 44823 not shown) Histogram of bond angle deviations from ideal: 97.97 - 105.36: 518 105.36 - 112.76: 23471 112.76 - 120.15: 18232 120.15 - 127.54: 17798 127.54 - 134.93: 441 Bond angle restraints: 60460 Sorted by residual: angle pdb=" N PHEAq 557 " pdb=" CA PHEAq 557 " pdb=" C PHEAq 557 " ideal model delta sigma weight residual 108.67 97.97 10.70 1.55e+00 4.16e-01 4.76e+01 angle pdb=" N PHEAb 557 " pdb=" CA PHEAb 557 " pdb=" C PHEAb 557 " ideal model delta sigma weight residual 108.96 98.89 10.07 1.59e+00 3.96e-01 4.01e+01 angle pdb=" C PHEAb 557 " pdb=" CA PHEAb 557 " pdb=" CB PHEAb 557 " ideal model delta sigma weight residual 110.22 119.06 -8.84 1.67e+00 3.59e-01 2.80e+01 angle pdb=" N ALAAb 416 " pdb=" CA ALAAb 416 " pdb=" C ALAAb 416 " ideal model delta sigma weight residual 111.28 116.79 -5.51 1.09e+00 8.42e-01 2.56e+01 angle pdb=" C LYSAq 418 " pdb=" CA LYSAq 418 " pdb=" CB LYSAq 418 " ideal model delta sigma weight residual 109.29 101.05 8.24 1.82e+00 3.02e-01 2.05e+01 ... (remaining 60455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 26029 17.38 - 34.77: 753 34.77 - 52.15: 127 52.15 - 69.54: 15 69.54 - 86.92: 71 Dihedral angle restraints: 26995 sinusoidal: 11085 harmonic: 15910 Sorted by residual: dihedral pdb=" CA THRAb 310 " pdb=" C THRAb 310 " pdb=" N PROAb 311 " pdb=" CA PROAb 311 " ideal model delta harmonic sigma weight residual 180.00 145.63 34.37 0 5.00e+00 4.00e-02 4.73e+01 dihedral pdb=" CA THRAq 310 " pdb=" C THRAq 310 " pdb=" N PROAq 311 " pdb=" CA PROAq 311 " ideal model delta harmonic sigma weight residual 180.00 146.81 33.19 0 5.00e+00 4.00e-02 4.41e+01 dihedral pdb=" CA LEUAb 209 " pdb=" C LEUAb 209 " pdb=" N VALAb 210 " pdb=" CA VALAb 210 " ideal model delta harmonic sigma weight residual -180.00 -147.96 -32.04 0 5.00e+00 4.00e-02 4.11e+01 ... (remaining 26992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4356 0.045 - 0.089: 1632 0.089 - 0.134: 373 0.134 - 0.178: 64 0.178 - 0.223: 7 Chirality restraints: 6432 Sorted by residual: chirality pdb=" CA SERAn 95 " pdb=" N SERAn 95 " pdb=" C SERAn 95 " pdb=" CB SERAn 95 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA LEUAj 148 " pdb=" N LEUAj 148 " pdb=" C LEUAj 148 " pdb=" CB LEUAj 148 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CG LEUAb 209 " pdb=" CB LEUAb 209 " pdb=" CD1 LEUAb 209 " pdb=" CD2 LEUAb 209 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 6429 not shown) Planarity restraints: 7916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLUAe 94 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" C GLUAe 94 " 0.045 2.00e-02 2.50e+03 pdb=" O GLUAe 94 " -0.017 2.00e-02 2.50e+03 pdb=" N SERAe 95 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SERAb 687 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PROAb 688 " -0.109 5.00e-02 4.00e+02 pdb=" CA PROAb 688 " 0.033 5.00e-02 4.00e+02 pdb=" CD PROAb 688 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILEAb 332 " 0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PROAb 333 " -0.105 5.00e-02 4.00e+02 pdb=" CA PROAb 333 " 0.031 5.00e-02 4.00e+02 pdb=" CD PROAb 333 " 0.034 5.00e-02 4.00e+02 ... (remaining 7913 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3234 2.74 - 3.28: 42619 3.28 - 3.82: 72837 3.82 - 4.36: 83655 4.36 - 4.90: 146757 Nonbonded interactions: 349102 Sorted by model distance: nonbonded pdb=" O GLYAb 415 " pdb=" N GLYAb 420 " model vdw 2.196 2.520 nonbonded pdb=" O GLUAb 266 " pdb=" ND2 ASNAb 270 " model vdw 2.207 2.520 nonbonded pdb=" OG1 THRAc 174 " pdb=" OH TYRAw 168 " model vdw 2.242 2.440 nonbonded pdb=" OH TYRAh 168 " pdb=" OG1 THRAu 174 " model vdw 2.246 2.440 nonbonded pdb=" OH TYRAi 168 " pdb=" OG1 THRAx 174 " model vdw 2.249 2.440 ... (remaining 349097 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'Aa' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ac' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ad' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ae' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Af' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ag' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ah' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ai' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Aj' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ak' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Al' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Am' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'An' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ao' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ap' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ar' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'As' and (resid 5 through 86 or resid 88 through 176)) selection = chain 'At' selection = (chain 'Au' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Av' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Aw' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ax' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Ay' and (resid 5 through 86 or resid 88 through 176)) selection = (chain 'Az' and (resid 5 through 86 or resid 88 through 176)) } ncs_group { reference = chain 'Ab' selection = (chain 'Aq' and (resid 121 through 667 or resid 669 through 756)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.030 Extract box with map and model: 5.400 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 80.540 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.160 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:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.900 ------------------------------------------------------------------------------- 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 : 3.423 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 outliers start: 8 outliers final: 1 residues processed: 675 average time/residue: 0.5101 time to fit residues: 557.7404 Evaluate side-chains 390 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 389 time to evaluate : 3.463 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3149 time to fit residues: 5.7875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 450 optimal weight: 0.9990 chunk 404 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 273 optimal weight: 5.9990 chunk 216 optimal weight: 20.0000 chunk 418 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 254 optimal weight: 0.9990 chunk 311 optimal weight: 4.9990 chunk 484 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 11 ASN ** Aa 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 118 HIS Ab 171 ASN Ab 197 GLN Ab 483 ASN Ab 493 ASN ** Ab 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 733 ASN Ab 747 ASN Ac 105 HIS Ac 154 ASN Ac 173 HIS Ad 7 GLN Ad 21 ASN Ad 73 GLN Ad 118 HIS Ae 105 HIS Ae 118 HIS Ae 173 HIS Af 11 ASN Af 111 ASN ** Ag 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 74 ASN Ag 118 HIS Ag 173 HIS Ah 25 ASN Ai 11 ASN ** Ai 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 109 ASN Ai 112 GLN Ai 118 HIS Ai 151 HIS Ai 154 ASN Ai 173 HIS Aj 11 ASN Aj 73 GLN Aj 75 GLN Aj 105 HIS Ak 73 GLN Al 11 ASN Al 60 HIS Al 98 ASN ** Al 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 128 HIS Al 136 HIS Am 25 ASN Am 57 HIS ** Am 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 173 HIS An 13 HIS ** Ao 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 136 HIS Ap 14 GLN Ap 75 GLN Ap 109 ASN Ap 118 HIS Ap 136 HIS Ap 173 HIS Aq 164 ASN Aq 171 ASN Aq 172 GLN Aq 234 HIS Aq 493 ASN ** Aq 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 603 HIS Aq 684 HIS Aq 733 ASN Aq 747 ASN Ar 65 HIS Ar 128 HIS Ar 141 GLN Ar 154 ASN Ar 173 HIS As 7 GLN As 11 ASN ** As 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 74 ASN ** As 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** As 154 ASN As 173 HIS At 11 ASN At 109 ASN At 173 HIS ** Au 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 105 HIS ** Au 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Au 154 ASN Au 173 HIS ** Av 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Av 136 HIS Aw 21 ASN Aw 73 GLN Aw 105 HIS ** Aw 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 136 HIS Aw 173 HIS Ax 7 GLN Ax 75 GLN Ax 125 ASN Ax 173 HIS Ay 11 ASN ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 112 GLN Total number of N/Q/H flips: 89 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1328 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 44828 Z= 0.224 Angle : 0.646 10.869 60460 Z= 0.339 Chirality : 0.041 0.296 6432 Planarity : 0.005 0.062 7916 Dihedral : 4.969 28.989 5845 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.37 % Allowed : 5.15 % Favored : 93.48 % 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: 0.57 (0.11), residues: 5332 helix: 1.60 (0.08), residues: 3593 sheet: -1.13 (0.36), residues: 190 loop : -2.46 (0.14), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRPAn 93 HIS 0.011 0.002 HISAh 151 PHE 0.031 0.002 PHEAz 41 TYR 0.030 0.002 TYRAl 54 ARG 0.011 0.001 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 485 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 420 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 35 residues processed: 460 average time/residue: 0.4593 time to fit residues: 350.6562 Evaluate side-chains 368 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 333 time to evaluate : 3.481 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3674 time to fit residues: 28.2622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 269 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 403 optimal weight: 5.9990 chunk 330 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 485 optimal weight: 6.9990 chunk 524 optimal weight: 0.9980 chunk 432 optimal weight: 3.9990 chunk 481 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 389 optimal weight: 0.1980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 615 ASN Ab 626 ASN Ab 684 HIS Ae 75 GLN Ae 109 ASN ** Ae 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 118 HIS Ah 25 ASN Aj 13 HIS ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 11 ASN An 11 ASN An 83 GLN Ao 7 GLN Ao 128 HIS Aq 164 ASN Aq 388 ASN Aq 615 ASN ** Ar 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 21 ASN ** As 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 118 HIS At 11 ASN ** At 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 