Starting phenix.real_space_refine on Wed Mar 4 22:04:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oo2_20142/03_2026/6oo2_20142.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oo2_20142/03_2026/6oo2_20142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oo2_20142/03_2026/6oo2_20142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oo2_20142/03_2026/6oo2_20142.map" model { file = "/net/cci-nas-00/data/ceres_data/6oo2_20142/03_2026/6oo2_20142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oo2_20142/03_2026/6oo2_20142.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 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: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 45 5.16 5 Be 3 3.05 5 C 10334 2.51 5 N 2982 2.21 5 O 3304 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16691 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2427 Classifications: {'peptide': 314} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "C" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2482 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 304} Chain breaks: 1 Chain: "D" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2482 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 304} Chain breaks: 1 Chain: "E" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2351 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 286} Chain breaks: 1 Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 39 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 1498 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 258} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 287} Chain breaks: 2 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 902 Unresolved non-hydrogen angles: 1146 Unresolved non-hydrogen dihedrals: 745 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLU:plan': 24, 'ASN:plan1': 9, 'TRP:plan': 4, 'ASP:plan': 20, 'PHE:plan': 12, 'HIS:plan': 2, 'ARG:plan': 16, 'TYR:plan': 5, 'GLN:plan1': 8} Unresolved non-hydrogen planarities: 448 Chain: "H" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 205 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "I" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 250 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 48} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 64 Chain: "J" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 205 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "K" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 250 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 48} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 64 Chain: "L" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 205 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "M" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 250 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 48} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 64 Chain: "N" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 205 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "O" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 250 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 48} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 64 Chain: "P" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 205 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "Q" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 250 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 48} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 64 Chain: "R" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 205 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "S" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 210 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 57 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.30, per 1000 atoms: 0.26 Number of scatterers: 16691 At special positions: 0 Unit cell: (81.75, 161.32, 155.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 45 16.00 P 10 15.00 Mg 4 11.99 F 9 9.00 O 3304 8.00 N 2982 7.00 C 10334 6.00 Be 3 4.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 831.6 milliseconds 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4598 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 13 sheets defined 60.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 116 through 122 removed outlier: 3.783A pdb=" N LEU A 119 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A 120 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 121 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 122 " --> pdb=" O LEU A 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 122' Processing helix chain 'A' and resid 138 through 155 Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 208 through 224 removed outlier: 4.005A pdb=" N VAL A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 245 through 260 removed outlier: 4.709A pdb=" N ARG A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 335 through 356 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'A' and resid 418 through 433 removed outlier: 3.891A pdb=" N LEU A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 178 through 190 Processing helix chain 'B' and resid 208 through 224 removed outlier: 4.313A pdb=" N VAL B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 261 Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 300 through 313 removed outlier: 3.584A pdb=" N GLY B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 335 through 356 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 402 through 413 removed outlier: 3.998A pdb=" N PHE B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 433 Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 138 through 155 Proline residue: C 152 - end of helix Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'C' and resid 209 through 224 removed outlier: 3.608A pdb=" N LEU C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 261 removed outlier: 4.056A pdb=" N ASN C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 290 Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 335 through 356 Proline residue: C 350 - end of helix Processing helix chain 'C' and resid 402 through 413 removed outlier: 3.967A pdb=" N PHE C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 131 through 135 removed outlier: 3.569A pdb=" N VAL D 135 " --> pdb=" O TRP D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 155 Proline residue: D 152 - end of helix Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.735A pdb=" N LEU D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 224 removed outlier: 3.659A pdb=" N ASN D 224 " --> pdb=" O MET D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 245 through 261 removed outlier: 4.202A pdb=" N ASN D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 300 through 312 Processing helix chain 'D' and resid 320 through 331 Processing helix chain 'D' and resid 335 through 356 Proline residue: D 350 - end of helix Processing helix chain 'D' and resid 402 through 413 removed outlier: 3.943A pdb=" N PHE D 406 " --> pdb=" O THR D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 433 Processing helix