Starting phenix.real_space_refine on Fri Nov 17 13:00:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feq_31560/11_2023/7feq_31560.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feq_31560/11_2023/7feq_31560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feq_31560/11_2023/7feq_31560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feq_31560/11_2023/7feq_31560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feq_31560/11_2023/7feq_31560.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7feq_31560/11_2023/7feq_31560.pdb" } resolution = 3.2 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= 0.002 sd= 0.123 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 12222 2.51 5 N 3206 2.21 5 O 3710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 18": "OD1" <-> "OD2" Residue "B ASP 26": "OD1" <-> "OD2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B ASP 78": "OD1" <-> "OD2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ASP 26": "OD1" <-> "OD2" Residue "C PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ASP 147": "OD1" <-> "OD2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "E TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 27": "NH1" <-> "NH2" Residue "E PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 27": "NH1" <-> "NH2" Residue "F TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F ARG 141": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "F PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 27": "NH1" <-> "NH2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 146": "NH1" <-> "NH2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "G GLU 181": "OE1" <-> "OE2" Residue "I ARG 27": "NH1" <-> "NH2" Residue "I ASP 36": "OD1" <-> "OD2" Residue "I GLU 53": "OE1" <-> "OE2" Residue "I TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 141": "NH1" <-> "NH2" Residue "I ASP 147": "OD1" <-> "OD2" Residue "I ASP 169": "OD1" <-> "OD2" Residue "J TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 27": "NH1" <-> "NH2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 78": "OD1" <-> "OD2" Residue "J PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 147": "OD1" <-> "OD2" Residue "J GLU 165": "OE1" <-> "OE2" Residue "J ARG 170": "NH1" <-> "NH2" Residue "J PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 181": "OE1" <-> "OE2" Residue "J ASP 186": "OD1" <-> "OD2" Residue "K TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 22": "NH1" <-> "NH2" Residue "K ASP 54": "OD1" <-> "OD2" Residue "K GLU 58": "OE1" <-> "OE2" Residue "K TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 141": "NH1" <-> "NH2" Residue "K ARG 146": "NH1" <-> "NH2" Residue "K PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 18": "OD1" <-> "OD2" Residue "L ARG 22": "NH1" <-> "NH2" Residue "L ARG 111": "NH1" <-> "NH2" Residue "L ARG 146": "NH1" <-> "NH2" Residue "L ASP 147": "OD1" <-> "OD2" Residue "M TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 36": "OD1" <-> "OD2" Residue "M GLU 53": "OE1" <-> "OE2" Residue "M ASP 54": "OD1" <-> "OD2" Residue "M TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 147": "OD1" <-> "OD2" Residue "M GLU 165": "OE1" <-> "OE2" Residue "M GLU 181": "OE1" <-> "OE2" Residue "N TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 54": "OD1" <-> "OD2" Residue "N TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 111": "NH1" <-> "NH2" Residue "N TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 134": "OE1" <-> "OE2" Residue "N GLU 165": "OE1" <-> "OE2" Residue "H TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 141": "NH1" <-> "NH2" Residue "H ARG 170": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 19236 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1374 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Chain: "B" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1374 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Chain: "C" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1374 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Chain: "D" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1374 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Chain: "E" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1374 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Chain: "F" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1374 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Chain: "G" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1374 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Chain: "I" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1374 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Chain: "J" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1374 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Chain: "K" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1374 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Chain: "L" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1374 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Chain: "M" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1374 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Chain: "N" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1374 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Chain: "H" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1374 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain breaks: 1 Time building chain proxies: 10.27, per 1000 atoms: 0.53 Number of scatterers: 19236 At special positions: 0 Unit cell: (119.475, 115.425, 111.375, 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 98 16.00 O 3710 8.00 N 3206 7.00 C 12222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.01 Conformation dependent library (CDL) restraints added in 4.2 seconds 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4676 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 35 sheets defined 39.8% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 19 through 26 removed outlier: 3.972A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 51 removed outlier: 3.620A pdb=" N ALA A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 83 removed outlier: 3.776A pdb=" N TYR A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 104 removed outlier: 3.880A pdb=" N