73 GLN ** Av 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 75 GLN ** Aw 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 75 GLN ** Ax 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 65 HIS ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 74 ASN Ay 75 GLN Az 128 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1467 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 44828 Z= 0.161 Angle : 0.521 10.974 60460 Z= 0.274 Chirality : 0.037 0.271 6432 Planarity : 0.004 0.056 7916 Dihedral : 4.594 27.461 5845 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.41 % Allowed : 6.63 % Favored : 91.96 % 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: 1.55 (0.11), residues: 5332 helix: 2.30 (0.08), residues: 3623 sheet: -0.62 (0.37), residues: 190 loop : -2.08 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPAn 93 HIS 0.014 0.001 HISAr 13 PHE 0.019 0.002 PHEAv 51 TYR 0.020 0.002 TYRAr 34 ARG 0.006 0.001 ARGAx 76 *********************** 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 446 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 379 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 27 residues processed: 429 average time/residue: 0.4472 time to fit residues: 322.0450 Evaluate side-chains 353 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 326 time to evaluate : 3.438 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3393 time to fit residues: 22.2267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 479 optimal weight: 5.9990 chunk 365 optimal weight: 30.0000 chunk 252 optimal weight: 4.9990 chunk 53 optimal weight: 30.0000 chunk 231 optimal weight: 6.9990 chunk 326 optimal weight: 40.0000 chunk 487 optimal weight: 8.9990 chunk 516 optimal weight: 5.9990 chunk 254 optimal weight: 0.9980 chunk 462 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 348 ASN Ab 608 ASN Ac 11 ASN Ad 60 HIS ** Ae 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 105 HIS Ae 109 ASN ** Ae 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 7 GLN Af 21 ASN Af 60 HIS Af 141 GLN ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 60 HIS Ag 75 GLN Ag 141 GLN Ah 7 GLN Ah 25 ASN ** Ah 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 10 GLN Ai 139 ASN ** Aj 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 141 GLN ** Al 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 136 HIS Al 154 ASN ** Am 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 141 GLN ** An 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 74 ASN An 83 GLN ** An 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 11 ASN Ao 50 ASN ** Ao 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 14 GLN ** Ap 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 65 HIS Aq 300 HIS ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** At 11 ASN At 112 GLN ** At 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Au 128 HIS Av 7 GLN Av 10 GLN ** Av 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 73 GLN Av 105 HIS ** Aw 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 23 GLN Ax 60 HIS ** Ax 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 14 GLN Ay 58 GLN ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 75 GLN ** Ay 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Az 128 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1953 moved from start: 0.6481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 44828 Z= 0.244 Angle : 0.684 10.311 60460 Z= 0.359 Chirality : 0.042 0.240 6432 Planarity : 0.005 0.075 7916 Dihedral : 5.089 34.568 5845 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.94 % Allowed : 8.20 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.11), residues: 5332 helix: 1.65 (0.08), residues: 3623 sheet: -0.53 (0.36), residues: 200 loop : -2.12 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPAn 93 HIS 0.013 0.002 HISAr 13 PHE 0.029 0.002 PHEAa 132 TYR 0.031 0.002 TYRAl 39 ARG 0.014 0.001 ARGAu 76 *********************** 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 494 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 402 time to evaluate : 3.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 38 residues processed: 472 average time/residue: 0.4780 time to fit residues: 371.8323 Evaluate side-chains 377 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 339 time to evaluate : 3.507 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.3398 time to fit residues: 29.2646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 429 optimal weight: 2.9990 chunk 293 optimal weight: 20.0000 chunk 7 optimal weight: 0.0270 chunk 384 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 440 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 263 optimal weight: 5.9990 chunk 463 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 10 GLN ** Aa 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 136 HIS Ab 164 ASN ** Ab 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 141 GLN Ad 7 GLN ** Ae 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 65 HIS ** Ag 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 151 HIS ** Ah 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 57 HIS