Starting phenix.real_space_refine on Fri Aug 9 09:34:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9s_29877/08_2024/8g9s_29877.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9s_29877/08_2024/8g9s_29877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9s_29877/08_2024/8g9s_29877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9s_29877/08_2024/8g9s_29877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9s_29877/08_2024/8g9s_29877.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9s_29877/08_2024/8g9s_29877.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.034 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: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 108 5.16 5 C 16056 2.51 5 N 4594 2.21 5 O 4958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 6": "NH1" <-> "NH2" Residue "B ASP 33": "OD1" <-> "OD2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B ARG 99": "NH1" <-> "NH2" Residue "B ARG 105": "NH1" <-> "NH2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 179": "NH1" <-> "NH2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B ASP 237": "OD1" <-> "OD2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "C ARG 6": "NH1" <-> "NH2" Residue "C PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ASP 237": "OD1" <-> "OD2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "D ARG 6": "NH1" <-> "NH2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D ARG 99": "NH1" <-> "NH2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D ARG 224": "NH1" <-> "NH2" Residue "D ASP 237": "OD1" <-> "OD2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ASP 262": "OD1" <-> "OD2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "E ARG 6": "NH1" <-> "NH2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E ARG 99": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E ASP 138": "OD1" <-> "OD2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 179": "NH1" <-> "NH2" Residue "E ARG 224": "NH1" <-> "NH2" Residue "E TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 237": "OD1" <-> "OD2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "E GLU 256": "OE1" <-> "OE2" Residue "E ARG 259": "NH1" <-> "NH2" Residue "E ARG 280": "NH1" <-> "NH2" Residue "F ARG 6": "NH1" <-> "NH2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F ARG 68": "NH1" <-> "NH2" Residue "F ARG 99": "NH1" <-> "NH2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "F TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 135": "NH1" <-> "NH2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 179": "NH1" <-> "NH2" Residue "F ARG 224": "NH1" <-> "NH2" Residue "F ARG 246": "NH1" <-> "NH2" Residue "F ARG 259": "NH1" <-> "NH2" Residue "F ASP 270": "OD1" <-> "OD2" Residue "F ARG 280": "NH1" <-> "NH2" Residue "G ARG 6": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "G ARG 105": "NH1" <-> "NH2" Residue "G ASP 108": "OD1" <-> "OD2" Residue "G ARG 110": "NH1" <-> "NH2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "G PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 179": "NH1" <-> "NH2" Residue "G PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 211": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "G ARG 246": "NH1" <-> "NH2" Residue "G ARG 259": "NH1" <-> "NH2" Residue "G ASP 262": "OD1" <-> "OD2" Residue "G ARG 280": "NH1" <-> "NH2" Residue "H ARG 5": "NH1" <-> "NH2" Residue "H ARG 7": "NH1" <-> "NH2" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 38": "OD1" <-> "OD2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "I ARG 5": "NH1" <-> "NH2" Residue "I ARG 7": "NH1" <-> "NH2" Residue "I ASP 9": "OD1" <-> "OD2" Residue "I PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 22": "OE1" <-> "OE2" Residue "I PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I GLU 78": "OE1" <-> "OE2" Residue "J ARG 5": "NH1" <-> "NH2" Residue "J ARG 7": "NH1" <-> "NH2" Residue "J GLU 22": "OE1" <-> "OE2" Residue "J PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 71": "NH1" <-> "NH2" Residue "J GLU 78": "OE1" <-> "OE2" Residue "M ARG 6": "NH1" <-> "NH2" Residue "M ARG 68": "NH1" <-> "NH2" Residue "M ARG 99": "NH1" <-> "NH2" Residue "M ARG 105": "NH1" <-> "NH2" Residue "M ARG 110": "NH1" <-> "NH2" Residue "M ARG 135": "NH1" <-> "NH2" Residue "M ARG 165": "NH1" <-> "NH2" Residue "M ARG 169": "NH1" <-> "NH2" Residue "M TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 179": "NH1" <-> "NH2" Residue "M ARG 224": "NH1" <-> "NH2" Residue "M ARG 246": "NH1" <-> "NH2" Residue "M ARG 259": "NH1" <-> "NH2" Residue "M TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 280": "NH1" <-> "NH2" Residue "N ARG 2": "NH1" <-> "NH2" Residue "N ARG 16": "NH1" <-> "NH2" Residue "N GLU 22": "OE1" <-> "OE2" Residue "N ARG 35": "NH1" <-> "NH2" Residue "N ARG 48": "NH1" <-> "NH2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N GLU 84": "OE1" <-> "OE2" Residue "N TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 128": "NH1" <-> "NH2" Residue "N ARG 143": "NH1" <-> "NH2" Residue "N ARG 150": "NH1" <-> "NH2" Residue "N ARG 183": "NH1" <-> "NH2" Residue "N TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 278": "NH1" <-> "NH2" Residue "K ARG 336": "NH1" <-> "NH2" Residue "K ARG 340": "NH1" <-> "NH2" Residue "K GLU 344": "OE1" <-> "OE2" Residue "K ARG 379": "NH1" <-> "NH2" Residue "K ARG 409": "NH1" <-> "NH2" Residue "K ARG 433": "NH1" <-> "NH2" Residue "K ARG 443": "NH1" <-> "NH2" Residue "K ARG 446": "NH1" <-> "NH2" Residue "K ARG 449": "NH1" <-> "NH2" Residue "K ARG 462": "NH1" <-> "NH2" Residue "K ARG 464": "NH1" <-> "NH2" Residue "K GLU 479": "OE1" <-> "OE2" Residue "K GLU 484": "OE1" <-> "OE2" Residue "K ARG 514": "NH1" <-> "NH2" Residue "K ARG 528": "NH1" <-> "NH2" Residue "K ARG 545": "NH1" <-> "NH2" Residue "K TYR 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 5": "NH1" <-> "NH2" Residue "L ARG 7": "NH1" <-> "NH2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 71": "NH1" <-> "NH2" Residue "L PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25758 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "C" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "D" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "F" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2124 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain breaks: 1 Chain: "G" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2173 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "H" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "I" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "J" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "M" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2110 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 8, 'TRANS': 255} Chain breaks: 1 Chain: "N" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1673 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "O" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 895 Classifications: {'RNA': 42} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 20, 'rna3p': 21} Chain: "K" Number of atoms: 3223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3223 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 390} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 2 Chain: "A" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 578 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Time building chain proxies: 14.73, per 1000 atoms: 0.57 Number of scatterers: 25758 At special positions: 0 Unit cell: (120.054, 129.941, 206.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 42 15.00 O 4958 8.00 N 4594 7.00 C 16056 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: 10.98 Conformation dependent library (CDL) restraints added in 4.5 seconds 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5728 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 38 sheets defined 41.6% alpha, 15.2% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 8.78 Creating SS restraints... Processing helix chain 'B' and resid 42 through 58 removed outlier: 3.955A pdb=" N LEU B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 83 through 89 removed outlier: 3.530A pdb=" N LYS B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 106 removed outlier: 3.644A pdb=" N THR B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.714A pdb=" N GLN B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR B 192 " --> pdb=" O PHE B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 208 Processing helix chain 'B' and resid 209 through 213 removed outlier: 3.799A pdb=" N HIS B 212 " --> pdb=" O MET B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 247 removed outlier: 4.181A pdb=" N LEU B 243 " --> pdb=" O PRO B 239 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 4.098A pdb=" N GLU B 274 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 275 " --> pdb=" O ASN B 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 275' Processing helix chain 'C' and resid 42 through 58 removed outlier: 3.843A pdb=" N LEU C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 82 Processing helix chain 'C' and resid 93 through 106 Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 186 through 193 removed outlier: 4.002A pdb=" N GLN C 191 " --> pdb=" O HIS C 187 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR C 192 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 208 Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.567A pdb=" N THR C 276 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 58 removed outlier: 3.913A pdb=" N LEU D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.638A pdb=" N ALA D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS D 81 " --> pdb=" O ILE D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 106 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 188 through 193 removed outlier: 3.700A pdb=" N THR D 192 " --> pdb=" O PHE D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 208 removed outlier: 3.668A pdb=" N VAL D 207 " --> pdb=" O TRP D 203 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 208 " --> pdb=" O GLN D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 245 removed outlier: 3.737A pdb=" N LEU D 243 " --> pdb=" O PRO D 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 58 removed outlier: 3.931A pdb=" N LEU E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 84 removed outlier: 3.725A pdb=" N LEU E 76 " --> pdb=" O ILE E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 90 through 106 Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 115 through 119 removed outlier: 4.169A pdb=" N THR E 118 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY E 119 " --> pdb=" O MET E 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 115 through 119' Processing helix chain 'E' and resid 185 through 193 removed outlier: 4.275A pdb=" N ALA E 189 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN E 191 " --> pdb=" O HIS E 187 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR E 192 " --> pdb=" O