ALA A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 158 removed outlier: 4.095A pdb=" N ALA A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 168 removed outlier: 3.732A pdb=" N ILE A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.819A pdb=" N LEU B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 24' Processing helix chain 'B' and resid 38 through 51 removed outlier: 3.986A pdb=" N SER B 42 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 83 removed outlier: 3.772A pdb=" N TYR B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 81 " --> pdb=" O TYR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 104 removed outlier: 3.828A pdb=" N ALA B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.574A pdb=" N ARG B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.601A pdb=" N GLU B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.706A pdb=" N ILE B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.899A pdb=" N GLU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.775A pdb=" N LEU C 23 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 19 through 24' Processing helix chain 'C' and resid 39 through 54 removed outlier: 3.866A pdb=" N ASP C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.605A pdb=" N MET C 74 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 99 through 104 removed outlier: 3.740A pdb=" N ALA C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.570A pdb=" N ARG C 141 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP C 147 " --> pdb=" O LEU C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 158 Processing helix chain 'C' and resid 160 through 168 removed outlier: 3.646A pdb=" N ILE C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.871A pdb=" N GLU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 removed outlier: 3.564A pdb=" N ARG D 22 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 23 " --> pdb=" O ILE D 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 18 through 23' Processing helix chain 'D' and resid 24 through 26 No H-bonds generated for 'chain 'D' and resid 24 through 26' Processing helix chain 'D' and resid 38 through 52 Processing helix chain 'D' and resid 73 through 78 removed outlier: 3.644A pdb=" N TYR D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP D 78 " --> pdb=" O MET D 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 78' Processing helix chain 'D' and resid 99 through 104 removed outlier: 3.756A pdb=" N ALA D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 148 removed outlier: 3.784A pdb=" N ARG D 141 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU D 143 " --> pdb=" O ALA D 139 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP D 147 " --> pdb=" O LEU D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 158 removed outlier: 3.950A pdb=" N LEU D 153 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU D 155 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 168 removed outlier: 3.681A pdb=" N ILE D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 removed outlier: 3.860A pdb=" N TYR D 182 " --> pdb=" O GLU D 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 24 removed outlier: 3.905A pdb=" N LEU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 19 through 24' Processing helix chain 'E' and resid 39 through 52 Processing helix chain 'E' and resid 70 through 83 removed outlier: 3.780A pdb=" N ALA E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ILE E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN E 81 " --> pdb=" O TYR E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 104 removed outlier: 3.714A pdb=" N ALA E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.894A pdb=" N ALA E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 150 removed outlier: 3.682A pdb=" N ARG E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS E 148 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 157 Processing helix chain 'E' and resid 160 through 168 removed outlier: 3.523A pdb=" N ILE E 164 " --> pdb=" O PRO E 160 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 183 removed outlier: 3.712A pdb=" N TYR E 182 " --> pdb=" O GLU E 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 24 removed outlier: 3.822A pdb=" N LEU F 23 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F 24 " --> pdb=" O TYR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 54 removed outlier: 3.689A pdb=" N ALA F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU F 53 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 83 removed outlier: 3.700A pdb=" N TYR F 77 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN F 81 " --> pdb=" O TYR F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 104 removed outlier: 3.656A pdb=" N ALA F 104 " --> pdb=" O ALA F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 140 removed outlier: 3.781A pdb=" N ALA F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 150 removed outlier: 3.652A pdb=" N ARG F 146 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP F 147 " --> pdb=" O LEU F 143 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 158 removed outlier: 3.931A pdb=" N GLU F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 168 removed outlier: 3.781A pdb=" N ILE F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR F 168 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 183 removed outlier: 4.084A pdb=" N GLU F 181 " --> pdb=" O GLU F 177 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR F 182 " --> pdb=" O GLU F 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 52 removed outlier: 3.501A pdb=" N SER G 42 " --> pdb=" O ASN G 38 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 72 Processing helix chain 'G' and resid 73 through 83 removed outlier: 3.863A pdb=" N TYR G 77 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN G 81 " --> pdb=" O TYR G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 104 removed outlier: 3.642A pdb=" N ALA G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 139 removed outlier: 3.793A pdb=" N ALA G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 147 removed outlier: 3.764A pdb=" N ASP G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 158 removed outlier: 3.709A pdb=" N