chain 'E' and resid 138 through 155 Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 178 through 190 Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.755A pdb=" N VAL E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 224 removed outlier: 3.592A pdb=" N ASN E 224 " --> pdb=" O MET E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 removed outlier: 3.719A pdb=" N THR E 238 " --> pdb=" O VAL E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 261 Processing helix chain 'E' and resid 283 through 290 Processing helix chain 'E' and resid 300 through 313 removed outlier: 4.146A pdb=" N GLY E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 331 Processing helix chain 'E' and resid 335 through 356 Proline residue: E 350 - end of helix removed outlier: 3.557A pdb=" N GLN E 355 " --> pdb=" O ILE E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 413 removed outlier: 3.966A pdb=" N PHE E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 432 removed outlier: 3.643A pdb=" N LEU E 423 " --> pdb=" O GLU E 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 135 Processing helix chain 'F' and resid 138 through 155 Proline residue: F 152 - end of helix Processing helix chain 'F' and resid 156 through 159 Processing helix chain 'F' and resid 178 through 191 Processing helix chain 'F' and resid 199 through 204 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 209 through 224 Processing helix chain 'F' and resid 245 through 261 removed outlier: 3.555A pdb=" N LEU F 256 " --> pdb=" O ILE F 252 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL F 258 " --> pdb=" O THR F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 264 No H-bonds generated for 'chain 'F' and resid 262 through 264' Processing helix chain 'F' and resid 278 through 282 Processing helix chain 'F' and resid 283 through 290 removed outlier: 3.577A pdb=" N ARG F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE F 290 " --> pdb=" O ILE F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 313 Processing helix chain 'F' and resid 320 through 330 Processing helix chain 'F' and resid 335 through 348 removed outlier: 3.936A pdb=" N MET F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 356 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 402 through 413 removed outlier: 3.743A pdb=" N PHE F 406 " --> pdb=" O THR F 402 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 433 Processing helix chain 'H' and resid 291 through 309 removed outlier: 3.510A pdb=" N GLN H 298 " --> pdb=" O ILE H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 330 removed outlier: 3.837A pdb=" N THR H 321 " --> pdb=" O LYS H 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 309 Processing helix chain 'I' and resid 312 through 330 removed outlier: 3.837A pdb=" N THR I 321 " --> pdb=" O LYS I 317 " (cutoff:3.500A) Processing helix chain 'J' and resid 291 through 309 Processing helix chain 'J' and resid 312 through 330 removed outlier: 3.839A pdb=" N THR J 321 " --> pdb=" O LYS J 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 309 Processing helix chain 'K' and resid 312 through 330 removed outlier: 3.839A pdb=" N THR K 321 " --> pdb=" O LYS K 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 309 removed outlier: 3.585A pdb=" N GLN L 298 " --> pdb=" O ILE L 294 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS L 299 " --> pdb=" O GLU L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 330 removed outlier: 3.839A pdb=" N THR L 321 " --> pdb=" O LYS L 317 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 309 Processing helix chain 'M' and resid 312 through 330 removed outlier: 3.708A pdb=" N THR M 321 " --> pdb=" O LYS M 317 " (cutoff:3.500A) Processing helix chain 'N' and resid 291 through 309 Processing helix chain 'N' and resid 312 through 330 removed outlier: 3.682A pdb=" N THR N 321 " --> pdb=" O LYS N 317 " (cutoff:3.500A) Processing helix chain 'O' and resid 282 through 309 Processing helix chain 'O' and resid 312 through 330 removed outlier: 3.839A pdb=" N THR O 321 " --> pdb=" O LYS O 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 291 through 309 removed outlier: 3.850A pdb=" N ILE P 297 " --> pdb=" O LYS P 293 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLN P 298 " --> pdb=" O ILE P 294 " (cutoff:3.500A) Processing helix chain 'P' and resid 312 through 330 removed outlier: 3.693A pdb=" N THR P 321 " --> pdb=" O LYS P 317 " (cutoff:3.500A) Processing helix chain 'Q' and resid 282 through 309 Processing helix chain 'Q' and resid 312 through 330 removed outlier: 3.688A pdb=" N THR Q 321 " --> pdb=" O LYS Q 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 291 through 309 Processing helix chain 'R' and resid 312 through 330 removed outlier: 3.722A pdb=" N THR R 321 " --> pdb=" O LYS R 317 " (cutoff:3.500A) Processing helix chain 'S' and resid 290 through 309 Processing helix chain 'S' and resid 312 through 330 removed outlier: 3.698A pdb=" N THR S 321 " --> pdb=" O LYS S 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 276 removed outlier: 8.619A pdb=" N THR A 276 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU A 171 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 170 " --> pdb=" O ILE A 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 363 removed outlier: 4.037A pdb=" N LYS A 372 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 193 through 197 removed outlier: 6.363A pdb=" N THR B 193 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE B 230 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE B 195 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP B 232 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL B 197 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 275 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU B 170 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 360 through 362 Processing sheet with id=AA6, first strand: chain 'C' and resid 193 through 197 removed outlier: 3.503A pdb=" N ILE C 228 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C 232 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 275 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLY C 168 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE C 294 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU C 170 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG C 293 " --> pdb=" O GLN C 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 373 through 375 Processing sheet with id=AA8, first strand: chain 'D' and resid 193 through 197 removed outlier: 6.447A pdb=" N THR D 193 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE D 230 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE D 195 " --> pdb=" O PHE D 230 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP D 232 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL D 197 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU D 273 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE D 229 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA D 275 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE D 231 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 