PHE E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 208 removed outlier: 3.846A pdb=" N VAL E 207 " --> pdb=" O TRP E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 213 Processing helix chain 'E' and resid 239 through 246 removed outlier: 3.728A pdb=" N LEU E 243 " --> pdb=" O PRO E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'F' and resid 42 through 58 removed outlier: 3.750A pdb=" N LEU F 46 " --> pdb=" O THR F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 82 Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 106 through 112 removed outlier: 3.571A pdb=" N ARG F 110 " --> pdb=" O TYR F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 193 Processing helix chain 'F' and resid 195 through 208 Processing helix chain 'F' and resid 239 through 246 Processing helix chain 'G' and resid 42 through 59 Processing helix chain 'G' and resid 73 through 82 removed outlier: 4.100A pdb=" N ALA G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 106 removed outlier: 3.923A pdb=" N GLU G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 112 removed outlier: 3.952A pdb=" N ARG G 110 " --> pdb=" O TYR G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 193 Processing helix chain 'G' and resid 195 through 213 removed outlier: 3.779A pdb=" N VAL G 207 " --> pdb=" O TRP G 203 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N PHE G 210 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASP G 211 " --> pdb=" O VAL G 207 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP G 213 " --> pdb=" O MET G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 247 Processing helix chain 'H' and resid 9 through 29 Processing helix chain 'H' and resid 35 through 47 removed outlier: 4.567A pdb=" N GLY H 42 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N SER H 43 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 65 removed outlier: 3.505A pdb=" N ARG H 57 " --> pdb=" O GLY H 53 " (cutoff:3.500A) Proline residue: H 60 - end of helix Processing helix chain 'H' and resid 68 through 86 removed outlier: 3.986A pdb=" N HIS H 85 " --> pdb=" O GLN H 81 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N CYS H 86 " --> pdb=" O ILE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 3.612A pdb=" N GLN H 110 " --> pdb=" O TYR H 106 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE H 111 " --> pdb=" O HIS H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 125 removed outlier: 3.504A pdb=" N ALA H 125 " --> pdb=" O LEU H 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 29 Processing helix chain 'I' and resid 35 through 47 removed outlier: 5.301A pdb=" N GLY I 42 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N SER I 43 " --> pdb=" O ARG I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 66 removed outlier: 4.770A pdb=" N VAL I 51 " --> pdb=" O THR I 47 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Proline residue: I 60 - end of helix Processing helix chain 'I' and resid 68 through 84 removed outlier: 3.910A pdb=" N GLU I 84 " --> pdb=" O ARG I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 114 removed outlier: 3.537A pdb=" N ALA I 102 " --> pdb=" O GLN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 124 Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 35 through 47 removed outlier: 4.282A pdb=" N ARG J 39 " --> pdb=" O THR J 35 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLY J 42 " --> pdb=" O ASP J 38 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N SER J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 66 removed outlier: 4.086A pdb=" N VAL J 51 " --> pdb=" O THR J 47 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLY J 53 " --> pdb=" O ILE J 49 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU J 58 " --> pdb=" O THR J 54 " (cutoff:3.500A) Proline residue: J 60 - end of helix Processing helix chain 'J' and resid 68 through 84 Processing helix chain 'J' and resid 94 through 114 removed outlier: 3.651A pdb=" N ALA J 102 " --> pdb=" O GLN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 125 Processing helix chain 'M' and resid 42 through 58 removed outlier: 4.022A pdb=" N LEU M 46 " --> pdb=" O THR M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 106 Processing helix chain 'M' and resid 106 through 112 Processing helix chain 'M' and resid 185 through 193 removed outlier: 3.610A pdb=" N ALA M 189 " --> pdb=" O SER M 185 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN M 191 " --> pdb=" O HIS M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 208 Processing helix chain 'M' and resid 239 through 246 removed outlier: 3.866A pdb=" N LEU M 243 " --> pdb=" O PRO M 239 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 262 No H-bonds generated for 'chain 'M' and resid 260 through 262' Processing helix chain 'M' and resid 272 through 276 removed outlier: 3.656A pdb=" N THR M 276 " --> pdb=" O LEU M 273 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 42 removed outlier: 3.635A pdb=" N ARG N 35 " --> pdb=" O PRO N 31 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN N 36 " --> pdb=" O ALA N 32 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU N 42 " --> pdb=" O LEU N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 85 Processing helix chain 'N' and resid 117 through 132 Processing helix chain 'K' and resid 2 through 16 removed outlier: 3.572A pdb=" N SER K 16 " --> pdb=" O ARG K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 260 Processing helix chain 'K' and