GLU G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 24 removed outlier: 3.836A pdb=" N LEU I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 54 removed outlier: 3.834A pdb=" N VAL I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER I 45 " --> pdb=" O ASN I 41 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 83 removed outlier: 3.641A pdb=" N THR I 79 " --> pdb=" O ALA I 75 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN I 81 " --> pdb=" O TYR I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 104 removed outlier: 3.513A pdb=" N PHE I 101 " --> pdb=" O SER I 97 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU I 102 " --> pdb=" O MET I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 140 removed outlier: 3.849A pdb=" N ALA I 138 " --> pdb=" O GLU I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 148 removed outlier: 3.874A pdb=" N ASP I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 143 through 148' Processing helix chain 'I' and resid 152 through 158 Processing helix chain 'I' and resid 160 through 168 removed outlier: 3.751A pdb=" N ILE I 164 " --> pdb=" O PRO I 160 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG I 166 " --> pdb=" O GLU I 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 23 removed outlier: 3.711A pdb=" N LEU J 23 " --> pdb=" O ILE J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 52 removed outlier: 3.727A pdb=" N SER J 45 " --> pdb=" O ASN J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 72 No H-bonds generated for 'chain 'J' and resid 70 through 72' Processing helix chain 'J' and resid 73 through 83 removed outlier: 3.746A pdb=" N TYR J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN J 81 " --> pdb=" O TYR J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 104 Processing helix chain 'J' and resid 133 through 143 removed outlier: 3.732A pdb=" N ALA J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG J 141 " --> pdb=" O ILE J 137 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU J 143 " --> pdb=" O ALA J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 158 Processing helix chain 'J' and resid 160 through 168 removed outlier: 3.760A pdb=" N ILE J 164 " --> pdb=" O PRO J 160 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 183 removed outlier: 3.741A pdb=" N TYR J 182 " --> pdb=" O GLU J 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 24 removed outlier: 3.795A pdb=" N LEU K 23 " --> pdb=" O ILE K 19 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU K 24 " --> pdb=" O TYR K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 52 removed outlier: 3.689A pdb=" N VAL K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER K 45 " --> pdb=" O ASN K 41 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN K 46 " --> pdb=" O SER K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 72 Processing helix chain 'K' and resid 73 through 83 removed outlier: 3.853A pdb=" N TYR K 77 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN K 81 " --> pdb=" O TYR K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 104 Processing helix chain 'K' and resid 134 through 147 removed outlier: 3.870A pdb=" N ALA K 138 " --> pdb=" O GLU K 134 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS K 140 " --> pdb=" O GLU K 136 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG K 141 " --> pdb=" O ILE K 137 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE K 142 " --> pdb=" O ALA K 138 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU K 143 " --> pdb=" O ALA K 139 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU K 144 " --> pdb=" O LYS K 140 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP K 147 " --> pdb=" O LEU K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 157 removed outlier: 3.811A pdb=" N GLU K 155 " --> pdb=" O LYS K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 168 removed outlier: 3.730A pdb=" N ILE K 164 " --> pdb=" O PRO K 160 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG K 166 " --> pdb=" O GLU K 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 26 Processing helix chain 'L' and resid 39 through 54 removed outlier: 3.786A pdb=" N VAL L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER L 45 " --> pdb=" O ASN L 41 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN L 46 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP L 54 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 83 removed outlier: 3.693A pdb=" N GLN L 81 " --> pdb=" O TYR L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 104 removed outlier: 3.785A pdb=" N ALA L 104 " --> pdb=" O ALA L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 150 removed outlier: 3.797A pdb=" N ALA L 138 " --> pdb=" O GLU L 134 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS L 140 " --> pdb=" O GLU L 136 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG L 141 " --> pdb=" O ILE L 137 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE L 142 " --> pdb=" O ALA L 138 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU L 143 " --> pdb=" O ALA L 139 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU L 144 " --> pdb=" O LYS L 140 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS L 148 " --> pdb=" O LEU L 144 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU L 149 " --> pdb=" O LEU L 145 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 158 removed outlier: 3.545A pdb=" N GLY L 158 " --> pdb=" O ALA L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 168 removed outlier: 3.682A pdb=" N ILE L 164 " --> pdb=" O PRO L 160 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR L 168 " --> pdb=" O ILE L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 183 Processing helix chain 'M' and resid 18 through 23 removed outlier: 3.899A pdb=" N LEU M 23 " --> pdb=" O ILE M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 52 removed outlier: 3.531A pdb=" N SER M 42 " --> pdb=" O ASN M 38 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER M 45 " --> pdb=" O ASN M 41 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 83 removed outlier: 3.640A pdb=" N THR M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 104 removed outlier: 3.822A pdb=" N ALA M 104 " --> pdb=" O ALA