372 through 375 removed outlier: 4.222A pdb=" N LYS D 372 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 363 " --> pdb=" O LYS D 372 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.672A pdb=" N THR E 193 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE E 230 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE E 195 " --> pdb=" O PHE E 230 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP E 232 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER E 227 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU E 273 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE E 229 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA E 275 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE E 231 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 372 through 375 removed outlier: 4.256A pdb=" N LYS E 372 " --> pdb=" O VAL E 363 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 124 through 126 removed outlier: 6.563A pdb=" N GLY F 168 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE F 294 " --> pdb=" O GLY F 168 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU F 170 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 372 through 375 removed outlier: 4.076A pdb=" N LYS F 372 " --> pdb=" O VAL F 363 " (cutoff:3.500A) 1066 hydrogen bonds defined for protein. 3129 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: 2.54 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3009 1.32 - 1.44: 3847 1.44 - 1.56: 9906 1.56 - 1.69: 40 1.69 - 1.81: 80 Bond restraints: 16882 Sorted by residual: bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.386 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.387 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.388 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" CA ILE J 305 " pdb=" CB ILE J 305 " ideal model delta sigma weight residual 1.538 1.588 -0.049 1.06e-02 8.90e+03 2.14e+01 bond pdb=" CA ILE R 305 " pdb=" CB ILE R 305 " ideal model delta sigma weight residual 1.538 1.587 -0.049 1.06e-02 8.90e+03 2.10e+01 ... (remaining 16877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 22333 2.99 - 5.97: 552 5.97 - 8.96: 87 8.96 - 11.94: 15 11.94 - 14.93: 3 Bond angle restraints: 22990 Sorted by residual: angle pdb=" N ASN Q 328 " pdb=" CA ASN Q 328 " pdb=" C ASN Q 328 " ideal model delta sigma weight residual 113.50 105.26 8.24 1.23e+00 6.61e-01 4.49e+01 angle pdb=" N ASN M 328 " pdb=" CA ASN M 328 " pdb=" C ASN M 328 " ideal model delta sigma weight residual 113.50 105.31 8.19 1.23e+00 6.61e-01 4.44e+01 angle pdb=" N ASN K 328 " pdb=" CA ASN K 328 " pdb=" C ASN K 328 " ideal model delta sigma weight residual 113.50 105.33 8.17 1.23e+00 6.61e-01 4.42e+01 angle pdb=" N ASN O 328 " pdb=" CA ASN O 328 " pdb=" C ASN O 328 " ideal model delta sigma weight residual 113.50 105.34 8.16 1.23e+00 6.61e-01 4.40e+01 angle pdb=" N ASN S 328 " pdb=" CA ASN S 328 " pdb=" C ASN S 328 " ideal model delta sigma weight residual 113.50 105.37 8.13 1.23e+00 6.61e-01 4.36e+01 ... (remaining 22985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 10060 33.70 - 67.40: 162 67.40 - 101.11: 15 101.11 - 134.81: 2 134.81 - 168.51: 4 Dihedral angle restraints: 10243 sinusoidal: 3204 harmonic: 7039 Sorted by residual: dihedral pdb=" C5' ADP B 501 " pdb=" O5' ADP B 501 " pdb=" PA ADP B 501 " pdb=" O2A ADP B 501 " ideal model delta sinusoidal sigma weight residual 300.00 131.49 168.51 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' ADP C 501 " pdb=" O5' ADP C 501 " pdb=" PA ADP C 501 " pdb=" O2A ADP C 501 " ideal model delta sinusoidal sigma weight residual 300.00 136.64 163.37 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 88.99 -148.99 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 10240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2141 0.073 - 0.147: 470 0.147 - 0.220: 130 0.220 - 0.294: 27 0.294 - 0.367: 5 Chirality restraints: 2773 Sorted by residual: chirality pdb=" CA ILE F 278 " pdb=" N ILE F 278 " pdb=" C ILE F 278 " pdb=" CB ILE F 278 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA ASP F 394 " pdb=" N ASP F 394 " pdb=" C ASP F 394 " pdb=" CB ASP F 394 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA MET F 386 " pdb=" N MET F 386 " pdb=" C MET F 386 " pdb=" CB MET F 386 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 2770 not shown) Planarity restraints: 3027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 379 " -0.023 2.00e-02 2.50e+03 4.80e-02 2.30e+01 pdb=" C GLY F 379 " 0.083 2.00e-02 2.50e+03 pdb=" O GLY F 379 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP F 380 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 237 " 0.023 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C LEU F 237 " -0.081 2.00e-02 2.50e+03 pdb=" O LEU F 237 " 0.031 2.00e-02 2.50e+03 pdb=" N THR F 238 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 297 " 0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C PRO F 297 " -0.073 2.00e-02 2.50e+03 pdb=" O PRO F 297 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU F 298 " 0.024 2.00e-02 2.50e+03 ... (remaining 3024 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 255 2.61 - 3.18: 14321 3.18 - 3.75: 25854 3.75 - 4.33: 32778 4.33 - 4.90: 54779 Nonbonded interactions: 127987 Sorted by model distance: nonbonded pdb=" OG SER A 180 " pdb="MG MG A 503 " model vdw 2.037 2.170 nonbonded pdb=" OG SER C 180 " pdb="MG MG C 503 " model vdw 2.038 2.170 nonbonded pdb=" OG SER B 180 " pdb="MG MG B 503 " model vdw 2.038 2.170 nonbonded pdb=" O2B ADP A 501 " pdb="MG MG A 503 " model vdw 2.038 2.170 nonbonded pdb=" F1 BEF C 502 " pdb="MG MG C 503 " model vdw 2.038 2.120 ... (remaining 127982 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 'A' and ((resid 126 through 136 and (name N or name CA or name C or name \ O or name CB )) or resid 137 or (resid 138 through 139 and (name N or name CA or \ name C or name O or name CB )) or (resid 140 through 160 and (name N or name CA \ or name C or name O or name CB )) or resid 161 or (resid 162 through 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 or (resid 169 th \ rough 172 and (name N or name CA or name C or name O or name CB )) or resid 173 \ or (resid 174 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 and (name N or name CA or name C or name O or name \ CB )) or resid 178 or (resid 179 through 207 and (name N or name CA or name C o \ r name O or name CB )) or resid 208 or (resid 209 through 238 and (name N or nam \ e CA or name C or name O or name CB )) or resid 239 or (resid 240 through 241 an \ d (name N or name CA or name C or name O or name CB )) or resid 242 or (resid 24 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 244 or (resi \ d 245 through 261 and (name N or name CA or name C or name O or name CB )) or re \ sid 262 or (resid 263 and (name N or name CA or name C or name O or name CB )) o \ r resid 264 or (resid 265 and (name N or name CA or name C or name O or name CB \ )) or (resid 268 and (name N or name CA or name C or name O or name CB )) or res \ id 269 or (resid 270 through 273 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 