resid 281 through 290 removed outlier: 5.401A pdb=" N SER K 287 " --> pdb=" O GLU K 283 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N MET K 288 " --> pdb=" O SER K 284 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN K 290 " --> pdb=" O ALA K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 303 Processing helix chain 'K' and resid 304 through 312 removed outlier: 3.527A pdb=" N TYR K 308 " --> pdb=" O VAL K 304 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR K 312 " --> pdb=" O TYR K 308 " (cutoff:3.500A) Processing helix chain 'K' and resid 318 through 322 removed outlier: 3.908A pdb=" N LYS K 322 " --> pdb=" O PRO K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 347 through 362 Processing helix chain 'K' and resid 376 through 383 Processing helix chain 'K' and resid 393 through 408 removed outlier: 3.629A pdb=" N LEU K 397 " --> pdb=" O LEU K 393 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN K 400 " --> pdb=" O ASP K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 412 through 427 removed outlier: 3.885A pdb=" N LEU K 416 " --> pdb=" O PRO K 412 " (cutoff:3.500A) Processing helix chain 'K' and resid 432 through 448 Processing helix chain 'K' and resid 466 through 486 Processing helix chain 'K' and resid 492 through 504 removed outlier: 6.511A pdb=" N GLY K 499 " --> pdb=" O ASP K 495 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N SER K 500 " --> pdb=" O ARG K 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 504 through 523 removed outlier: 3.837A pdb=" N VAL K 508 " --> pdb=" O THR K 504 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY K 510 " --> pdb=" O ILE K 506 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N THR K 511 " --> pdb=" O ALA K 507 " (cutoff:3.500A) Proline residue: K 517 - end of helix Processing helix chain 'K' and resid 525 through 541 Processing helix chain 'K' and resid 551 through 570 Processing helix chain 'K' and resid 573 through 582 removed outlier: 3.651A pdb=" N ALA K 582 " --> pdb=" O LEU K 578 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 29 removed outlier: 3.784A pdb=" N ASN L 29 " --> pdb=" O GLN L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 47 removed outlier: 6.531A pdb=" N GLY L 42 " --> pdb=" O ASP L 38 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N SER L 43 " --> pdb=" O ARG L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 66 removed outlier: 4.051A pdb=" N VAL L 51 " --> pdb=" O THR L 47 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY L 53 " --> pdb=" O ILE L 49 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR L 54 " --> pdb=" O ALA L 50 " (cutoff:3.500A) Proline residue: L 60 - end of helix Processing helix chain 'L' and resid 70 through 85 removed outlier: 4.194A pdb=" N HIS L 85 " --> pdb=" O GLN L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 113 Processing helix chain 'L' and resid 116 through 125 Processing helix chain 'A' and resid 38 through 52 removed outlier: 3.542A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 41 removed outlier: 3.604A pdb=" N SER B 134 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU B 131 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE B 183 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N PHE B 133 " --> pdb=" O HIS B 181 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N HIS B 181 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 7 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP B 14 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ALA B 223 " --> pdb=" O ASP B 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA3, first strand: chain 'B' and resid 145 through 148 removed outlier: 3.746A pdb=" N HIS B 145 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AA5, first strand: chain 'C' and resid 40 through 41 removed outlier: 3.629A pdb=" N ARG C 135 " --> pdb=" O ARG C 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 40 through 41 removed outlier: 3.629A pdb=" N ARG C 135 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR C 7 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AA8, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AA9, first strand: chain 'C' and resid 247 through 250 Processing sheet with id=AB1, first strand: chain 'D' and resid 40 through 41 Processing sheet with id=AB2, first strand: chain 'D' and resid 40 through 41 removed outlier: 6.533A pdb=" N ASP D 14 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ALA D 223 " --> pdb=" O ASP D 14 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AB4, first strand: chain 'D' and resid 143 through 146 Processing sheet with id=AB5, first strand: chain 'D' and resid 247 through 251 Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 33 removed outlier: 3.676A pdb=" N GLU E 38 " --> pdb=" O ASP E 33 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLY E 39 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG E 135 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG E 179 " --> pdb=" O ARG E 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 129 through 131 Processing sheet with id=AB8, first strand: chain 'E' and resid 247 through 251 Processing sheet with id=AB9, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.583A pdb=" N ARG F 135 " --> pdb=" O ARG F 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.583A pdb=" N ARG F 135 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR F 7 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG F 6 " --> pdb=" O