M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 139 removed outlier: 3.838A pdb=" N ALA M 138 " --> pdb=" O GLU M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 158 removed outlier: 3.794A pdb=" N ASP M 147 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS M 148 " --> pdb=" O LEU M 144 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU M 149 " --> pdb=" O LEU M 145 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS M 151 " --> pdb=" O ASP M 147 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL M 152 " --> pdb=" O LYS M 148 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA M 154 " --> pdb=" O ASN M 150 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU M 155 " --> pdb=" O LYS M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 168 removed outlier: 3.761A pdb=" N ILE M 164 " --> pdb=" O PRO M 160 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG M 166 " --> pdb=" O GLU M 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 24 removed outlier: 3.713A pdb=" N LEU N 24 " --> pdb=" O TYR N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 52 removed outlier: 3.652A pdb=" N VAL N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER N 45 " --> pdb=" O ASN N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 83 removed outlier: 3.876A pdb=" N TYR N 77 " --> pdb=" O GLY N 73 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP N 78 " --> pdb=" O MET N 74 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR N 79 " --> pdb=" O ALA N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 135 through 158 removed outlier: 3.653A pdb=" N ARG N 141 " --> pdb=" O ILE N 137 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE N 142 " --> pdb=" O ALA N 138 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU N 143 " --> pdb=" O ALA N 139 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU N 144 " --> pdb=" O LYS N 140 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP N 147 " --> pdb=" O LEU N 143 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS N 148 " --> pdb=" O LEU N 144 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS N 151 " --> pdb=" O ASP N 147 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL N 152 " --> pdb=" O LYS N 148 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA N 154 " --> pdb=" O ASN N 150 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU N 155 " --> pdb=" O LYS N 151 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR N 157 " --> pdb=" O LEU N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 165 removed outlier: 3.681A pdb=" N ILE N 164 " --> pdb=" O PRO N 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 24 removed outlier: 3.918A pdb=" N LEU H 23 " --> pdb=" O ILE H 19 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 52 Processing helix chain 'H' and resid 73 through 83 removed outlier: 3.754A pdb=" N TYR H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN H 81 " --> pdb=" O TYR H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 104 Processing helix chain 'H' and resid 133 through 149 removed outlier: 3.774A pdb=" N ALA H 138 " --> pdb=" O GLU H 134 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU H 143 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU H 144 " --> pdb=" O LYS H 140 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP H 147 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU H 149 " --> pdb=" O LEU H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 168 removed outlier: 3.697A pdb=" N ILE H 164 " --> pdb=" O PRO H 160 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG H 166 " --> pdb=" O GLU H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 183 removed outlier: 3.771A pdb=" N TYR H 182 " --> pdb=" O GLU H 178 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 7.073A pdb=" N ILE A 29 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 59 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE A 90 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU A 61 " --> pdb=" O ILE A 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 96 removed outlier: 7.005A pdb=" N ALA A 95 " --> pdb=" O MET A 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 131 Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.592A pdb=" N ILE B 59 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE B 90 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU B 61 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N TYR B 112 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR B 89 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 187 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 113 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 94 through 96 Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 131 Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 31 removed outlier: 5.486A pdb=" N SER C 65 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N MET C 94 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N MET C 120 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA C 95 " --> pdb=" O MET C 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 112 through 113 Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 129 Processing sheet with id=AB1, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.992A pdb=" N ILE D 29 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE D 59 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE D 90 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU D 61 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 95 through 96 removed outlier: 7.057A pdb=" N ALA D 95 " --> pdb=" O MET D 120 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 121 " --> pdb=" O ASN D 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=AB4, first strand: chain 'D' and resid 125 through 131 Processing sheet with id=AB5, first strand: chain 'E' and resid 28 through 31 removed outlier: 6.990A pdb=" N ILE E 29 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ASN E 64 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU E 31 " --> pdb=" O ASN E 64 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE E 59 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU E 61 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE E 92 