274 through 312 and (name N or name CA or name C or name O o \ r name CB )) or resid 313 or (resid 314 through 327 and (name N or name CA or na \ me C or name O or name CB )) or (resid 328 through 332 and (name N or name CA or \ name C or name O or name CB )) or resid 333 or (resid 334 through 335 and (name \ N or name CA or name C or name O or name CB )) or resid 336 or (resid 337 throu \ gh 364 and (name N or name CA or name C or name O or name CB )) or (resid 371 th \ rough 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 through 381 and (name N or name CA or name C or name O or name CB \ )) or (resid 382 through 432 and (name N or name CA or name C or name O or name \ CB )) or resid 433)) selection = (chain 'B' and ((resid 126 through 136 and (name N or name CA or name C or name \ O or name CB )) or resid 137 or (resid 138 through 139 and (name N or name CA or \ name C or name O or name CB )) or (resid 140 through 160 and (name N or name CA \ or name C or name O or name CB )) or resid 161 or (resid 162 through 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 or (resid 169 th \ rough 172 and (name N or name CA or name C or name O or name CB )) or resid 173 \ or (resid 174 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 and (name N or name CA or name C or name O or name \ CB )) or resid 178 or (resid 179 through 207 and (name N or name CA or name C o \ r name O or name CB )) or resid 208 or (resid 209 through 238 and (name N or nam \ e CA or name C or name O or name CB )) or resid 239 or (resid 240 through 241 an \ d (name N or name CA or name C or name O or name CB )) or resid 242 or (resid 24 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 244 or (resi \ d 245 through 261 and (name N or name CA or name C or name O or name CB )) or re \ sid 262 or (resid 263 and (name N or name CA or name C or name O or name CB )) o \ r resid 264 or (resid 265 and (name N or name CA or name C or name O or name CB \ )) or (resid 268 and (name N or name CA or name C or name O or name CB )) or res \ id 269 or (resid 270 through 273 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 274 through 312 and (name N or name CA or name C or name O o \ r name CB )) or resid 313 or (resid 314 through 327 and (name N or name CA or na \ me C or name O or name CB )) or (resid 328 through 332 and (name N or name CA or \ name C or name O or name CB )) or resid 333 or (resid 334 through 335 and (name \ N or name CA or name C or name O or name CB )) or resid 336 or (resid 337 throu \ gh 364 and (name N or name CA or name C or name O or name CB )) or (resid 371 th \ rough 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 through 381 and (name N or name CA or name C or name O or name CB \ )) or (resid 382 through 432 and (name N or name CA or name C or name O or name \ CB )) or resid 433)) selection = (chain 'C' and ((resid 126 through 136 and (name N or name CA or name C or name \ O or name CB )) or resid 137 or (resid 138 through 139 and (name N or name CA or \ name C or name O or name CB )) or (resid 140 through 160 and (name N or name CA \ or name C or name O or name CB )) or resid 161 or (resid 162 through 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 or (resid 169 th \ rough 172 and (name N or name CA or name C or name O or name CB )) or resid 173 \ or (resid 174 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 and (name N or name CA or name C or name O or name \ CB )) or resid 178 or (resid 179 through 207 and (name N or name CA or name C o \ r name O or name CB )) or resid 208 or (resid 209 through 238 and (name N or nam \ e CA or name C or name O or name CB )) or resid 239 or (resid 240 through 241 an \ d (name N or name CA or name C or name O or name CB )) or resid 242 or (resid 24 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 244 or (resi \ d 245 through 261 and (name N or name CA or name C or name O or name CB )) or re \ sid 262 or (resid 263 and (name N or name CA or name C or name O or name CB )) o \ r resid 264 or (resid 265 and (name N or name CA or name C or name O or name CB \ )) or (resid 268 and (name N or name CA or name C or name O or name CB )) or res \ id 269 or (resid 270 through 273 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 274 through 312 and (name N or name CA or name C or name O o \ r name CB )) or resid 313 or (resid 314 through 327 and (name N or name CA or na \ me C or name O or name CB )) or (resid 328 through 332 and (name N or name CA or \ name C or name O or name CB )) or resid 333 or (resid 334 through 335 and (name \ N or name CA or name C or name O or name CB )) or resid 336 or (resid 337 throu \ gh 364 and (name N or name CA or name C or name O or name CB )) or (resid 371 th \ rough 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 through 381 and (name N or name CA or name C or name O or name CB \ )) or (resid 382 through 432 and (name N or name CA or name C or name O or name \ CB )) or resid 433)) selection = (chain 'D' and ((resid 126 through 136 and (name N or name CA or name C or name \ O or name CB )) or resid 137 or (resid 138 through 139 and (name N or name CA or \ name C or name O or name CB )) or (resid 140 through 160 and (name N or name CA \ or name C or name O or name CB )) or resid 161 or (resid 162 through 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 or (resid 169 th \ rough 172 and (name N or name CA or name C or name O or name CB )) or resid 173 \ or (resid 174 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 and (name N or name CA or name C or name O or name \ CB )) or resid 178 or (resid 179 through 207 and (name N or name CA or name C o \ r name O or name CB )) or resid 208 or (resid 209 through 238 and (name N or nam \ e CA or name C or name O or name CB )) or resid 239 or (resid 240 through 241 an \ d (name N or name CA or name C or name O or name CB )) or resid 242 or (resid 24 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 244 or (resi \ d 245 through 261 and (name N or name CA or name C or name O or name CB )) or re \ sid 262 or (resid 263 and (name N or name CA or name C or name O or name CB )) o \ r resid 264 or (resid 265 and (name N or name CA or name C or name O or name CB \ )) or (resid 268 and (name N or name CA or name C or name O or name CB )) or res \ id 269 or (resid 270 through 273 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 274 through 312 and (name N or name CA or name C or name O o \ r name CB )) or resid 313 or (resid 314 through 327 and (name N or name CA or na \ me C or name O or name CB )) or (resid 328 through 332 and (name N or name CA or \ name C or name O or name CB )) or resid 333 or (resid 334 through 335 and (name \ N or name CA or name C or name O or name CB )) or resid 336 or (resid 337 throu \ gh 364 and (name N or name CA or name C or name O or name CB )) or (resid 371 th \ rough 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 through 381 and (name N or name CA or name C or name O or name CB \ )) or (resid 382 through 432 and (name N or name CA or name C or name O or name \ CB )) or resid 433)) selection = (chain 