Ai 141 GLN ** Aj 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 74 ASN ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 25 ASN ** An 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 25 ASN An 128 HIS Ao 7 GLN Ao 125 ASN ** Ap 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 105 HIS Aq 215 ASN ** Aq 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 128 HIS ** As 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** At 141 GLN Au 75 GLN ** Av 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 128 HIS Av 141 GLN Aw 65 HIS ** Ax 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 11 ASN Ay 25 ASN ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2148 moved from start: 0.7723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 44828 Z= 0.244 Angle : 0.675 10.962 60460 Z= 0.354 Chirality : 0.041 0.189 6432 Planarity : 0.005 0.080 7916 Dihedral : 5.236 36.038 5845 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.56 % Allowed : 10.22 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.11), residues: 5332 helix: 1.48 (0.08), residues: 3608 sheet: -0.58 (0.37), residues: 191 loop : -2.04 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPAz 93 HIS 0.011 0.002 HISAy 60 PHE 0.028 0.002 PHEAr 41 TYR 0.036 0.002 TYRAm 39 ARG 0.007 0.001 ARGAr 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 451 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 377 time to evaluate : 3.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 29 residues processed: 437 average time/residue: 0.4489 time to fit residues: 330.9798 Evaluate side-chains 345 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 316 time to evaluate : 3.480 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3363 time to fit residues: 23.2904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 173 optimal weight: 0.7980 chunk 464 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 516 optimal weight: 2.9990 chunk 428 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 chunk 271 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 65 HIS ** Aa 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 348 ASN ** Ac 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 23 GLN ** Ae 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 73 GLN ** 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 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 11 ASN Ag 141 GLN ** Ag 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 60 HIS ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 141 GLN ** Am 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 11 ASN ** An 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 74 ASN An 151 HIS ** Ao 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 125 ASN ** Ap 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 300 HIS ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 57 HIS ** As 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 112 GLN ** Au 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Au 128 HIS Au 136 HIS Av 11 ASN ** Av 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 65 HIS Aw 118 HIS ** Ax 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 11 ASN ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Az 7 GLN Az 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2318 moved from start: 0.8718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 44828 Z= 0.253 Angle : 0.704 14.836 60460 Z= 0.367 Chirality : 0.042 0.364 6432 Planarity : 0.005 0.082 7916 Dihedral : 5.426 35.438 5845 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.62 % Allowed : 11.91 % Favored : 86.47 % 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: 0.33 (0.11), residues: 5332 helix: 1.20 (0.08), residues: 3606 sheet: -0.47 (0.38), residues: 191 loop : -2.10 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPAu 93 HIS 0.015 0.002 HISAq 302 PHE 0.026 0.002 PHEAb 442 TYR 0.033 0.002 TYRAu 34 ARG 0.008 0.001 ARGAi 9 *********************** 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 431 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 354 time to evaluate : 3.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 32 residues processed: 407 average time/residue: 0.4605 time to fit residues: 314.7727 Evaluate side-chains 353 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 321 time to evaluate : 3.480 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3597 time to fit residues: 26.4155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 294 optimal weight: 0.7980 chunk 377 optimal weight: 7.9990 chunk 292 optimal weight: 0.9990 chunk 434 optimal weight: 4.9990 chunk 288 optimal weight: 0.8980 chunk 514 optimal weight: 7.9990 chunk 322 optimal weight: 8.9990 chunk 313 optimal weight: 0.7980 chunk 237 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 10 GLN Aa 73 GLN Ab 408 GLN ** Ac 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 11 ASN ** Ae 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 73 GLN Ae 75 GLN ** Ae 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 151 HIS ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 11 ASN ** Ah 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 