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ILE E 63 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N MET E 94 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS E 91 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 28 through 31 removed outlier: 6.990A pdb=" N ILE E 29 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ASN E 64 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU E 31 " --> pdb=" O ASN E 64 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE E 59 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU E 61 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE E 92 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ILE E 63 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N MET E 94 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N MET E 120 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA E 95 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 125 through 131 Processing sheet with id=AB8, first strand: chain 'F' and resid 28 through 31 removed outlier: 6.607A pdb=" N ILE F 59 " --> pdb=" O SER F 88 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE F 90 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU F 61 " --> pdb=" O ILE F 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 128 through 131 removed outlier: 3.504A pdb=" N GLY F 130 " --> pdb=" O GLY J 126 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 28 through 31 removed outlier: 6.727A pdb=" N ILE G 59 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE G 90 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU G 61 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE G 92 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE G 63 " --> pdb=" O ILE G 92 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N MET G 94 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N MET G 120 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ALA G 95 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 28 through 31 removed outlier: 6.727A pdb=" N ILE G 59 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE G 90 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU G 61 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE G 92 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE G 63 " --> pdb=" O ILE G 92 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N MET G 94 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N TYR G 112 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR G 89 " --> pdb=" O TYR G 112 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 125 through 129 Processing sheet with id=AC4, first strand: chain 'I' and resid 28 through 31 removed outlier: 6.990A pdb=" N ILE I 29 " --> pdb=" O TYR I 62 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASN I 64 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU I 31 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE I 63 " --> pdb=" O ILE I 92 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N MET I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 112 through 113 Processing sheet with id=AC6, first strand: chain 'I' and resid 120 through 121 removed outlier: 3.685A pdb=" N ILE I 121 " --> pdb=" O ASN I 172 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN I 172 " --> pdb=" O ILE I 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'J' and resid 28 through 31 removed outlier: 6.726A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ILE J 63 " --> pdb=" O ILE J 92 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N MET J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N MET J 120 " --> pdb=" O GLY J 93 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA J 95 " --> pdb=" O MET J 120 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE J 121 " --> pdb=" O ASN J 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN J 172 " --> pdb=" O ILE J 121 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 28 through 31 removed outlier: 6.726A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ILE J 63 " --> pdb=" O ILE J 92 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N MET J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N TYR J 112 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR J 89 " --> pdb=" O TYR J 112 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS J 187 " --> pdb=" O ARG J 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 28 through 31 removed outlier: 6.954A pdb=" N ILE K 29 " --> pdb=" O TYR K 62 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ASN K 64 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU K 31 " --> pdb=" O ASN K 64 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE K 92 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE K 63 " --> pdb=" O ILE K 92 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N MET K 94 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS K 187 " --> pdb=" O ARG K 111 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 120 through 121 removed outlier: 3.855A pdb=" N ILE K 121 " --> pdb=" O ASN K 172 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN K 172 " --> pdb=" O ILE K 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'L' and resid 28 through 31 removed outlier: 7.031A pdb=" N ILE L 29 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU L 61 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N TYR L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR L 89 " --> pdb=" O TYR L 112 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS L 187 " --> pdb=" O ARG L 111 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 95 through 96 removed outlier: 6.978A pdb=" N ALA L 95 " --> pdb=" O MET L 120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 28 through 31 removed outlier: 7.021A pdb=" N ILE M 29 " --> pdb=" O TYR M 62 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'M' and resid 95 through 96 removed outlier: 7.145A pdb=" N ALA M 95 " --> pdb=" O MET M 120 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL M 119 " --> pdb=" O LYS M 174 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE M 121 " --> pdb=" O ASN M 172 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN M 172 " --> pdb=" O ILE M 121 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 28 through 31 removed