GLU F 230 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU F 230 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP F 8 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL F 228 " --> pdb=" O ASP F 8 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL F 10 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU F 226 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU F 12 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN F 220 " --> pdb=" O GLN F 16 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 145 through 146 Processing sheet with id=AC3, first strand: chain 'F' and resid 247 through 250 Processing sheet with id=AC4, first strand: chain 'G' and resid 40 through 41 Processing sheet with id=AC5, first strand: chain 'G' and resid 40 through 41 removed outlier: 6.535A pdb=" N ASP G 14 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ALA G 223 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLN G 16 " --> pdb=" O MET G 221 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET G 221 " --> pdb=" O GLN G 16 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG G 224 " --> pdb=" O GLY G 284 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLY G 284 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU G 226 " --> pdb=" O LEU G 282 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU G 282 " --> pdb=" O LEU G 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 145 through 146 Processing sheet with id=AC7, first strand: chain 'G' and resid 248 through 251 Processing sheet with id=AC8, first strand: chain 'M' and resid 178 through 183 removed outlier: 6.929A pdb=" N ASP M 8 " --> pdb=" O VAL M 228 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL M 228 " --> pdb=" O ASP M 8 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL M 10 " --> pdb=" O LEU M 226 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU M 226 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU M 12 " --> pdb=" O ARG M 224 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN M 220 " --> pdb=" O GLN M 16 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL M 228 " --> pdb=" O ARG M 280 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 114 through 115 Processing sheet with id=AD1, first strand: chain 'M' and resid 143 through 145 Processing sheet with id=AD2, first strand: chain 'M' and resid 166 through 167 removed outlier: 3.583A pdb=" N MET M 167 " --> pdb=" O TYR A 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'M' and resid 248 through 251 Processing sheet with id=AD4, first strand: chain 'N' and resid 62 through 70 removed outlier: 6.786A pdb=" N ASP N 10 " --> pdb=" O ASP N 97 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA N 99 " --> pdb=" O SER N 8 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER N 8 " --> pdb=" O ALA N 99 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG N 101 " --> pdb=" O GLU N 6 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU N 6 " --> pdb=" O ARG N 101 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N HIS N 103 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE N 4 " --> pdb=" O HIS N 103 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 62 through 70 removed outlier: 6.580A pdb=" N ARG N 101 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE N 54 " --> pdb=" O ARG N 101 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N HIS N 103 " --> pdb=" O LEU N 52 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 170 through 172 Processing sheet with id=AD7, first strand: chain 'K' and resid 192 through 194 Processing sheet with id=AD8, first strand: chain 'K' and resid 210 through 211 Processing sheet with id=AD9, first strand: chain 'K' and resid 324 through 325 Processing sheet with id=AE1, first strand: chain 'K' and resid 331 through 332 Processing sheet with id=AE2, first strand: chain 'A' and resid 20 through 24 removed outlier: 3.532A pdb=" N ILE A 12 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A 65 " --> pdb=" O ILE A 12 " (cutoff:3.500A) 1058 hydrogen bonds defined for protein. 3009 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 8.10 Time building geometry restraints manager: 11.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6747 1.33 - 1.45: 5476 1.45 - 1.57: 13865 1.57 - 1.70: 83 1.70 - 1.82: 185 Bond restraints: 26356 Sorted by residual: bond pdb=" CA ASP C 213 " pdb=" CB ASP C 213 " ideal model delta sigma weight residual 1.523 1.489 0.034 1.35e-02 5.49e+03 6.37e+00 bond pdb=" CG1 ILE M 147 " pdb=" CD1 ILE M 147 " ideal model delta sigma weight residual 1.513 1.427 0.086 3.90e-02 6.57e+02 4.87e+00 bond pdb=" CA ASP C 8 " pdb=" CB ASP C 8 " ideal model delta sigma weight residual 1.534 1.496 0.037 1.72e-02 3.38e+03 4.74e+00 bond pdb=" CA GLY B 22 " pdb=" C GLY B 22 " ideal model delta sigma weight residual 1.520 1.506 0.014 7.30e-03 1.88e+04 3.70e+00 bond pdb=" CB VAL C 50 " pdb=" CG2 VAL C 50 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.38e+00 ... (remaining 26351 not shown) Histogram of bond angle deviations from ideal: 96.26 - 103.83: 410 103.83 - 111.39: 11223 111.39 - 118.95: 9899 118.95 - 126.52: 13830 126.52 - 134.08: 369 Bond angle restraints: 35731 Sorted by residual: angle pdb=" C ARG B 224 " pdb=" N GLY B 225 " pdb=" CA GLY B 225 " ideal model delta sigma weight residual 122.33 119.18 3.15 7.30e-01 1.88e+00 1.86e+01 angle pdb=" N VAL G 258 " pdb=" CA VAL G 258 " pdb=" C VAL G 258 " ideal model delta sigma weight residual 106.21 109.99 -3.78 1.07e+00 8.73e-01 1.25e+01 angle pdb=" C ASP M 157 " pdb=" N ALA M 158 " pdb=" CA ALA M 158 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" CB ARG D 259 " pdb=" CG ARG D 259 " pdb=" CD ARG D 259 " ideal model delta sigma weight residual 111.30 119.09 -7.79 2.30e+00 1.89e-01 1.15e+01 angle pdb=" CA MET E 209 " pdb=" CB MET E 209 " pdb=" CG MET E 209 " ideal model delta sigma weight residual 114.10 107.56 6.54 2.00e+00 2.50e-01 1.07e+01 ... (remaining 35726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 15483 35.76 - 71.53: 345 71.53 - 107.29: 53 107.29 - 143.05: 3 143.05 - 178.81: 3 Dihedral angle restraints: 15887 sinusoidal: 6974 harmonic: 8913 Sorted by residual: dihedral pdb=" O4' C O 14 " pdb=" C1' C O 14 " pdb=" N1 C O 14 " pdb=" C2 C O 14 " ideal model delta sinusoidal sigma weight residual 200.00 42.17 157.83 1 1.50e+01 4.44e-03 8.22e+01 dihedral pdb=" O4' C O 38 " pdb=" C1' C O 38 " pdb=" N1 C O 38 " pdb=" C2 C O 38 " ideal model delta sinusoidal sigma weight residual 200.00 53.15 146.85 1 1.50e+01 4.44e-03 7.84e+01 dihedral pdb=" O4' C O 8 " pdb=" C1' C O 8 " pdb=" N1 C O 8 " pdb=" C2 C O 8 " ideal model delta sinusoidal sigma weight residual 200.00 66.11 133.89 1 1.50e+01 4.44e-03 7.22e+01 ... (remaining 15884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3195 0.063 - 0.125: 605 0.125 - 0.188: 62 0.188 - 0.251: 3 0.251 - 0.314: 1 Chirality restraints: 3866 Sorted by residual: chirality pdb=" C3' U O 24 " pdb=" C4' U O 24 " pdb=" O3' U O 24 " pdb=" C2' U O 24 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB THR K 279 " pdb=" CA THR K 279 " pdb=" OG1 THR K 279 " pdb=" CG2 THR K 279 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C1' C O 31 " pdb=" O4' C O 31 " pdb=" C2' C O 31 " pdb=" N1 C O 31 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 3863 not shown) Planarity restraints: 4570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 77 " -0.021 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP L 77 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP L 77 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP L 77 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 77 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP L 77 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 77 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 77 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 77 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP L 77 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR H 47 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO H 48 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO H 48 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 48 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 127 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO D 128 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 128 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 128 " -0.033 5.00e-02 4.00e+02 ... (remaining 4567 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 540 2.61 - 3.18: 25668 3.18 - 3.75: 40805 3.75 - 4.33: 55110 4.33 - 4.90: 86984 Nonbonded interactions: 209107 Sorted by model distance: nonbonded pdb=" OG SER M 195 " pdb=" OD1 ASN M 197 " model vdw 2.037 3.040 nonbonded pdb=" OD2 ASP B 237 " pdb=" OG1 THR B 276 " model vdw 2.086 3.040 nonbonded pdb=" NH2 ARG B 51 " pdb=" OP1 U O 13 " model vdw 2.086 3.120 nonbonded pdb=" NH2 ARG E 51 " pdb=" OP1 C O 31 " model vdw 2.094 3.120 nonbonded pdb=" OD2 ASP M 237 " pdb=" OG1 THR M 276 " model vdw 2.097 3.040 ... (remaining 209102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 through 74 or resid 94 through 148 or resid 167 through \ 284)) selection = (chain 'C' and (resid 2 through 74 or resid 94 through 148 or resid 167 through \ 284)) selection = (chain 'D' and (resid 2 through 74 or resid 94 through 148 or resid 167 through \ 284)) selection = (chain 'E' and (resid 2 through 74 or resid 94 through 148 or resid 167 through \ 284)) selection = (chain 'F' and (resid 2 through 74 or resid 94 through 284)) selection = (chain 'G' and (resid 2 through 74 or resid 94 through 148 or resid 167 through \ 284)) selection = (chain 'M' and (resid 2 through 148 or resid 167 through 284)) } ncs_group { reference = (chain 'H' and (resid 2 through 67 or resid 70 through 85 or resid 94 through 12 \ 5)) selection = (chain 'I' and (resid 2 through 67 or resid 70 through 85 or resid 94 through 12 \ 5)) selection = (chain 'J' and (resid 2 through 67 or resid 70 through 85 or resid 94 through 12 \ 5)) selection = chain 'L' } 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: 1.200 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: 1.030 Check model and map are aligned: 0.180 Set scattering table: 0.260 Process input model: 75.170 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 : 0.008 0.086 26356 Z= 0.498 Angle : 0.851 8.889 35731 Z= 0.488 Chirality : 0.048 0.314 3866 Planarity : 0.005 0.061 4570 Dihedral : 16.325 178.815 10159 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 24.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.52 % Favored : 91.44 % Rotamer: Outliers : 0.04 % Allowed : 0.57 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.15), residues: 3062 helix: 0.42 (0.15), residues: 1116 sheet: -1.13 (0.21), residues: 585 loop : -2.25 (0.15), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP L 77 HIS 0.020 0.002 HIS G 62 PHE 0.030 0.003 PHE M 11 TYR 0.027 0.003 TYR H 12 ARG 0.016 0.001 ARG G 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 261 time to evaluate : 3.