'E' and ((resid 126 through 136 and (name N or name CA or name C or name \ O or name CB )) or resid 137 or (resid 138 through 139 and (name N or name CA or \ name C or name O or name CB )) or (resid 140 through 160 and (name N or name CA \ or name C or name O or name CB )) or resid 161 or (resid 162 through 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 or (resid 169 th \ rough 172 and (name N or name CA or name C or name O or name CB )) or resid 173 \ or (resid 174 through 175 and (name N or name CA or name C or name O or name CB \ )) or resid 176 or (resid 177 and (name N or name CA or name C or name O or name \ CB )) or resid 178 or (resid 179 through 207 and (name N or name CA or name C o \ r name O or name CB )) or resid 208 or (resid 209 through 238 and (name N or nam \ e CA or name C or name O or name CB )) or resid 239 or (resid 240 through 241 an \ d (name N or name CA or name C or name O or name CB )) or resid 242 or (resid 24 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 244 or (resi \ d 245 through 261 and (name N or name CA or name C or name O or name CB )) or re \ sid 262 or (resid 263 and (name N or name CA or name C or name O or name CB )) o \ r resid 264 or (resid 265 and (name N or name CA or name C or name O or name CB \ )) or (resid 268 and (name N or name CA or name C or name O or name CB )) or res \ id 269 or (resid 270 through 273 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 274 through 312 and (name N or name CA or name C or name O o \ r name CB )) or resid 313 or (resid 314 through 327 and (name N or name CA or na \ me C or name O or name CB )) or (resid 328 through 332 and (name N or name CA or \ name C or name O or name CB )) or resid 333 or (resid 334 through 335 and (name \ N or name CA or name C or name O or name CB )) or resid 336 or (resid 337 throu \ gh 364 and (name N or name CA or name C or name O or name CB )) or (resid 371 th \ rough 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 through 381 and (name N or name CA or name C or name O or name CB \ )) or (resid 382 through 432 and (name N or name CA or name C or name O or name \ CB )) or resid 433)) selection = (chain 'F' and resid 126 through 433) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = (chain 'S' and resid 290 through 330) } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.190 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 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 : 0.012 0.709 16885 Z= 1.059 Angle : 1.145 14.931 22990 Z= 0.754 Chirality : 0.072 0.367 2773 Planarity : 0.006 0.056 3027 Dihedral : 13.965 168.510 5645 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.09 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.14), residues: 2383 helix: -2.12 (0.11), residues: 1356 sheet: -2.00 (0.35), residues: 194 loop : -2.54 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 304 TYR 0.008 0.001 TYR C 181 PHE 0.012 0.001 PHE A 308 TRP 0.010 0.001 TRP E 280 HIS 0.001 0.000 HIS E 157 Details of bonding type rmsd covalent geometry : bond 0.00706 (16882) covalent geometry : angle 1.14458 (22990) hydrogen bonds : bond 0.18685 ( 1066) hydrogen bonds : angle 8.26067 ( 3129) Misc. bond : bond 0.70641 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.594 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: A 202 LEU cc_start: 0.8551 (mt) cc_final: 0.8120 (tt) REVERT: A 307 MET cc_start: 0.8242 (ttm) cc_final: 0.7537 (tpp) REVERT: B 307 MET cc_start: 0.8205 (ttm) cc_final: 0.7469 (tpp) REVERT: C 341 VAL cc_start: 0.9106 (m) cc_final: 0.8862 (p) REVERT: C 386 MET cc_start: 0.7700 (ptp) cc_final: 0.7410 (ptt) REVERT: C 427 GLN cc_start: 0.7117 (tp40) cc_final: 0.6656 (tp-100) REVERT: C 431 ASP cc_start: 0.6500 (m-30) cc_final: 0.6033 (m-30) REVERT: D 145 LEU cc_start: 0.9248 (mt) cc_final: 0.9039 (mt) REVERT: D 186 VAL cc_start: 0.9402 (t) cc_final: 0.9180 (p) REVERT: D 348 MET cc_start: 0.7827 (mmm) cc_final: 0.7559 (tpp) REVERT: D 386 MET cc_start: 0.6842 (ptp) cc_final: 0.6608 (ppp) REVERT: D 431 ASP cc_start: 0.7513 (m-30) cc_final: 0.6612 (m-30) REVERT: E 170 LEU cc_start: 0.8232 (tp) cc_final: 0.8002 (tt) REVERT: E 386 MET cc_start: 0.6916 (ptp) cc_final: 0.6595 (ptp) REVERT: E 418 ASN cc_start: 0.8800 (t0) cc_final: 0.8569 (m-40) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1274 time to fit residues: 39.0683 Evaluate side-chains 100 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 9.9990 chunk 235 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN B 216 GLN C 281 GLN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN C 437 ASN D 216 GLN D 418 ASN D 427 GLN E 265 ASN E 311 ASN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.040788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.031107 restraints weight = 213027.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.031765 restraints weight = 142368.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.032227 restraints weight = 107777.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.032569 restraints weight = 88801.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.032719 restraints weight = 76823.637| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 16885 Z= 0.316 Angle : 0.799 9.837 22990 Z= 0.416 Chirality : 0.043 0.238 2773 Planarity : 0.006 0.059 3027 Dihedral : 9.138 175.280 2580 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.30 % Allowed : 6.97 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.17), residues: 2383 helix: 0.13 (0.14), residues: 1412 sheet: -1.31 (0.35), residues: 218 loop : -1.58 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 289 TYR 0.020 0.002 TYR B 334 PHE 0.027 0.003 PHE C 195 TRP 0.045 0.004 TRP C 132 HIS 0.012 0.004 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00615 (16882) covalent geometry : angle 0.79909 (22990) hydrogen bonds : bond 0.03853 ( 1066) hydrogen bonds : angle 5.27278 ( 3129) Misc. bond : bond 0.00357 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.9722 (mt) cc_final: 0.9189 (tp) REVERT: A 260 MET cc_start: 0.9250 (ttt) cc_final: 0.9013 (ptm) REVERT: A 307 MET cc_start: 0.9279 (ttm) cc_final: 0.9050 (ttm) REVERT: B 233 GLU cc_start: 0.9220 (mp0) cc_final: 0.9006 (mp0) REVERT: B 260 MET cc_start: 0.9213 (ttt) cc_final: 0.8890 (ppp) REVERT: B 307 MET cc_start: 0.9422 (ttm) cc_final: 0.9047 (ttt) REVERT: C 348 MET cc_start: 0.8955 (mmm) cc_final: 0.8309 (mmm) REVERT: C 386 MET cc_start: 0.8657 (ptp) cc_final: 0.8347 (ptp) REVERT: C 427 GLN cc_start: 0.9170 (tp40) cc_final: 0.8760 (tp-100) REVERT: D 233 GLU cc_start: 0.8164 (mp0) cc_final: 0.7786 (mp0) REVERT: D 251 ARG cc_start: 0.9380 (mtt90) cc_final: 0.9115 (ttm-80) REVERT: D 260 MET cc_start: 0.9216 (tmm) cc_final: 0.8967 (tmm) REVERT: D 307 MET cc_start: 0.9332 (mtt) cc_final: 0.9066 (mmm) REVERT: D 348 MET cc_start: 0.9351 (mmm) cc_final: 0.9084 (mmp) REVERT: D 386 MET cc_start: 0.8640 (ptp) cc_final: 0.7960 (ppp) REVERT: E 233 GLU cc_start: 0.9024 (mp0) cc_final: 0.8745 (mp0) outliers start: 4 outliers final: 1 residues processed: 96 average time/residue: 0.1056 time to fit residues: 17.2808 Evaluate side-chains 77 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 146 optimal weight: 0.0970 chunk 108 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 172 optimal weight: 50.0000 chunk 137 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN C 281 GLN E 265 ASN E 359 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.040086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.030355 restraints weight = 178189.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.031024 restraints weight = 127013.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.031528 restraints weight = 97971.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.031849 restraints weight = 81069.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.032068 restraints weight = 70803.399| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16885 Z= 0.102 Angle : 0.542 6.911 22990 Z= 0.269 Chirality : 0.040 0.199 2773 Planarity : 0.004 0.050 3027 Dihedral : 8.617 177.298 2580 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.07 % Allowed : 2.15 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.18), residues: 2383 helix: 1.64 (0.14), residues: 1408 sheet: -1.02 (0.36), residues: 205 loop : -1.11 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 287 TYR 0.014 0.001 TYR C 181 PHE 0.028 0.001 PHE C 308 TRP 0.012 0.001 TRP A 388 HIS 0.006 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00204 (16882) covalent geometry : angle 0.54250 (22990) hydrogen bonds : bond 0.02510 ( 1066) hydrogen bonds : angle 4.32676 ( 3129) Misc. bond : bond 0.00065 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.9724 (mt) cc_final: 0.9086 (tp) REVERT: A 307 MET cc_start: 0.9252 (ttm) cc_final: 0.8968 (ttt) REVERT: B 233 GLU cc_start: 0.9293 (mp0) cc_final: 0.8964 (mp0) REVERT: B 307 MET cc_start: 0.9483 (ttm) cc_final: 0.9164 (ttt) REVERT: C 207 MET cc_start: 0.8456 (tpp) cc_final: 0.7485 (mmp) REVERT: C 330 MET cc_start: 0.9126 (mpp) cc_final: 0.8609 (tpp) REVERT: C 348 MET cc_start: 0.9138 (mmm) cc_final: 0.8565 (mmm) REVERT: C 386 MET cc_start: 0.8778 (ptp) cc_final: 0.8361 (ptp) REVERT: C 427 GLN cc_start: 0.9306 (tp40) cc_final: 0.8906 (tp-100) REVERT: D 233 GLU cc_start: 0.8485 (mp0) cc_final: 0.8051 (mp0) REVERT: D 251 ARG cc_start: 0.9461 (mtt90) cc_final: 0.9168 (ttm-80) REVERT: D 260 MET cc_start: 0.9171 (tmm) cc_final: 0.8881 (tmm) REVERT: D 330 MET cc_start: 0.9215 (mmp) cc_final: 0.8961 (mmm) REVERT: D 386 MET cc_start: 0.8370 (ptp) cc_final: 0.7502 (ppp) REVERT: E 233 GLU cc_start: 0.9050 (mp0) cc_final: 0.8764 (mp0) REVERT: E 418 ASN cc_start: 0.9323 (t0) cc_final: 0.9106 (p0) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.1113 time to fit residues: 18.6205 Evaluate side-chains 82 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 115 optimal weight: 0.7980 chunk 128 optimal weight: 8.9990 chunk 154 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN E 265 ASN E 311 ASN E 427 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.038684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.029573 restraints weight = 180583.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.030122 restraints weight = 128461.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.030573 restraints weight = 99401.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.030879 restraints weight = 83580.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.031090 restraints weight = 72907.441| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16885 Z= 0.177 Angle : 0.615 7.011 22990 Z= 0.312 Chirality : 0.041 0.220 2773 Planarity : 0.004 0.052 3027 Dihedral : 8.377 173.466 2580 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.18), residues: 2383 helix: 2.05 (0.14), residues: 1410 sheet: -0.83 (0.36), residues: 210 loop : -0.90 (0.25), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 251 TYR 0.027 0.002 TYR B 181 PHE 0.021 0.002 PHE C 308 TRP 0.016 0.002 TRP A 388 HIS 0.007 0.002 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00359 (16882) covalent geometry : angle 0.61520 (22990) hydrogen bonds : bond 0.02823 ( 1066) hydrogen bonds : angle 4.36454 ( 3129) Misc. bond : bond 0.00150 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 202 LEU cc_start: 0.9756 (mt) cc_final: 0.9130 (tp) REVERT: A 260 MET cc_start: 0.9185 (ttt) cc_final: 0.8964 (ptm) REVERT: A 307 MET cc_start: 0.9328 (ttm) cc_final: 0.9085 (ttm) REVERT: B 233 GLU cc_start: 0.9244 (mp0) cc_final: 0.8849 (mp0) REVERT: B 260 MET cc_start: 0.9089 (ttp) cc_final: 0.8838 (tmm) REVERT: B 281 GLN cc_start: 0.9065 (mt0) cc_final: 0.8488 (tm-30) REVERT: C 348 MET cc_start: 0.9441 (mmm) cc_final: 0.8816 (mmm) REVERT: C 381 ASP cc_start: 0.9128 (t0) cc_final: 0.8900 (p0) REVERT: C 386 MET cc_start: 0.8707 (ptp) cc_final: 0.8309 (ptp) REVERT: C 427 GLN cc_start: 0.9256 (tp40) cc_final: 0.8861 (tp-100) REVERT: D 233 GLU cc_start: 0.8415 (mp0) cc_final: 0.7964 (mp0) REVERT: D 260 MET cc_start: 0.9207 (tmm) cc_final: 0.8841 (tmm) REVERT: D 330 MET cc_start: 0.9220 (mmp) cc_final: 0.8977 (mmm) REVERT: E 233 GLU cc_start: 0.9108 (mp0) cc_final: 0.8801 (mp0) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1135 time to fit residues: 17.0088 Evaluate side-chains 70 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 174 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.037204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.028430 restraints weight = 190897.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.029015 restraints weight = 133398.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.029413 restraints weight = 102763.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.029693 restraints weight = 85624.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.029822 restraints weight = 74866.705| |-----------------------------------------------------------------------------| r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 16885 Z= 0.263 Angle : 0.720 9.390 22990 Z= 0.373 Chirality : 0.043 0.314 2773 Planarity : 0.005 0.057 3027 Dihedral : 8.357 162.284 2580 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.18), residues: 2383 helix: 1.61 (0.14), residues: 1426 sheet: -0.89 (0.35), residues: 210 loop : -1.03 (0.25), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG E 250 TYR 0.016 0.002 TYR A 324 PHE 0.025 0.003 PHE E 230 TRP 0.031 0.003 TRP C 388 HIS 0.007 0.002 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00526 (16882) covalent geometry : angle 0.71978 (22990) hydrogen bonds : bond 0.03524 ( 1066) hydrogen bonds : angle 4.83728 ( 3129) Misc. bond : bond 0.00126 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 330 MET cc_start: 0.9313 (mmp) cc_final: 0.8948 (mmm) REVERT: B 233 GLU cc_start: 0.9354 (mp0) cc_final: 0.9149 (mp0) REVERT: B 260 MET cc_start: 0.9269 (ttp) cc_final: 0.9026 (ttt) REVERT: B 281 GLN cc_start: 0.9173 (mt0) cc_final: 0.8432 (tm-30) REVERT: B 386 MET cc_start: 0.7654 (tmm) cc_final: 0.7374 (tmm) REVERT: C 307 MET cc_start: 0.9569 (mtp) cc_final: 0.9156 (mtp) REVERT: C 348 MET cc_start: 0.9577 (mmm) cc_final: 0.9052 (mmm) REVERT: C 381 ASP cc_start: 0.9168 (t0) cc_final: 0.8925 (p0) REVERT: C 386 MET cc_start: 0.8758 (ptp) cc_final: 0.8402 (ptp) REVERT: C 427 GLN cc_start: 0.9179 (tp40) cc_final: 0.8809 (tp-100) REVERT: D 260 MET cc_start: 0.9204 (tmm) cc_final: 0.8815 (tmm) REVERT: D 307 MET cc_start: 0.9486 (mtt) cc_final: 0.9129 (mmm) REVERT: D 386 MET cc_start: 0.8185 (pmm) cc_final: 0.6249 (ppp) REVERT: E 233 GLU cc_start: 0.9199 (mp0) cc_final: 0.8871 (mp0) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1020 time to fit residues: 12.8795 Evaluate side-chains 65 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 179 optimal weight: 40.0000 chunk 167 optimal weight: 9.9990 chunk 169 optimal weight: 50.0000 chunk 138 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.037191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.028239 restraints weight = 193833.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.028833 restraints weight = 134610.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.029213 restraints weight = 103241.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.029508 restraints weight = 86023.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.029725 restraints weight = 75219.185| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.6981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 16885 Z= 0.193 Angle : 0.615 6.858 22990 Z= 0.314 Chirality : 0.041 0.220 2773 Planarity : 0.004 0.049 3027 Dihedral : 7.980 158.136 2580 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.18), residues: 2383 helix: 1.91 (0.14), residues: 1416 sheet: -0.79 (0.36), residues: 194 loop : -0.94 (0.25), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 289 TYR 0.014 0.002 TYR C 181 PHE 0.016 0.002 PHE E 230 TRP 0.023 0.002 TRP A 388 HIS 0.006 0.002 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00388 (16882) covalent geometry : angle 0.61542 (22990) hydrogen bonds : bond 0.03080 ( 1066) hydrogen bonds : angle 4.55795 ( 3129) Misc. bond : bond 0.00067 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: B 233 GLU cc_start: 0.9305 (mp0) cc_final: 0.9102 (mp0) REVERT: B 281 GLN cc_start: 0.9113 (mt0) cc_final: 0.8372 (tm-30) REVERT: B 427 GLN cc_start: 0.9602 (tt0) cc_final: 0.9340 (tp-100) REVERT: C 307 MET cc_start: 0.9586 (mtp) cc_final: 0.9341 (mtt) REVERT: C 348 MET cc_start: 0.9555 (mmm) cc_final: 0.9087 (mmm) REVERT: C 381 ASP cc_start: 0.9136 (t0) cc_final: 0.8932 (p0) REVERT: C 427 GLN cc_start: 0.9186 (tp40) cc_final: 0.8831 (tp-100) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1026 time to fit residues: 12.9260 Evaluate side-chains 63 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 65 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 172 optimal weight: 50.0000 chunk 22 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 173 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN C 281 GLN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.037344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.028369 restraints weight = 185332.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.029010 restraints weight = 128382.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.029424 restraints weight = 97044.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.029667 restraints weight = 79888.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.029930 restraints weight = 70355.397| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.7114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16885 Z= 0.134 Angle : 0.572 7.030 22990 Z= 0.287 Chirality : 0.041 0.209 2773 Planarity : 0.004 0.047 3027 Dihedral : 7.837 159.516 2580 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.07 % Allowed : 1.26 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.18), residues: 2383 helix: 2.23 (0.14), residues: 1424 sheet: -0.72 (0.36), residues: 194 loop : -0.84 (0.25), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 251 TYR 0.009 0.001 TYR D 295 PHE 0.014 0.001 PHE A 218 TRP 0.017 0.001 TRP A 388 HIS 0.005 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00271 (16882) covalent geometry : angle 0.57209 (22990) hydrogen bonds : bond 0.02769 ( 1066) hydrogen bonds : angle 4.31186 ( 3129) Misc. bond : bond 0.00050 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.669 Fit side-chains REVERT: B 233 GLU cc_start: 0.9243 (mp0) cc_final: 0.8822 (mp0) REVERT: B 260 MET cc_start: 0.9107 (ttp) cc_final: 0.8820 (tmm) REVERT: B 281 GLN cc_start: 0.9051 (mt0) cc_final: 0.8531 (tp-100) REVERT: B 330 MET cc_start: 0.9484 (mmm) cc_final: 0.9212 (tpp) REVERT: B 427 GLN cc_start: 0.9615 (tt0) cc_final: 0.9343 (tp40) REVERT: C 281 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7987 (pp30) REVERT: C 307 MET cc_start: 0.9586 (mtp) cc_final: 0.9365 (mtp) REVERT: C 348 MET cc_start: 0.9544 (mmm) cc_final: 0.9103 (mmm) REVERT: C 386 MET cc_start: 0.8868 (ptt) cc_final: 0.7418 (ptp) REVERT: C 427 GLN cc_start: 0.9225 (tp40) cc_final: 0.8886 (tp-100) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1043 time to fit residues: 13.3335 Evaluate side-chains 64 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 240 optimal weight: 50.0000 chunk 132 optimal weight: 6.9990 chunk 236 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 194 optimal weight: 30.0000 chunk 118 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 208 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 152 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.037773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.028871 restraints weight = 223322.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.029516 restraints weight = 143732.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.029927 restraints weight = 106548.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.030257 restraints weight = 86322.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.030496 restraints weight = 73397.474| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.7652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 16885 Z= 0.222 Angle : 0.658 7.052 22990 Z= 0.334 Chirality : 0.041 0.236 2773 Planarity : 0.004 0.050 3027 Dihedral : 8.056 159.276 2580 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.18), residues: 2383 helix: 2.04 (0.14), residues: 1428 sheet: -0.80 (0.36), residues: 207 loop : -0.96 (0.25), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 251 TYR 0.012 0.002 TYR A 324 PHE 0.021 0.002 PHE E 230 TRP 0.026 0.003 TRP A 206 HIS 0.009 0.002 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00441 (16882) covalent geometry : angle 0.65821 (22990) hydrogen bonds : bond 0.03227 ( 1066) hydrogen bonds : angle 4.57835 ( 3129) Misc. bond : bond 0.00071 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.495 Fit side-chains REVERT: A 260 MET cc_start: 0.9172 (ptm) cc_final: 0.8911 (tmm) REVERT: A 330 MET cc_start: 0.9323 (mmp) cc_final: 0.8971 (mmm) REVERT: B 260 MET cc_start: 0.9255 (ttp) cc_final: 0.8882 (tmm) REVERT: B 281 GLN cc_start: 0.9051 (mt0) cc_final: 0.8371 (tm-30) REVERT: B 427 GLN cc_start: 0.9615 (tt0) cc_final: 0.9293 (tp40) REVERT: C 281 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8657 (tm-30) REVERT: C 307 MET cc_start: 0.9583 (mtp) cc_final: 0.9260 (mtp) REVERT: C 348 MET cc_start: 0.9535 (mmm) cc_final: 0.9154 (mmm) REVERT: C 427 GLN cc_start: 0.9190 (tp40) cc_final: 0.8814 (tp-100) REVERT: D 251 ARG cc_start: 0.9688 (mtt-85) cc_final: 0.9377 (mtm-85) REVERT: D 307 MET cc_start: 0.9431 (mtt) cc_final: 0.9213 (mmm) REVERT: E 330 MET cc_start: 0.9185 (mpp) cc_final: 0.8964 (mpp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1068 time to fit residues: 12.9040 Evaluate side-chains 62 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 52 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 29 optimal weight: 50.0000 chunk 192 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 137 optimal weight: 7.9990 chunk 157 optimal weight: 20.0000 chunk 195 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 201 optimal weight: 30.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.036671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.027926 restraints weight = 193890.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.028585 restraints weight = 132831.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.028989 restraints weight = 100047.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.029283 restraints weight = 81718.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.029487 restraints weight = 70761.840| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.7782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 16885 Z= 0.169 Angle : 0.610 8.834 22990 Z= 0.308 Chirality : 0.041 0.217 2773 Planarity : 0.004 0.049 3027 Dihedral : 7.945 158.254 2580 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.18), residues: 2383 helix: 2.16 (0.14), residues: 1432 sheet: -0.76 (0.36), residues: 202 loop : -0.92 (0.25), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 251 TYR 0.009 0.001 TYR D 295 PHE 0.016 0.002 PHE E 230 TRP 0.020 0.002 TRP A 388 HIS 0.006 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00342 (16882) covalent geometry : angle 0.60990 (22990) hydrogen bonds : bond 0.03027 ( 1066) hydrogen bonds : angle 4.44364 ( 3129) Misc. bond : bond 0.00058 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 260 MET cc_start: 0.9059 (ptm) cc_final: 0.8854 (tmm) REVERT: B 233 GLU cc_start: 0.9350 (mp0) cc_final: 0.9078 (mp0) REVERT: B 260 MET cc_start: 0.9201 (ttp) cc_final: 0.8900 (tmm) REVERT: B 281 GLN cc_start: 0.9084 (mt0) cc_final: 0.8358 (tm-30) REVERT: B 330 MET cc_start: 0.9530 (mmm) cc_final: 0.9249 (tpp) REVERT: B 427 GLN cc_start: 0.9628 (tt0) cc_final: 0.9351 (tp40) REVERT: C 281 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8494 (tm-30) REVERT: C 307 MET cc_start: 0.9629 (mtp) cc_final: 0.9306 (mtp) REVERT: C 348 MET cc_start: 0.9560 (mmm) cc_final: 0.9181 (mmm) REVERT: C 427 GLN cc_start: 0.9242 (tp40) cc_final: 0.8900 (tp-100) REVERT: D 251 ARG cc_start: 0.9712 (mtt-85) cc_final: 0.9186 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1141 time to fit residues: 14.0029 Evaluate side-chains 66 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 162 optimal weight: 40.0000 chunk 117 optimal weight: 4.9990 chunk 216 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 226 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.036901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.028312 restraints weight = 226585.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.028958 restraints weight = 144651.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.029373 restraints weight = 105983.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.029696 restraints weight = 85445.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.029881 restraints weight = 72616.912| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.8507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 16885 Z= 0.293 Angle : 0.743 9.242 22990 Z= 0.384 Chirality : 0.043 0.244 2773 Planarity : 0.005 0.067 3027 Dihedral : 8.398 159.359 2580 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.18), residues: 2383 helix: 1.69 (0.14), residues: 1427 sheet: -1.09 (0.35), residues: 226 loop : -1.18 (0.25), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 289 TYR 0.015 0.002 TYR C 324 PHE 0.025 0.003 PHE E 230 TRP 0.030 0.003 TRP A 388 HIS 0.010 0.002 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00584 (16882) covalent geometry : angle 0.74290 (22990) hydrogen bonds : bond 0.03842 ( 1066) hydrogen bonds : angle 5.01280 ( 3129) Misc. bond : bond 0.00166 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 330 MET cc_start: 0.9298 (mmp) cc_final: 0.8965 (mmm) REVERT: B 233 GLU cc_start: 0.9223 (mp0) cc_final: 0.8888 (mp0) REVERT: B 281 GLN cc_start: 0.9098 (mt0) cc_final: 0.8430 (tm-30) REVERT: B 427 GLN cc_start: 0.9616 (tt0) cc_final: 0.9329 (tp40) REVERT: C 281 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8620 (tm-30) REVERT: C 348 MET cc_start: 0.9514 (mmm) cc_final: 0.9137 (mmm) REVERT: C 427 GLN cc_start: 0.9134 (tp40) cc_final: 0.8755 (tp-100) REVERT: D 251 ARG cc_start: 0.9665 (mtt-85) cc_final: 0.9365 (mtm-85) REVERT: D 307 MET cc_start: 0.9457 (mtt) cc_final: 0.9242 (mmm) REVERT: D 386 MET cc_start: 0.8144 (pmm) cc_final: 0.7822 (pmm) REVERT: E 260 MET cc_start: 0.9375 (tmm) cc_final: 0.9121 (tmm) REVERT: E 348 MET cc_start: 0.8431 (mmt) cc_final: 0.8065 (mmm) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1111 time to fit residues: 13.0596 Evaluate side-chains 60 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 48 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 232 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 170 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 223 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 GLN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.036880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.028181 restraints weight = 188538.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.028827 restraints weight = 128017.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.029263 restraints weight = 95981.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.029558 restraints weight = 77909.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.029796 restraints weight = 67604.183| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.8314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16885 Z= 0.114 Angle : 0.584 8.320 22990 Z= 0.289 Chirality : 0.041 0.181 2773 Planarity : 0.004 0.048 3027 Dihedral : 7.889 158.732 2580 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.18), residues: 2383 helix: 2.22 (0.14), residues: 1427 sheet: -0.78 (0.35), residues: 222 loop : -0.79 (0.26), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 251 TYR 0.009 0.001 TYR D 295 PHE 0.013 0.001 PHE C 428 TRP 0.019 0.002 TRP A 132 HIS 0.004 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00234 (16882) covalent geometry : angle 0.58409 (22990) hydrogen bonds : bond 0.02840 ( 1066) hydrogen bonds : angle 4.35298 ( 3129) Misc. bond : bond 0.00027 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2113.72 seconds wall clock time: 37 minutes 35.96 seconds (2255.96 seconds total)