75 GLN Ak 112 GLN ** Al 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 109 ASN An 151 HIS ** Ao 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 172 GLN ** Aq 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** At 25 ASN At 136 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 141 GLN ** 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 60 HIS ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 154 ASN Ay 173 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2130 moved from start: 0.8665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 44828 Z= 0.153 Angle : 0.545 9.715 60460 Z= 0.284 Chirality : 0.037 0.249 6432 Planarity : 0.004 0.085 7916 Dihedral : 4.834 30.727 5845 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.01 % Allowed : 12.89 % Favored : 86.10 % 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: 1.22 (0.11), residues: 5332 helix: 1.95 (0.08), residues: 3610 sheet: -0.38 (0.38), residues: 190 loop : -1.93 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAp 93 HIS 0.010 0.001 HISAb 684 PHE 0.025 0.001 PHEAz 132 TYR 0.034 0.002 TYRAw 34 ARG 0.005 0.000 ARGAv 43 *********************** 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 403 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 355 time to evaluate : 3.734 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 outliers start: 48 outliers final: 28 residues processed: 386 average time/residue: 0.4566 time to fit residues: 296.6806 Evaluate side-chains 358 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 330 time to evaluate : 3.483 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3375 time to fit residues: 22.6918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 318 optimal weight: 0.0470 chunk 205 optimal weight: 10.0000 chunk 307 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 327 optimal weight: 0.0870 chunk 350 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 404 optimal weight: 0.9980 overall best weight: 1.0258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 73 GLN ** Ac 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 65 HIS ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 11 ASN ** Ag 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** ** Aj 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 300 HIS ** Aq 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 57 HIS ** Ar 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 75 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 65 HIS ** Ax 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 11 ASN ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2111 moved from start: 0.8785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 44828 Z= 0.149 Angle : 0.530 10.096 60460 Z= 0.274 Chirality : 0.037 0.155 6432 Planarity : 0.004 0.068 7916 Dihedral : 4.608 30.472 5845 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.48 % Allowed : 13.76 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.12), residues: 5332 helix: 2.29 (0.08), residues: 3617 sheet: -0.28 (0.39), residues: 181 loop : -1.83 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAa 93 HIS 0.006 0.001 HISAd 128 PHE 0.038 0.001 PHEAq 542 TYR 0.020 0.001 TYRAs 39 ARG 0.009 0.000 ARGAn 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 384 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 361 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 372 average time/residue: 0.4675 time to fit residues: 291.8776 Evaluate side-chains 345 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 336 time to evaluate : 3.482 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5050 time to fit residues: 12.4094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 468 optimal weight: 5.9990 chunk 493 optimal weight: 9.9990 chunk 449 optimal weight: 10.0000 chunk 479 optimal weight: 10.0000 chunk 492 optimal weight: 20.0000 chunk 288 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 376 optimal weight: 40.0000 chunk 147 optimal weight: 0.9980 chunk 433 optimal weight: 3.9990 chunk 453 optimal weight: 0.7980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 684 HIS ** Ac 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 65 HIS ** Ae 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 13 HIS ** Ai 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 73 GLN ** Ao 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 11 ASN Ar 57 HIS ** Ar 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 98 ASN Au 136 HIS Av 21 ASN ** Av 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 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 Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2296 moved from start: 0.9347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 44828 Z= 0.209 Angle : 0.626 14.031 60460 Z= 0.321 Chirality : 0.039 0.228 6432 Planarity : 0.004 0.063 7916 Dihedral : 4.916 32.465 5845 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.59 % Allowed : 14.03 % Favored : 85.38 % 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: 1.17 (0.11), residues: 5332 helix: 1.90 (0.08), residues: 3605 sheet: -0.27 (0.38), residues: 186 loop : -1.92 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPAw 93 HIS 0.009 0.001 HISAb 684 PHE 0.024 0.002 PHEAo 170 TYR 0.038 0.002 TYRAy 34 ARG 0.013 0.001 ARGAi 156 *********************** 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 374 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 346 time to evaluate : 4.193 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 outliers start: 28 outliers final: 16 residues processed: 366 average time/residue: 0.4650 time to fit residues: 285.1878 Evaluate side-chains 339 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 323 time to evaluate : 3.486 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3412 time to fit residues: 15.3488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 477 optimal weight: 0.8980 chunk 314 optimal weight: 3.9990 chunk 507 optimal weight: 5.9990 chunk 309 optimal weight: 3.9990 chunk 240 optimal weight: 0.0050 chunk 352 optimal weight: 50.0000 chunk 532 optimal weight: 8.9990 chunk 489 optimal weight: 0.7980 chunk 423 optimal weight: 0.5980 chunk 43 optimal weight: 40.0000 chunk 327 optimal weight: 40.0000 overall best weight: 1.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 684 HIS ** Ac 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 65 HIS ** Ae 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 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 13 HIS Ai 23 GLN ** Ai 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 21 ASN ** Aj 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 172 GLN Aq 300 HIS ** Aq 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 57 HIS ** Ar 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 136 HIS Av 75 GLN ** Av 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 65 HIS Aw 141 GLN ** Ax 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2198 moved from start: 0.9396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 44828 Z= 0.158 Angle : 0.560 14.195 60460 Z= 0.288 Chirality : 0.037 0.202 6432 Planarity : 0.004 0.066 7916 Dihedral : 4.664 30.916 5845 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.38 % Allowed : 14.35 % Favored : 85.28 % 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: 1.52 (0.11), residues: 5332 helix: 2.18 (0.08), residues: 3612 sheet: -0.08 (0.38), residues: 191 loop : -1.87 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPAw 93 HIS 0.006 0.001 HISAd 128 PHE 0.030 0.001 PHEAb 243 TYR 0.022 0.001 TYRAb 211 ARG 0.007 0.000 ARGAn 76 ********************** 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 366 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 348 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 354 average time/residue: 0.4637 time to fit residues: 273.8009 Evaluate side-chains 337 residues out of total 4754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 333 time to evaluate : 3.481 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3378 time to fit residues: 7.6632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 259 optimal weight: 2.9990 chunk 336 optimal weight: 0.0000 chunk 451 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 390 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 424 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 435 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 21 ASN Ae 65 HIS ** Ae 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 21 ASN ** Af 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 50 ASN ** An 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 11 ASN ** Ao 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 388 ASN ** Ar 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 57 HIS ** Ar 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 75 GLN ** As 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 136 HIS ** Av 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 65 HIS ** Ax 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 21 ASN ** Ay 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.246192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.218842 restraints weight = 100760.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.221750 restraints weight = 60726.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.223583 restraints weight = 39497.525| |-----------------------------------------------------------------------------| r_work (final): 0.4668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2411 moved from start: 0.9663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 44828 Z= 0.174 Angle : 0.590 13.596 60460 Z= 0.302 Chirality : 0.038 0.200 6432 Planarity : 0.004 0.065 7916 Dihedral : 4.706 31.465 5845 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.32 % Allowed : 14.83 % Favored : 84.85 % 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: 1.46 (0.11), residues: 5332 helix: 2.15 (0.08), residues: 3605 sheet: -0.34 (0.37), residues: 201 loop : -1.86 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPAw 93 HIS 0.007 0.001 HISAw 60 PHE 0.029 0.002 PHEAb 243 TYR 0.031 0.002 TYRAq 168 ARG 0.008 0.000 ARGAf 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6914.05 seconds wall clock time: 126 minutes 5.09 seconds (7565.09 seconds total)