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 CYS cc_start: 0.8560 (m) cc_final: 0.8201 (m) REVERT: C 272 ASN cc_start: 0.8958 (m110) cc_final: 0.8673 (m-40) REVERT: D 150 MET cc_start: 0.8868 (tpt) cc_final: 0.8487 (tpp) REVERT: E 111 THR cc_start: 0.8628 (m) cc_final: 0.8428 (p) REVERT: E 167 MET cc_start: 0.7910 (mmp) cc_final: 0.7501 (mmm) REVERT: F 116 MET cc_start: 0.9324 (mpp) cc_final: 0.8326 (mpp) REVERT: G 116 MET cc_start: 0.9063 (mpp) cc_final: 0.8420 (mpp) REVERT: H 116 ASP cc_start: 0.9299 (p0) cc_final: 0.8953 (t0) REVERT: I 25 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8972 (tm-30) REVERT: I 41 PHE cc_start: 0.9192 (t80) cc_final: 0.8856 (t80) REVERT: I 68 PHE cc_start: 0.7757 (t80) cc_final: 0.7530 (t80) REVERT: I 88 ARG cc_start: 0.8786 (tmm-80) cc_final: 0.8550 (ttp80) REVERT: J 65 LYS cc_start: 0.9026 (ttpp) cc_final: 0.8772 (tttm) REVERT: N 165 THR cc_start: 0.6275 (p) cc_final: 0.5982 (p) REVERT: K 300 HIS cc_start: 0.8694 (m90) cc_final: 0.8149 (m-70) REVERT: K 327 LEU cc_start: 0.9340 (mm) cc_final: 0.8904 (pp) REVERT: L 9 ASP cc_start: 0.8702 (m-30) cc_final: 0.8480 (m-30) REVERT: L 56 MET cc_start: 0.8742 (mmp) cc_final: 0.8206 (ttt) REVERT: A 11 LYS cc_start: 0.8666 (tptt) cc_final: 0.8430 (tppt) REVERT: A 12 ILE cc_start: 0.8814 (tt) cc_final: 0.8456 (tt) REVERT: A 22 LYS cc_start: 0.8891 (mppt) cc_final: 0.8667 (mmmt) REVERT: A 28 GLU cc_start: 0.8426 (mp0) cc_final: 0.8225 (mp0) REVERT: A 67 LYS cc_start: 0.9501 (pptt) cc_final: 0.9137 (pptt) outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.3872 time to fit residues: 157.9150 Evaluate side-chains 214 residues out of total 2654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 9.9990 chunk 234 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 180 optimal weight: 9.9990 chunk 280 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN C 85 ASN ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 HIS M 124 GLN ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 HIS ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26356 Z= 0.294 Angle : 0.674 7.760 35731 Z= 0.364 Chirality : 0.045 0.283 3866 Planarity : 0.005 0.100 4570 Dihedral : 13.817 169.546 4057 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.83 % Allowed : 7.84 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3062 helix: 0.86 (0.15), residues: 1171 sheet: -0.75 (0.23), residues: 527 loop : -2.04 (0.15), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 77 HIS 0.006 0.001 HIS F 187 PHE 0.025 0.002 PHE H 111 TYR 0.016 0.002 TYR K 250 ARG 0.008 0.001 ARG K 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 257 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 CYS cc_start: 0.8372 (m) cc_final: 0.8033 (m) REVERT: C 167 MET cc_start: 0.8942 (mmm) cc_final: 0.8554 (mmp) REVERT: D 272 ASN cc_start: 0.9132 (t0) cc_final: 0.8919 (t0) REVERT: E 150 MET cc_start: 0.9340 (tpp) cc_final: 0.9061 (tpp) REVERT: F 116 MET cc_start: 0.9361 (mpp) cc_final: 0.8387 (mpp) REVERT: F 141 MET cc_start: 0.8277 (mpp) cc_final: 0.8075 (mpp) REVERT: F 209 MET cc_start: 0.7886 (ttp) cc_final: 0.7617 (tmm) REVERT: H 77 TRP cc_start: 0.8625 (t60) cc_final: 0.8286 (t60) REVERT: H 87 GLN cc_start: 0.7917 (pp30) cc_final: 0.7690 (pp30) REVERT: H 89 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7142 (t80) REVERT: I 55 LEU cc_start: 0.9450 (mt) cc_final: 0.9206 (mt) REVERT: I 68 PHE cc_start: 0.7831 (t80) cc_final: 0.7363 (t80) REVERT: I 88 ARG cc_start: 0.8834 (tmm-80) cc_final: 0.8529 (ttp80) REVERT: I 106 TYR cc_start: 0.9087 (m-80) cc_final: 0.8880 (m-80) REVERT: N 171 MET cc_start: 0.9017 (tpp) cc_final: 0.8761 (tpt) REVERT: K 300 HIS cc_start: 0.8478 (m90) cc_final: 0.8056 (m-70) REVERT: K 327 LEU cc_start: 0.9244 (mm) cc_final: 0.8775 (pp) REVERT: L 9 ASP cc_start: 0.8647 (m-30) cc_final: 0.8425 (m-30) REVERT: L 40 TYR cc_start: 0.9133 (m-80) cc_final: 0.8928 (m-80) REVERT: A 24 TYR cc_start: 0.8912 (m-80) cc_final: 0.8707 (m-80) outliers start: 22 outliers final: 11 residues processed: 267 average time/residue: 0.4056 time to fit residues: 170.4056 Evaluate side-chains 228 residues out of total 2654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 216 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 363 MET Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 68 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 20.0000 chunk 87 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 281 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 chunk 278 optimal weight: 0.3980 chunk 95 optimal weight: 0.8980 chunk 225 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN D 75 ASN E 21 ASN F 74 ASN F 234 ASN ** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26356 Z= 0.211 Angle : 0.603 8.319 35731 Z= 0.323 Chirality : 0.042 0.244 3866 Planarity : 0.004 0.097 4570 Dihedral : 13.636 166.406 4057 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.13 % Allowed : 11.69 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3062 helix: 1.18 (0.16), residues: 1175 sheet: -0.42 (0.23), residues: 520 loop : -1.94 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 43 HIS 0.007 0.001 HIS G 81 PHE 0.026 0.001 PHE H 111 TYR 0.021 0.002 TYR G 178 ARG 0.005 0.000 ARG L 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 244 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 209 MET cc_start: 0.8427 (tmm) cc_final: 0.7028 (tmm) REVERT: C 103 