outlier: 6.837A pdb=" N ILE N 29 " --> pdb=" O TYR N 62 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ASN N 64 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU N 31 " --> pdb=" O ASN N 64 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE N 63 " --> pdb=" O ILE N 92 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N MET N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLU N 118 " --> pdb=" O CYS N 91 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLY N 93 " --> pdb=" O GLU N 118 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N MET N 120 " --> pdb=" O GLY N 93 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA N 95 " --> pdb=" O MET N 120 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL N 119 " --> pdb=" O LYS N 174 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE N 121 " --> pdb=" O ASN N 172 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN N 172 " --> pdb=" O ILE N 121 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 28 through 31 removed outlier: 6.837A pdb=" N ILE N 29 " --> pdb=" O TYR N 62 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ASN N 64 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU N 31 " --> pdb=" O ASN N 64 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE N 63 " --> pdb=" O ILE N 92 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N MET N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N TYR N 112 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR N 89 " --> pdb=" O TYR N 112 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA N 113 " --> pdb=" O LYS N 187 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 28 through 31 removed outlier: 6.965A pdb=" N ILE H 29 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ASN H 64 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU H 31 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE H 63 " --> pdb=" O ILE H 92 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N MET H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TYR H 112 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR H 89 " --> pdb=" O TYR H 112 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS H 187 " --> pdb=" O ARG H 111 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1380 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: 5.23 Time building geometry restraints manager: 7.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3360 1.28 - 1.41: 4118 1.41 - 1.54: 11703 1.54 - 1.67: 97 1.67 - 1.80: 182 Bond restraints: 19460 Sorted by residual: bond pdb=" C ILE H 43 " pdb=" O ILE H 43 " ideal model delta sigma weight residual 1.236 1.156 0.081 1.19e-02 7.06e+03 4.58e+01 bond pdb=" C LEU H 47 " pdb=" O LEU H 47 " ideal model delta sigma weight residual 1.237 1.150 0.087 1.31e-02 5.83e+03 4.41e+01 bond pdb=" C SER H 42 " pdb=" O SER H 42 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.39e-02 5.18e+03 2.91e+01 bond pdb=" C GLN H 46 " pdb=" O GLN H 46 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.26e-02 6.30e+03 2.78e+01 bond pdb=" CA SER H 42 " pdb=" CB SER H 42 " ideal model delta sigma weight residual 1.533 1.458 0.075 1.60e-02 3.91e+03 2.19e+01 ... (remaining 19455 not shown) Histogram of bond angle deviations from ideal: 94.48 - 104.27: 329 104.27 - 114.06: 11368 114.06 - 123.86: 14061 123.86 - 133.65: 490 133.65 - 143.44: 2 Bond angle restraints: 26250 Sorted by residual: angle pdb=" C HIS K 122 " pdb=" N GLN K 123 " pdb=" CA GLN K 123 " ideal model delta sigma weight residual 120.49 143.44 -22.95 1.42e+00 4.96e-01 2.61e+02 angle pdb=" C HIS C 122 " pdb=" N GLN C 123 " pdb=" CA GLN C 123 " ideal model delta sigma weight residual 120.68 132.45 -11.77 1.52e+00 4.33e-01 6.00e+01 angle pdb=" N GLU I 181 " pdb=" CA GLU I 181 " pdb=" C GLU I 181 " ideal model delta sigma weight residual 114.75 105.58 9.17 1.26e+00 6.30e-01 5.30e+01 angle pdb=" N VAL H 152 " pdb=" CA VAL H 152 " pdb=" C VAL H 152 " ideal model delta sigma weight residual 109.34 94.48 14.86 2.08e+00 2.31e-01 5.10e+01 angle pdb=" C SER H 45 " pdb=" N GLN H 46 " pdb=" CA GLN H 46 " ideal model delta sigma weight residual 121.54 134.18 -12.64 1.91e+00 2.74e-01 4.38e+01 ... (remaining 26245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 10798 18.00 - 35.99: 1058 35.99 - 53.99: 187 53.99 - 71.98: 31 71.98 - 89.98: 8 Dihedral angle restraints: 12082 sinusoidal: 4830 harmonic: 7252 Sorted by residual: dihedral pdb=" CA MET F 94 " pdb=" C MET F 94 " pdb=" N ALA F 95 " pdb=" CA ALA F 95 " ideal model delta harmonic sigma weight residual -180.00 -136.36 -43.64 0 5.00e+00 4.00e-02 7.62e+01 dihedral pdb=" CA VAL H 152 " pdb=" C VAL H 152 " pdb=" N LEU H 153 " pdb=" CA LEU H 153 " ideal model delta harmonic sigma weight residual -180.00 -141.16 -38.84 0 5.00e+00 4.00e-02 6.03e+01 dihedral pdb=" CA GLY N 106 " pdb=" C GLY N 106 " pdb=" N GLU N 107 " pdb=" CA GLU N 107 " ideal model delta harmonic sigma weight residual -180.00 -141.22 -38.78 0 5.00e+00 4.00e-02 6.02e+01 ... (remaining 12079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2826 0.103 - 0.206: 274 0.206 - 0.309: 12 0.309 - 0.412: 9 0.412 - 0.515: 1 Chirality restraints: 3122 Sorted by residual: chirality pdb=" CA VAL H 44 " pdb=" N VAL H 44 " pdb=" C VAL H 44 " pdb=" CB VAL H 44 " both_signs ideal model delta sigma weight residual False 2.44 2.96 -0.51 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" CB ILE B 3 " pdb=" CA ILE B 3 " pdb=" CG1 ILE B 3 " pdb=" CG2 ILE B 3 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CB ILE E 92 " pdb=" CA ILE E 92 " pdb=" CG1 ILE E 92 " pdb=" CG2 ILE E 92 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 3119 not shown) Planarity restraints: 3360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 42 " -0.016 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C SER H 42 " 0.058 2.00e-02 2.50e+03 pdb=" O SER H 42 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE H 43 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 43 " 0.015 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ILE H 43 " -0.055 2.00e-02 2.50e+03 pdb=" O ILE H 43 " 0.021 2.00e-02 2.50e+03 pdb=" N VAL H 44 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE I 3 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.45e+00 pdb=" N PRO I 4 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO I 4 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 4 " 0.040 5.00e-02 4.00e+02 ... (remaining 3357 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1089 2.72 - 3.26: 16408 3.26 - 3.81: 26010 3.81 - 4.35: 34532 4.35 - 4.90: 62187 Nonbonded interactions: 140226 Sorted by model distance: nonbonded pdb=" O SER H 42 " pdb=" OG SER H 42 " model vdw 2.172 2.440 nonbonded pdb=" O SER H 45 " pdb=" OG SER H 45 " model vdw 2.188 2.440 nonbonded pdb=" O LEU I 114 " pdb=" OG SER I 117 " model vdw 2.286 2.440 nonbonded pdb=" N VAL H 152 " pdb=" O VAL H 152 " model vdw 2.299 2.496 nonbonded pdb=" OG SER H 175 " pdb=" N ALA H 176 " model vdw 2.333 2.520 ... (remaining 140221 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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 individual isotropic 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.000 Check model and map are aligned: 0.310 Set scattering table: 0.170 Process input model: 49.260 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.111 19460 Z= 0.663 Angle : 1.203 22.949 26250 Z= 0.641 Chirality : 0.065 0.515 3122 Planarity : 0.008 0.073 3360 Dihedral : 14.493 89.976 7406 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.57 % Allowed : 12.87 % Favored : 86.57 % Rotamer: Outliers : 0.19 % Allowed : 7.73 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.29 % 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: -6.13 (0.11), residues: 2464 helix: -4.35 (0.09), residues: 1120 sheet: -2.12 (0.28), residues: 308 loop : -4.25 (0.12), residues: 1036 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 327 time to evaluate : 2.385 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 331 average time/residue: 0.3420 time to fit residues: 165.7891 Evaluate side-chains 256 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 2.333 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1688 time to fit residues: 3.9233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.9990 chunk 191 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 0.0970 chunk 197 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 228 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN B 159 GLN C 46 GLN C 122 HIS D 81 GLN E 131 GLN F 46 GLN I 122 HIS K 46 GLN K 64 ASN K 122 HIS L 122 HIS M 122 HIS M 123 GLN N 122 HIS H 122 HIS H 159 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 19460 Z= 0.164 Angle : 0.654 10.325 26250 Z= 0.340 Chirality : 0.044 0.241 3122 Planarity : 0.005 0.053 3360 Dihedral : 6.461 38.208 2688 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.21 % Favored : 90.50 % Rotamer: Outliers : 0.78 % Allowed : 12.49 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.13), residues: 2464 helix: -3.49 (0.12), residues: 1092 sheet: -2.23 (0.26), residues: 336 loop : -3.80 (0.14), residues: 1036 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 293 time to evaluate : 2.213 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 304 average time/residue: 0.3168 time to fit residues: 145.4424 Evaluate side-chains 269 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 262 time to evaluate : 2.033 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2276 time to fit residues: 5.5197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 247 optimal weight: 0.9990 chunk 204 optimal weight: 7.9990 chunk 227 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS B 122 HIS E 81 GLN F 46 GLN F 116 ASN J 129 GLN N 122 HIS ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 19460 Z= 0.475 Angle : 0.831 12.274 26250 Z= 0.425 Chirality : 0.051 0.263 3122 Planarity : 0.006 0.053 3360 Dihedral : 6.767 38.449 2688 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.45 % Allowed : 12.78 % Favored : 86.77 % Rotamer: Outliers : 1.46 % Allowed : 14.92 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.13), residues: 2464 helix: -3.22 (0.13), residues: 1092 sheet: -1.97 (0.28), residues: 308 loop : -3.73 (0.14), residues: 1064 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 273 time to evaluate : 2.374 Fit side-chains outliers start: 30 outliers final: 13 residues processed: 293 average time/residue: 0.3149 time to fit residues: 139.9336 Evaluate side-chains 274 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 261 time to evaluate : 2.156 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1766 time to fit residues: 7.2842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 chunk 25 optimal weight: 0.0670 chunk 109 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN I 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19460 Z= 0.155 Angle : 0.616 9.400 26250 Z= 0.319 Chirality : 0.044 0.276 3122 Planarity : 0.005 0.046 3360 Dihedral : 6.026 38.252 2688 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.01 % Favored : 90.79 % Rotamer: Outliers : 1.12 % Allowed : 16.33 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.14), residues: 2464 helix: -2.91 (0.14), residues: 1092 sheet: 0.10 (0.37), residues: 168 loop : -3.46 (0.13), residues: 1204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 282 time to evaluate : 2.225 Fit side-chains outliers start: 23 outliers final: 10 residues processed: 296 average time/residue: 0.3153 time to fit residues: 141.9288 Evaluate side-chains 264 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 254 time to evaluate : 2.212 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1882 time to fit residues: 6.3416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 116 ASN N 159 GLN H 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 19460 Z= 0.418 Angle : 0.780 11.548 26250 Z= 0.398 Chirality : 0.050 0.253 3122 Planarity : 0.005 0.047 3360 Dihedral : 6.453 38.950 2688 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.70 % Favored : 86.97 % Rotamer: Outliers : 1.07 % Allowed : 17.59 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.14), residues: 2464 helix: -2.90 (0.13), residues: 1106 sheet: -1.83 (0.28), residues: 308 loop : -3.42 (0.15), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 279 time to evaluate : 2.362 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 292 average time/residue: 0.3181 time to fit residues: 141.1410 Evaluate side-chains 279 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 267 time to evaluate : 2.173 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1688 time to fit residues: 6.9232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19460 Z= 0.279 Angle : 0.698 10.552 26250 Z= 0.359 Chirality : 0.047 0.280 3122 Planarity : 0.005 0.046 3360 Dihedral : 6.282 39.013 2688 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.80 % Favored : 88.92 % Rotamer: Outliers : 0.87 % Allowed : 18.42 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.14), residues: 2464 helix: -2.79 (0.14), residues: 1106 sheet: 0.18 (0.36), residues: 168 loop : -3.34 (0.14), residues: 1190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 269 time to evaluate : 2.431 Fit side-chains outliers start: 18 outliers final: 6 residues processed: 279 average time/residue: 0.3205 time to fit residues: 135.7035 Evaluate side-chains 266 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 260 time to evaluate : 2.075 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1719 time to fit residues: 5.1133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 138 optimal weight: 0.0770 chunk 178 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 242 optimal weight: 0.0980 chunk 152 optimal weight: 10.0000 chunk 148 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19460 Z= 0.138 Angle : 0.591 8.598 26250 Z= 0.305 Chirality : 0.044 0.280 3122 Planarity : 0.004 0.045 3360 Dihedral : 5.576 37.311 2688 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.62 % Favored : 90.18 % Rotamer: Outliers : 0.73 % Allowed : 18.90 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.15), residues: 2464 helix: -2.58 (0.14), residues: 1120 sheet: 0.43 (0.35), residues: 168 loop : -3.09 (0.15), residues: 1176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 264 time to evaluate : 2.250 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 276 average time/residue: 0.3408 time to fit residues: 141.7642 Evaluate side-chains 257 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 251 time to evaluate : 2.542 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1900 time to fit residues: 5.0323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 190 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19460 Z= 0.212 Angle : 0.634 12.845 26250 Z= 0.325 Chirality : 0.046 0.239 3122 Planarity : 0.004 0.042 3360 Dihedral : 5.646 38.149 2688 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.96 % Favored : 88.84 % Rotamer: Outliers : 0.15 % Allowed : 19.48 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.77 (0.15), residues: 2464 helix: -2.43 (0.14), residues: 1106 sheet: 0.59 (0.36), residues: 168 loop : -3.08 (0.15), residues: 1190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 262 time to evaluate : 2.365 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 264 average time/residue: 0.3330 time to fit residues: 131.9331 Evaluate side-chains 255 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 2.237 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1688 time to fit residues: 3.4591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 225 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS J 122 HIS N 122 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19460 Z= 0.268 Angle : 0.680 13.131 26250 Z= 0.348 Chirality : 0.047 0.254 3122 Planarity : 0.005 0.043 3360 Dihedral : 5.900 38.148 2688 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.44 % Favored : 88.27 % Rotamer: Outliers : 0.19 % Allowed : 20.51 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.77 (0.15), residues: 2464 helix: -2.41 (0.14), residues: 1106 sheet: 0.55 (0.36), residues: 168 loop : -3.08 (0.15), residues: 1190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 262 time to evaluate : 2.368 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 264 average time/residue: 0.3289 time to fit residues: 129.3731 Evaluate side-chains 256 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 2.195 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1629 time to fit residues: 3.7078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.6980 chunk 146 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 231 optimal weight: 7.9990 chunk 199 optimal weight: 2.9990 chunk 20 optimal weight: 0.0370 chunk 154 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19460 Z= 0.184 Angle : 0.623 12.218 26250 Z= 0.321 Chirality : 0.045 0.262 3122 Planarity : 0.004 0.043 3360 Dihedral : 5.644 37.754 2688 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.31 % Favored : 89.49 % Rotamer: Outliers : 0.05 % Allowed : 20.70 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.62 (0.15), residues: 2464 helix: -2.28 (0.14), residues: 1106 sheet: 0.63 (0.36), residues: 168 loop : -3.01 (0.15), residues: 1190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 262 time to evaluate : 2.314 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 263 average time/residue: 0.3442 time to fit residues: 134.8143 Evaluate side-chains 254 residues out of total 2058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.052 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 184 optimal weight: 0.0020 chunk 29 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 200 optimal weight: 0.0970 chunk 83 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 175 optimal weight: 4.9990 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.098134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.088051 restraints weight = 23983.736| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.42 r_work: 0.2792 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19460 Z= 0.217 Angle : 0.641 12.412 26250 Z= 0.329 Chirality : 0.046 0.257 3122 Planarity : 0.005 0.043 3360 Dihedral : 5.651 37.541 2688 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.00 % Favored : 88.80 % Rotamer: Outliers : 0.15 % Allowed : 20.80 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.56 (0.15), residues: 2464 helix: -2.21 (0.14), residues: 1106 sheet: 0.67 (0.36), residues: 168 loop : -3.00 (0.15), residues: 1190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3844.93 seconds wall clock time: 70 minutes 24.23 seconds (4224.23 seconds total)