CYS cc_start: 0.8339 (m) cc_final: 0.8105 (p) REVERT: C 167 MET cc_start: 0.8879 (mmm) cc_final: 0.8592 (mmm) REVERT: D 271 LYS cc_start: 0.9246 (tppt) cc_final: 0.8963 (tppt) REVERT: D 272 ASN cc_start: 0.9270 (t0) cc_final: 0.9007 (t0) REVERT: E 102 MET cc_start: 0.9366 (mmt) cc_final: 0.9066 (mmm) REVERT: E 167 MET cc_start: 0.7339 (mmm) cc_final: 0.7034 (mmm) REVERT: F 116 MET cc_start: 0.9392 (mpp) cc_final: 0.8672 (mpp) REVERT: F 141 MET cc_start: 0.8295 (mpp) cc_final: 0.8031 (mpp) REVERT: F 209 MET cc_start: 0.8148 (ttp) cc_final: 0.7736 (tmm) REVERT: G 116 MET cc_start: 0.8916 (mpp) cc_final: 0.8134 (mpp) REVERT: G 178 TYR cc_start: 0.8603 (m-80) cc_final: 0.8257 (m-80) REVERT: H 87 GLN cc_start: 0.8289 (pp30) cc_final: 0.8028 (pp30) REVERT: H 89 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7230 (t80) REVERT: H 122 PHE cc_start: 0.8721 (t80) cc_final: 0.8480 (t80) REVERT: I 39 ARG cc_start: 0.8920 (mtp180) cc_final: 0.8653 (ttm170) REVERT: I 55 LEU cc_start: 0.9519 (mt) cc_final: 0.9268 (mt) REVERT: I 65 LYS cc_start: 0.9432 (pptt) cc_final: 0.9080 (pptt) REVERT: I 88 ARG cc_start: 0.8741 (tmm-80) cc_final: 0.8462 (ttp80) REVERT: I 106 TYR cc_start: 0.9076 (m-80) cc_final: 0.8761 (m-80) REVERT: J 22 GLU cc_start: 0.9398 (tm-30) cc_final: 0.8957 (tm-30) REVERT: J 68 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: N 171 MET cc_start: 0.9083 (tpp) cc_final: 0.8847 (tpt) REVERT: K 300 HIS cc_start: 0.8393 (m90) cc_final: 0.7851 (m-70) REVERT: K 327 LEU cc_start: 0.9182 (mm) cc_final: 0.8772 (pp) REVERT: L 9 ASP cc_start: 0.8629 (m-30) cc_final: 0.8409 (m-30) REVERT: L 56 MET cc_start: 0.8468 (mmp) cc_final: 0.7738 (ttt) outliers start: 30 outliers final: 18 residues processed: 263 average time/residue: 0.3789 time to fit residues: 157.2151 Evaluate side-chains 235 residues out of total 2654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 215 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 92 HIS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 363 MET Chi-restraints excluded: chain K residue 570 PHE Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 68 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 7.9990 chunk 211 optimal weight: 0.1980 chunk 145 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 282 optimal weight: 0.7980 chunk 298 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 267 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN I 85 HIS ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26356 Z= 0.226 Angle : 0.589 7.532 35731 Z= 0.314 Chirality : 0.042 0.246 3866 Planarity : 0.004 0.068 4570 Dihedral : 13.554 166.150 4057 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.77 % Allowed : 14.33 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3062 helix: 1.32 (0.16), residues: 1176 sheet: -0.46 (0.22), residues: 532 loop : -1.85 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 77 HIS 0.006 0.001 HIS H 92 PHE 0.028 0.001 PHE H 111 TYR 0.026 0.001 TYR N 139 ARG 0.008 0.000 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 235 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 209 MET cc_start: 0.8529 (tmm) cc_final: 0.6906 (tmm) REVERT: C 46 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7876 (tt) REVERT: C 103 CYS cc_start: 0.8355 (m) cc_final: 0.8038 (m) REVERT: C 167 MET cc_start: 0.8896 (mmm) cc_final: 0.8638 (mmm) REVERT: D 271 LYS cc_start: 0.9224 (tppt) cc_final: 0.8927 (tppt) REVERT: D 272 ASN cc_start: 0.9356 (t0) cc_final: 0.9039 (t0) REVERT: E 167 MET cc_start: 0.7304 (mmm) cc_final: 0.6975 (mmm) REVERT: E 209 MET cc_start: 0.7376 (tpp) cc_final: 0.7012 (tpt) REVERT: F 116 MET cc_start: 0.9426 (mpp) cc_final: 0.8680 (mpp) REVERT: F 141 MET cc_start: 0.8409 (mpp) cc_final: 0.8120 (mpp) REVERT: F 209 MET cc_start: 0.8118 (ttp) cc_final: 0.7692 (tmm) REVERT: G 178 TYR cc_start: 0.8688 (m-80) cc_final: 0.8263 (m-80) REVERT: G 209 MET cc_start: 0.4917 (tmm) cc_final: 0.4244 (ttt) REVERT: G 221 MET cc_start: 0.5337 (ptt) cc_final: 0.5102 (ptt) REVERT: H 87 GLN cc_start: 0.8453 (pp30) cc_final: 0.8234 (pp30) REVERT: H 89 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7339 (t80) REVERT: I 55 LEU cc_start: 0.9504 (mt) cc_final: 0.9256 (mt) REVERT: I 65 LYS cc_start: 0.9336 (pptt) cc_final: 0.8888 (ptmm) REVERT: I 88 ARG cc_start: 0.8757 (tmm-80) cc_final: 0.8456 (ttp80) REVERT: J 68 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: M 31 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7236 (mtt-85) REVERT: K 1 MET cc_start: 0.7220 (tpt) cc_final: 0.7000 (tpt) REVERT: K 300 HIS cc_start: 0.8381 (m90) cc_final: 0.7808 (m-70) REVERT: K 327 LEU cc_start: 0.9159 (mm) cc_final: 0.8891 (pp) REVERT: L 9 ASP cc_start: 0.8573 (m-30) cc_final: 0.8340 (m-30) REVERT: L 56 MET cc_start: 0.8438 (mmp) cc_final: 0.7722 (ttt) outliers start: 47 outliers final: 25 residues processed: 270 average time/residue: 0.3316 time to fit residues: 140.9877 Evaluate side-chains 245 residues out of total 2654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 216 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 92 HIS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 139 TYR Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 363 MET Chi-restraints excluded: chain K residue 570 PHE Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 68 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 254 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 268 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: