Starting phenix.real_space_refine on Tue Sep 15 03:11:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vof_21262/09_2026/6vof_21262.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vof_21262/09_2026/6vof_21262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vof_21262/09_2026/6vof_21262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vof_21262/09_2026/6vof_21262.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vof_21262/09_2026/6vof_21262.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vof_21262/09_2026/6vof_21262.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vof_21262/09_2026/6vof_21262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vof_21262/09_2026/6vof_21262.cif" } resolution = 4.51 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 98 5.16 5 C 21813 2.51 5 N 6336 2.21 5 O 6921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35182 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3796 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3832 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3829 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 481} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3589 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 451} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3600 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3610 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1360 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 173} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2444 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 308} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "e" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 926 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 58 Chain: "I" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 746 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'TRANS': 150} Unresolved non-hydrogen bonds: 486 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 385 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'ASN:plan1': 16, 'PHE:plan': 7, 'ASP:plan': 4, 'ARG:plan': 11, 'GLN:plan1': 12, 'GLU:plan': 14, 'TYR:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 287 Chain: "J" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 681 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 3, 'TRANS': 132} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 396 Unresolved non-hydrogen angles: 491 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'ASP:plan': 10, 'PHE:plan': 5, 'ASN:plan1': 3, 'GLU:plan': 15, 'TYR:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 8} Unresolved non-hydrogen planarities: 195 Chain: "a" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1082 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 185} Link IDs: {'PTRANS': 14, 'TRANS': 205} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 691 Unresolved non-hydrogen angles: 912 Unresolved non-hydrogen dihedrals: 583 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'HIS:plan': 3, 'PHE:plan': 17, 'TYR:plan': 8, 'TRP:plan': 5, 'GLN:plan1': 9, 'ARG:plan': 4, 'ASN:plan1': 6, 'GLU:plan': 9, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 340 Chain: "M" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 403 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "N" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 396 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 56 Chain: "O" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 390 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 2, 'PHE:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "P" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 392 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 1, 'PHE:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "Q" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 393 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 62 Chain: "R" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 392 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 1, 'PHE:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "S" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 396 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 57 Chain: "T" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 402 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 57 Chain: "U" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 400 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 57 Chain: "V" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 392 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 62 Chain: "W" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 406 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'TYR:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 47 Chain: "X" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 402 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'PHE:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 56 Chain: "Y" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 386 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 2, 'PHE:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "Z" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 386 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 2, 'PHE:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 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} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.79, per 1000 atoms: 0.22 Number of scatterers: 35182 At special positions: 0 Unit cell: (130, 203.84, 169.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 P 14 15.00 O 6921 8.00 N 6336 7.00 C 21813 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.00 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: 3.10 Conformation dependent library (CDL) restraints added in 1.7 seconds 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9402 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 29 sheets defined 60.7% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.395A pdb=" N MET A 82 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.588A pdb=" N TYR A 104 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 175 through 187 Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 217 through 221 removed outlier: 4.302A pdb=" N GLU A 220 " --> pdb=" O GLY A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 288 through 289 No H-bonds generated for 'chain 'A' and resid 288 through 289' Processing helix chain 'A' and resid 290 through 301 removed outlier: 3.586A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 373 through 395 removed outlier: 4.230A pdb=" N LEU A 385 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 removed outlier: 5.477A pdb=" N GLN A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 444 Processing helix chain 'A' and resid 445 through 449 removed outlier: 3.790A pdb=" N SER A 448 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 469 removed outlier: 3.984A pdb=" N ARG A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.526A pdb=" N GLN A 495 " --> pdb=" O LYS A 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.935A pdb=" N THR B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.819A pdb=" N TYR B 104 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 175 through 187 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 232 through 253 Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 288 through 289 No H-bonds generated for 'chain 'B' and resid 288 through 289' Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.311A pdb=" N ALA B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 397 removed outlier: 4.428A pdb=" N LYS B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 422 Processing helix chain 'B' and resid 430 through 443 Processing helix chain 'B' and resid 452 through 469 removed outlier: 4.547A pdb=" N LYS B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 480 removed outlier: 4.030A pdb=" N GLN B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 502 removed outlier: 3.877A pdb=" N GLN B 495 " --> pdb=" O LYS B 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 18 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.820A pdb=" N ASP C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 221 Processing helix chain 'C' and resid 232 through 252 Proline residue: C 240 - end of helix removed outlier: 3.599A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.971A pdb=" N ALA C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 289 No H-bonds generated for 'chain 'C' and resid 288 through 289' Processing helix chain 'C' and resid 290 through 301 removed outlier: 3.610A pdb=" N ARG C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 326 Processing helix chain 'C' and resid 330 through 338 removed outlier: 4.254A pdb=" N ILE C 336 " --> pdb=" O PRO C 332 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER C 337 " --> pdb=" O THR C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.437A pdb=" N ALA C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 381 Processing helix chain 'C' and resid 382 through 397 Processing helix chain 'C' and resid 404 through 421 Processing helix chain 'C' and resid 430 through 443 Processing helix chain 'C' and resid 444 through 449 removed outlier: 4.377A pdb=" N SER C 448 " --> pdb=" O GLY C 444 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU C 449 " --> pdb=" O TYR C 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 444 through 449' Processing helix chain 'C' and resid 453 through 469 Processing helix chain 'C' and resid 469 through 480 removed outlier: 4.436A pdb=" N GLN C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU C 474 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 503 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.545A pdb=" N LEU D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 177 through 193 Processing helix chain 'D' and resid 205 through 219 Processing helix chain 'D' and resid 242 through 263 removed outlier: 5.352A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 290 Processing helix chain 'D' and resid 301 through 311 removed outlier: 3.639A pdb=" N GLU D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 333 removed outlier: 3.621A pdb=" N ASP D 332 " --> pdb=" O VAL D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 381 through 409 removed outlier: 4.370A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA D 406 " --> pdb=" O GLN D 402 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 470 through 474 removed outlier: 3.516A pdb=" N ALA D 473 " --> pdb=" O PRO D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 495 Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 177 through 190 Processing helix chain 'E' and resid 205 through 219 Processing helix chain 'E' and resid 242 through 263 removed outlier: 4.081A pdb=" N ARG E 248 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 289 removed outlier: 3.502A pdb=" N PHE E 278 " --> pdb=" O ASN E 274 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 313 Processing helix chain 'E' and resid 330 through 333 removed outlier: 4.091A pdb=" N ASP E 333 " --> pdb=" O PRO E 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 330 through 333' Processing helix chain 'E' and resid 336 through 343 Processing helix chain 'E' and resid 353 through 359 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 383 through 409 removed outlier: 5.161A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 431 removed outlier: 4.643A pdb=" N THR E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA E 422 " --> pdb=" O ARG E 418 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 450 through 462 Processing helix chain 'E' and resid 465 through 469 removed outlier: 4.338A pdb=" N SER E 468 " --> pdb=" O GLU E 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 475 Processing helix chain 'E' and resid 479 through 496 Processing helix chain 'F' and resid 103 through 106 Processing helix chain 'F' and resid 153 through 160 Processing helix chain 'F' and resid 177 through 190 Processing helix chain 'F' and resid 205 through 220 Processing helix chain 'F' and resid 242 through 263 removed outlier: 4.669A pdb=" N GLY F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU F 251 " --> pdb=" O MET F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 290 removed outlier: 3.875A pdb=" N PHE F 278 " --> pdb=" O ASN F 274 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 329 through 333 removed outlier: 3.654A pdb=" N ASP F 332 " --> pdb=" O VAL F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 346 removed outlier: 3.813A pdb=" N THR F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.738A pdb=" N ALA F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 381 through 406 removed outlier: 4.054A pdb=" N THR F 394 " --> pdb=" O ARG F 390 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 431 Processing helix chain 'F' and resid 450 through 464 removed outlier: 4.471A pdb=" N PHE F 458 " --> pdb=" O THR F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 475 removed outlier: 3.863A pdb=" N PHE F 474 " --> pdb=" O GLU F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 493 Processing helix chain 'd' and resid 73 through 90 Processing helix chain 'd' and resid 91 through 107 Processing helix chain 'd' and resid 108 through 117 Processing helix chain 'd' and resid 121 through 137 Processing helix chain 'd' and resid 139 through 152 Processing helix chain 'd' and resid 153 through 156 removed outlier: 3.501A pdb=" N ASN d 156 " --> pdb=" O GLU d 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 153 through 156' Processing helix chain 'd' and resid 157 through 173 removed outlier: 4.264A pdb=" N ASP d 167 " --> pdb=" O ASN d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 203 Processing helix chain 'd' and resid 237 through 248 removed outlier: 4.193A pdb=" N LEU d 248 " --> pdb=" O ILE d 244 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 82 Processing helix chain 'g' and resid 82 through 100 Processing helix chain 'g' and resid 132 through 152 removed outlier: 4.841A pdb=" N LEU g 138 " --> pdb=" O ASN g 134 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 161 through 170 Processing helix chain 'g' and resid 187 through 204 removed outlier: 4.459A pdb=" N ILE g 194 " --> pdb=" O GLU g 190 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP g 197 " --> pdb=" O ALA g 193 " (cutoff:3.500A) Processing helix chain 'g' and resid 291 through 362 Proline residue: g 297 - end of helix removed outlier: 4.246A pdb=" N ASP g 328 " --> pdb=" O SER g 324 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 104 removed outlier: 3.540A pdb=" N LEU e 96 " --> pdb=" O ALA e 92 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU e 100 " --> pdb=" O LEU e 96 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 131 removed outlier: 3.677A pdb=" N GLU e 114 " --> pdb=" O ARG e 110 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN e 130 " --> pdb=" O VAL e 126 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR e 131 " --> pdb=" O GLU e 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 158 Processing helix chain 'I' and resid 162 through 182 Processing helix chain 'J' and resid 88 through 202 removed outlier: 4.005A pdb=" N THR J 110 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Proline residue: J 111 - end of helix Processing helix chain 'J' and resid 204 through 219 Processing helix chain 'a' and resid 37 through 58 Processing helix chain 'a' and resid 68 through 87 removed outlier: 3.699A pdb=" N PHE a 72 " --> pdb=" O GLY a 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 94 through 114 Processing helix chain 'a' and resid 129 through 132 Processing helix chain 'a' and resid 133 through 155 removed outlier: 3.976A pdb=" N THR a 137 " --> pdb=" O ASP a 133 " (cutoff:3.500A) Processing helix chain 'a' and resid 171 through 208 removed outlier: 3.545A pdb=" N ASN a 175 " --> pdb=" O LEU a 171 " (cutoff:3.500A) Proline residue: a 183 - end of helix removed outlier: 4.158A pdb=" N LEU a 190 " --> pdb=" O LEU a 186 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 244 removed outlier: 4.436A pdb=" N VAL a 216 " --> pdb=" O VAL a 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 21 removed outlier: 4.532A pdb=" N SER M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 42 removed outlier: 3.946A pdb=" N GLY M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 77 removed outlier: 3.523A pdb=" N ARG M 50 " --> pdb=" O GLU M 46 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER M 56 " --> pdb=" O THR M 52 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU M 63 " --> pdb=" O PHE M 59 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR M 64 " --> pdb=" O MET M 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 21 removed outlier: 4.403A pdb=" N SER N 21 " --> pdb=" O VAL N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 42 removed outlier: 3.579A pdb=" N GLY N 25 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL N 26 " --> pdb=" O ILE N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 76 Processing helix chain 'O' and resid 4 through 21 removed outlier: 3.944A pdb=" N SER O 21 " --> pdb=" O VAL O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 42 removed outlier: 3.816A pdb=" N VAL O 26 " --> pdb=" O ILE O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 76 removed outlier: 3.955A pdb=" N PHE O 59 " --> pdb=" O LEU O 55 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU O 63 " --> pdb=" O PHE O 59 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 42 Proline residue: P 24 - end of helix removed outlier: 3.979A pdb=" N GLY P 38 " --> pdb=" O GLN P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 75 removed outlier: 4.416A pdb=" N LEU P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER P 56 " --> pdb=" O THR P 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 Proline residue: Q 24 - end of helix Processing helix chain 'Q' and resid 45 through 76 removed outlier: 4.341A pdb=" N LEU Q 74 " --> pdb=" O VAL Q 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 42 removed outlier: 3.535A pdb=" N GLY R 14 " --> pdb=" O VAL R 10 " (cutoff:3.500A) Proline residue: R 24 - end of helix Processing helix chain 'R' and resid 45 through 76 Processing helix chain 'S' and resid 4 through 42 removed outlier: 3.747A pdb=" N GLY S 14 " --> pdb=" O VAL S 10 " (cutoff:3.500A) Proline residue: S 24 - end of helix Processing helix chain 'S' and resid 45 through 76 Processing helix chain 'T' and resid 4 through 42 removed outlier: 3.651A pdb=" N GLY T 14 " --> pdb=" O VAL T 10 " (cutoff:3.500A) Proline residue: T 24 - end of helix Processing helix chain 'T' and resid 45 through 76 Processing helix chain 'U' and resid 4 through 21 removed outlier: 3.624A pdb=" N SER U 21 " --> pdb=" O VAL U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 42 removed outlier: 4.892A pdb=" N GLY U 29 " --> pdb=" O GLY U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 76 removed outlier: 4.173A pdb=" N PHE U 59 " --> pdb=" O LEU U 55 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU U 63 " --> pdb=" O PHE U 59 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR U 64 " --> pdb=" O MET U 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 21 removed outlier: 3.543A pdb=" N SER V 21 " --> pdb=" O VAL V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 21 through 42 removed outlier: 3.805A pdb=" N GLY V 29 " --> pdb=" O GLY V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 78 removed outlier: 4.631A pdb=" N LEU V 63 " --> pdb=" O PHE V 59 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR V 64 " --> pdb=" O MET V 60 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA V 77 " --> pdb=" O ALA V 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 42 removed outlier: 4.134A pdb=" N VAL W 17 " --> pdb=" O ALA W 13 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER W 21 " --> pdb=" O VAL W 17 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE W 22 " --> pdb=" O GLY W 18 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY W 23 " --> pdb=" O LEU W 19 " (cutoff:3.500A) Proline residue: W 24 - end of helix removed outlier: 4.069A pdb=" N GLY W 29 " --> pdb=" O GLY W 25 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY W 38 " --> pdb=" O GLN W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 77 removed outlier: 3.746A pdb=" N LEU W 55 " --> pdb=" O GLY W 51 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU W 63 " --> pdb=" O PHE W 59 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR W 64 " --> pdb=" O MET W 60 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY W 67 " --> pdb=" O LEU W 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 21 removed outlier: 4.104A pdb=" N VAL X 17 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER X 21 " --> pdb=" O VAL X 17 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 42 removed outlier: 3.737A pdb=" N VAL X 26 " --> pdb=" O ILE X 22 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY X 29 " --> pdb=" O GLY X 25 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY X 38 " --> pdb=" O GLN X 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 45 through 76 removed outlier: 4.274A pdb=" N LEU X 63 " --> pdb=" O PHE X 59 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR X 64 " --> pdb=" O MET X 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 20 removed outlier: 3.516A pdb=" N VAL Y 17 " --> pdb=" O ALA Y 13 " (cutoff:3.500A) Processing helix chain 'Y' and resid 21 through 42 removed outlier: 3.547A pdb=" N GLY Y 29 " --> pdb=" O GLY Y 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY Y 38 " --> pdb=" O GLN Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 77 removed outlier: 4.813A pdb=" N LEU Y 63 " --> pdb=" O PHE Y 59 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR Y 64 " --> pdb=" O MET Y 60 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA Y 77 " --> pdb=" O ALA Y 73 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 20 removed outlier: 4.084A pdb=" N VAL Z 17 " --> pdb=" O ALA Z 13 " (cutoff:3.500A) Processing helix chain 'Z' and resid 22 through 42 removed outlier: 3.938A pdb=" N GLY Z 29 " --> pdb=" O GLY Z 25 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY Z 38 " --> pdb=" O GLN Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 77 removed outlier: 3.843A pdb=" N ALA Z 62 " --> pdb=" O ALA Z 58 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU Z 63 " --> pdb=" O PHE Z 59 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY Z 67 " --> pdb=" O LEU Z 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 67 removed outlier: 3.609A pdb=" N LEU A 33 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 63 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A 61 " --> pdb=" O MET A 77 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE F 26 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL F 61 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ALA F 34 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE F 23 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.644A pdb=" N GLU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 168 through 170 removed outlier: 5.953A pdb=" N ILE A 168 " --> pdb=" O VAL A 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 227 removed outlier: 8.289A pdb=" N VAL A 225 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR A 196 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLU A 227 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ALA A 198 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 258 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 23 through 27 removed outlier: 7.197A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN E 66 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU E 68 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL B 35 " --> pdb=" O LEU E 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 30 through 36 current: chain 'E' and resid 92 through 97 Processing sheet with id=AA6, first strand: chain 'E' and resid 23 through 27 removed outlier: 7.197A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN E 66 " --> pdb=" O ARG E 75 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 61 through 68 current: chain 'B' and resid 53 through 55 removed outlier: 5.613A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 66 " --> pdb=" O GLY B 73 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 30 through 36 current: chain 'E' and resid 92 through 97 Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.244A pdb=" N GLU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 109 removed outlier: 6.557A pdb=" N ILE B 193 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE B 260 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL B 195 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR B 257 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.545A pdb=" N VAL B 320 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'd' and resid 231 through 232 removed outlier: 3.824A pdb=" N VAL C 27 " --> pdb=" O LEU d 232 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU C 67 " --> pdb=" O ASN C 71 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 39 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N HIS C 43 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL C 32 " --> pdb=" O HIS C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.763A pdb=" N VAL C 100 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 193 through 198 removed outlier: 5.861A pdb=" N ILE C 193 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE C 260 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 195 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP C 262 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C 197 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE C 168 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU C 167 " --> pdb=" O ILE C 343 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 21 through 27 removed outlier: 3.587A pdb=" N ILE D 27 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL D 30 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN D 45 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA D 46 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS D 50 " --> pdb=" O GLU D 90 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU D 90 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY D 21 " --> pdb=" O VAL D 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AB6, first strand: chain 'D' and resid 148 through 149 removed outlier: 3.931A pdb=" N TYR D 162 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 267 through 272 removed outlier: 5.699A pdb=" N VAL D 268 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE D 324 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU D 270 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N THR D 350 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY D 169 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU D 352 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE D 171 " --> pdb=" O LEU D 352 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL D 351 " --> pdb=" O ASP D 366 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 197 through 204 removed outlier: 6.953A pdb=" N SER D 197 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL D 235 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N PHE D 199 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLY D 237 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLY D 201 " --> pdb=" O GLY D 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AC1, first strand: chain 'E' and resid 234 through 238 removed outlier: 4.051A pdb=" N GLY E 200 " --> pdb=" O PHE E 271 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL E 268 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE E 324 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU E 270 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA E 326 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE E 272 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N TYR E 328 " --> pdb=" O ILE E 272 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE E 168 " --> pdb=" O GLN E 325 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL E 327 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU E 170 " --> pdb=" O VAL E 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AC3, first strand: chain 'F' and resid 148 through 149 removed outlier: 3.796A pdb=" N PHE F 149 " --> pdb=" O TYR F 162 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR F 162 " --> pdb=" O PHE F 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 235 through 238 removed outlier: 5.541A pdb=" N GLY F 201 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP F 273 " --> pdb=" O GLY F 200 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LYS F 167 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR F 350 " --> pdb=" O LYS F 167 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY F 169 " --> pdb=" O THR F 350 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'd' and resid 178 through 179 removed outlier: 6.084A pdb=" N ALA d 178 " --> pdb=" O LYS d 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'g' and resid 178 through 180 removed outlier: 3.743A pdb=" N ARG g 178 " --> pdb=" O ILE g 157 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU g 120 " --> pdb=" O ILE g 158 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE g 160 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL g 122 " --> pdb=" O ILE g 160 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA g 119 " --> pdb=" O GLU g 211 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU g 213 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N MET g 121 " --> pdb=" O LEU g 213 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR g 214 " --> pdb=" O VAL g 226 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL g 226 " --> pdb=" O TYR g 214 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 253 through 256 removed outlier: 3.629A pdb=" N LEU g 254 " --> pdb=" O ASP g 269 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP g 269 " --> pdb=" O LEU g 254 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'g' and resid 283 through 284 removed outlier: 6.279A pdb=" N GLU g 283 " --> pdb=" O ALA e 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'e' and resid 12 through 15 removed outlier: 7.601A pdb=" N VAL e 7 " --> pdb=" O ILE e 14 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'e' and resid 18 through 19 removed outlier: 4.039A pdb=" N LEU e 3 " --> pdb=" O VAL e 19 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'e' and resid 22 through 25 2459 hydrogen bonds defined for protein. 7218 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: 7.22 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10548 1.33 - 1.45: 5498 1.45 - 1.57: 19304 1.57 - 1.69: 23 1.69 - 1.81: 185 Bond restraints: 35558 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.73e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.17e+01 bond pdb=" C4 ATP F 601 " pdb=" C5 ATP F 601 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.76e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.45e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.46e+01 ... (remaining 35553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.78: 48187 4.78 - 9.57: 232 9.57 - 14.35: 9 14.35 - 19.13: 2 19.13 - 23.91: 7 Bond angle restraints: 48437 Sorted by residual: angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 115.96 23.91 1.00e+00 1.00e+00 5.72e+02 angle pdb=" PA ATP F 601 " pdb=" O3A ATP F 601 " pdb=" PB ATP F 601 " ideal model delta sigma weight residual 136.83 114.95 21.88 1.00e+00 1.00e+00 4.79e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 118.11 21.76 1.00e+00 1.00e+00 4.74e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 118.96 20.91 1.00e+00 1.00e+00 4.37e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 116.98 19.85 1.00e+00 1.00e+00 3.94e+02 ... (remaining 48432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 20136 24.18 - 48.36: 1099 48.36 - 72.54: 121 72.54 - 96.72: 35 96.72 - 120.90: 3 Dihedral angle restraints: 21394 sinusoidal: 6742 harmonic: 14652 Sorted by residual: dihedral pdb=" CA TYR D 362 " pdb=" C TYR D 362 " pdb=" N PRO D 363 " pdb=" CA PRO D 363 " ideal model delta harmonic sigma weight residual 180.00 119.49 60.51 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CA ALA F 295 " pdb=" C ALA F 295 " pdb=" N VAL F 296 " pdb=" CA VAL F 296 " ideal model delta harmonic sigma weight residual 180.00 -122.15 -57.85 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -127.48 -52.52 0 5.00e+00 4.00e-02 1.10e+02 ... (remaining 21391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 5221 0.085 - 0.170: 602 0.170 - 0.255: 26 0.255 - 0.340: 7 0.340 - 0.425: 2 Chirality restraints: 5858 Sorted by residual: chirality pdb=" CB ILE B 331 " pdb=" CA ILE B 331 " pdb=" CG1 ILE B 331 " pdb=" CG2 ILE B 331 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CB ILE C 331 " pdb=" CA ILE C 331 " pdb=" CG1 ILE C 331 " pdb=" CG2 ILE C 331 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CG LEU C 421 " pdb=" CB LEU C 421 " pdb=" CD1 LEU C 421 " pdb=" CD2 LEU C 421 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 5855 not shown) Planarity restraints: 6483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 28 " 0.046 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO D 29 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 338 " 0.047 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO F 339 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO F 339 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 339 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 343 " 0.024 2.00e-02 2.50e+03 1.99e-02 6.92e+00 pdb=" CG PHE F 343 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE F 343 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE F 343 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 343 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 343 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE F 343 " 0.004 2.00e-02 2.50e+03 ... (remaining 6480 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2579 2.72 - 3.27: 40179 3.27 - 3.81: 65913 3.81 - 4.36: 74181 4.36 - 4.90: 120543 Nonbonded interactions: 303395 Sorted by model distance: nonbonded pdb=" OE1 GLN F 376 " pdb=" O2' ATP C 601 " model vdw 2.176 3.040 nonbonded pdb=" O ILE A 475 " pdb=" OG1 THR A 479 " model vdw 2.216 3.040 nonbonded pdb=" NZ LYS D 154 " pdb=" O PHE D 430 " model vdw 2.226 3.120 nonbonded pdb=" O VAL D 102 " pdb=" OG1 THR D 128 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR g 229 " pdb=" O CYS g 240 " model vdw 2.232 3.040 ... (remaining 303390 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 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 15 or (resid 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 23 or (resid 24 through 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 322 or (resid 323 thro \ ugh 324 and (name N or name CA or name C or name O or name CB )) or resid 325 th \ rough 398 or (resid 399 through 400 and (name N or name CA or name C or name O o \ r name CB )) or resid 401 through 471 or (resid 472 and (name N or name CA or na \ me C or name O or name CB )) or resid 473 through 601)) selection = (chain 'B' and (resid 8 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 393 or (resid 394 thro \ ugh 397 and (name N or name CA or name C or name O or name CB )) or resid 398 or \ (resid 399 through 400 and (name N or name CA or name C or name O or name CB )) \ or resid 401 through 432 or (resid 433 and (name N or name CA or name C or name \ O or name CB )) or resid 434 through 503 or resid 601)) selection = (chain 'C' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 23 or (resid 24 through 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 322 or (resid 323 through 324 and ( \ name N or name CA or name C or name O or name CB )) or resid 325 through 393 or \ (resid 394 through 397 and (name N or name CA or name C or name O or name CB )) \ or resid 398 through 432 or (resid 433 and (name N or name CA or name C or name \ O or name CB )) or resid 434 through 471 or (resid 472 and (name N or name CA or \ name C or name O or name CB )) or resid 473 through 503 or resid 601)) } ncs_group { reference = (chain 'D' and (resid 19 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 58 or (resid 59 and ( \ name N or name CA or name C or name O or name CB )) or resid 60 through 115 or ( \ resid 116 and (name N or name CA or name C or name O or name CB )) or resid 117 \ through 118 or (resid 119 and (name N or name CA or name C or name O or name CB \ )) or resid 120 through 260 or (resid 261 and (name N or name CA or name C or na \ me O or name CB )) or resid 262 through 310 or (resid 311 and (name N or name CA \ or name C or name O or name CB )) or resid 312 through 407 or (resid 408 and (n \ ame N or name CA or name C or name O or name CB )) or resid 409 through 416 or ( \ resid 417 and (name N or name CA or name C or name O or name CB )) or resid 418 \ through 494)) selection = (chain 'E' and (resid 19 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 78 or (resid 79 and (name N or nam \ e CA or name C or name O or name CB )) or resid 80 through 260 or (resid 261 and \ (name N or name CA or name C or name O or name CB )) or resid 262 through 331 o \ r (resid 332 through 333 and (name N or name CA or name C or name O or name CB ) \ ) or resid 334 through 407 or (resid 408 and (name N or name CA or name C or nam \ e O or name CB )) or resid 409 through 414 or (resid 415 and (name N or name CA \ or name C or name O or name CB )) or resid 416 through 446 or (resid 447 and (na \ me N or name CA or name C or name O or name CB )) or resid 448 through 464 or (r \ esid 465 and (name N or name CA or name C or name O or name CB )) or resid 466 t \ hrough 494)) selection = (chain 'F' and (resid 19 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 or (resid 59 and \ (name N or name CA or name C or name O or name CB )) or resid 60 through 78 or \ (resid 79 and (name N or name CA or name C or name O or name CB )) or resid 80 t \ hrough 115 or (resid 116 and (name N or name CA or name C or name O or name CB ) \ ) or resid 117 through 118 or (resid 119 and (name N or name CA or name C or nam \ e O or name CB )) or resid 120 through 310 or (resid 311 and (name N or name CA \ or name C or name O or name CB )) or resid 312 through 317 or (resid 318 and (na \ me N or name CA or name C or name O or name CB )) or resid 319 through 331 or (r \ esid 332 through 333 and (name N or name CA or name C or name O or name CB )) or \ resid 334 through 414 or (resid 415 and (name N or name CA or name C or name O \ or name CB )) or resid 416 or (resid 417 and (name N or name CA or name C or nam \ e O or name CB )) or resid 418 through 446 or (resid 447 and (name N or name CA \ or name C or name O or name CB )) or resid 448 through 464 or (resid 465 and (na \ me N or name CA or name C or name O or name CB )) or resid 466 through 494)) } ncs_group { reference = (chain 'M' and ((resid 3 through 42 and (name N or name CA or name C or name O o \ r name CB )) or resid 43 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or (resid 47 through 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 81)) selection = (chain 'N' and ((resid 3 through 42 and (name N or name CA or name C or name O o \ r name CB )) or resid 43 through 58 or (resid 59 through 66 and (name N or name \ CA or name C or name O or name CB )) or resid 67 through 81)) selection = (chain 'O' and (resid 3 through 47 or (resid 48 through 50 and (name N or name C \ A or name C or name O or name CB )) or resid 51 through 81)) selection = (chain 'P' and (resid 3 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB )) or resid 51 through 81)) selection = (chain 'Q' and (resid 3 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or (resid 47 through 66 and (name N or name CA or name \ C or name O or name CB )) or resid 67 through 81)) selection = (chain 'R' and (resid 3 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB )) or resid 51 through 81)) selection = (chain 'S' and (resid 3 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or (resid 47 through 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 81)) selection = (chain 'T' and (resid 3 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 or (resid 48 through 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 or (resid 52 through 66 and (n \ ame N or name CA or name C or name O or name CB )) or resid 67 through 81)) selection = (chain 'U' and (resid 3 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 or (resid 48 through 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 81)) selection = (chain 'V' and (resid 3 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or (resid 47 through 66 and (name N or name CA or name \ C or name O or name CB )) or resid 67 through 81)) selection = (chain 'W' and ((resid 3 through 42 and (name N or name CA or name C or name O o \ r name CB )) or resid 43 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or (resid 47 through 50 and (name N or name CA or name \ C or name O or name CB )) or (resid 51 through 66 and (name N or name CA or nam \ e C or name O or name CB )) or resid 67 through 81)) selection = (chain 'X' and ((resid 3 through 42 and (name N or name CA or name C or name O o \ r name CB )) or resid 43 through 47 or (resid 48 through 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 81)) selection = chain 'Y' selection = chain 'Z' } 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: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 32.400 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.080 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.007 0.116 35562 Z= 0.379 Angle : 1.029 23.913 48439 Z= 0.632 Chirality : 0.053 0.425 5858 Planarity : 0.006 0.070 6483 Dihedral : 15.348 120.901 11989 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.32 % Favored : 91.63 % Rotamer: Outliers : 0.76 % Allowed : 14.74 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.16 % 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: -3.59 (0.10), residues: 5123 helix: -1.66 (0.08), residues: 2866 sheet: -3.77 (0.19), residues: 438 loop : -2.98 (0.13), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 277 TYR 0.026 0.003 TYR A 439 PHE 0.045 0.003 PHE F 343 TRP 0.022 0.003 TRP e 15 HIS 0.010 0.002 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.37 (35558) covalent geometry : angle 1.02851 / 0.63 (48437) SS BOND : bond 0.02700 / 1.42 ( 1) SS BOND : angle 2.03369 / 1.12 ( 2) hydrogen bonds : bond 0.12116 / 7.99 ( 2444) hydrogen bonds : angle 6.52700 / 4.57 ( 7218) Misc. bond : bond 0.06944 / 3.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 365 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 ILE cc_start: 0.9463 (mm) cc_final: 0.9196 (mm) REVERT: A 223 ILE cc_start: 0.9158 (mp) cc_final: 0.8643 (mt) REVERT: A 261 TYR cc_start: 0.8033 (m-80) cc_final: 0.7682 (m-80) REVERT: A 292 PHE cc_start: 0.8370 (t80) cc_final: 0.6849 (t80) REVERT: A 295 HIS cc_start: 0.9045 (m170) cc_final: 0.8809 (m-70) REVERT: A 314 MET cc_start: 0.7926 (ttm) cc_final: 0.7623 (mtt) REVERT: A 344 PHE cc_start: 0.8453 (t80) cc_final: 0.8095 (t80) REVERT: A 421 LEU cc_start: 0.9238 (mt) cc_final: 0.8988 (mt) REVERT: B 56 PHE cc_start: 0.8778 (m-80) cc_final: 0.8521 (m-80) REVERT: B 77 MET cc_start: 0.8594 (mpp) cc_final: 0.8337 (mpp) REVERT: B 219 MET cc_start: 0.8115 (tpt) cc_final: 0.7909 (tpt) REVERT: B 223 ILE cc_start: 0.8489 (mt) cc_final: 0.8267 (mt) REVERT: B 263 ASP cc_start: 0.6744 (m-30) cc_final: 0.6369 (m-30) REVERT: B 274 MET cc_start: 0.9101 (ptm) cc_final: 0.7915 (ppp) REVERT: B 320 VAL cc_start: 0.9326 (OUTLIER) cc_final: 0.8937 (m) REVERT: B 418 ARG cc_start: 0.9079 (ttm170) cc_final: 0.8829 (ttp80) REVERT: C 37 ASP cc_start: 0.6969 (t0) cc_final: 0.6716 (t0) REVERT: C 49 MET cc_start: 0.6894 (tpt) cc_final: 0.6502 (tpt) REVERT: C 261 TYR cc_start: 0.8079 (m-80) cc_final: 0.7873 (m-80) REVERT: C 298 LEU cc_start: 0.9504 (tp) cc_final: 0.9273 (tp) REVERT: D 214 MET cc_start: 0.9011 (mtt) cc_final: 0.8688 (mmm) REVERT: D 324 ILE cc_start: 0.9598 (mp) cc_final: 0.9293 (mp) REVERT: D 374 MET cc_start: 0.8213 (mmp) cc_final: 0.7979 (mmm) REVERT: E 292 MET cc_start: 0.8023 (mtp) cc_final: 0.7819 (mmm) REVERT: E 343 PHE cc_start: 0.6713 (t80) cc_final: 0.6442 (t80) REVERT: E 374 MET cc_start: 0.7456 (tpp) cc_final: 0.6428 (tpp) REVERT: E 492 MET cc_start: 0.8729 (tpp) cc_final: 0.8476 (tpp) REVERT: F 79 MET cc_start: 0.8670 (mmm) cc_final: 0.8435 (mmm) REVERT: F 183 MET cc_start: 0.8599 (mtp) cc_final: 0.8340 (mtp) REVERT: F 305 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8747 (mm-30) REVERT: F 374 MET cc_start: 0.8056 (mmm) cc_final: 0.7854 (mmm) REVERT: F 390 ARG cc_start: 0.8677 (ttp-170) cc_final: 0.8406 (ttt180) REVERT: F 400 GLU cc_start: 0.8703 (tt0) cc_final: 0.8355 (tt0) REVERT: F 402 GLN cc_start: 0.8918 (tp40) cc_final: 0.8707 (tm-30) REVERT: F 428 GLU cc_start: 0.9363 (tm-30) cc_final: 0.8921 (tm-30) REVERT: F 488 MET cc_start: 0.8247 (tpt) cc_final: 0.7653 (tpt) REVERT: d 154 ARG cc_start: 0.8942 (mmm-85) cc_final: 0.8635 (mmm-85) REVERT: d 224 ARG cc_start: 0.9418 (ttm-80) cc_final: 0.8685 (ttp80) REVERT: g 94 TYR cc_start: 0.9008 (t80) cc_final: 0.8554 (t80) REVERT: g 121 MET cc_start: 0.8839 (tpt) cc_final: 0.8509 (tpp) REVERT: g 136 MET cc_start: 0.8591 (tmm) cc_final: 0.8262 (tmm) REVERT: g 180 PHE cc_start: 0.7623 (t80) cc_final: 0.7423 (t80) REVERT: g 199 PHE cc_start: 0.8335 (t80) cc_final: 0.8127 (t80) REVERT: g 212 MET cc_start: 0.8946 (tmm) cc_final: 0.8697 (tmm) REVERT: g 231 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8746 (pp) REVERT: X 41 ARG cc_start: 0.8336 (mtm110) cc_final: 0.8048 (tmm160) outliers start: 22 outliers final: 11 residues processed: 384 average time/residue: 0.2413 time to fit residues: 149.2149 Evaluate side-chains 264 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 251 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 494 optimal weight: 40.0000 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 214 GLN A 273 GLN A 497 GLN B 43 HIS B 110 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 HIS ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN B 468 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 334 ASN C 389 GLN D 45 ASN D 193 HIS D 274 ASN D 299 GLN D 433 GLN E 25 GLN E 42 ASN E 72 ASN E 133 HIS E 223 ASN E 240 ASN ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 479 ASN F 19 ASN F 42 ASN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 GLN F 489 ASN d 141 HIS d 199 GLN d 247 GLN g 76 GLN g 184 ASN g 286 GLN ** g 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 331 ASN e 36 ASN e 116 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.047512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.039064 restraints weight = 364903.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.040253 restraints weight = 229293.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.040814 restraints weight = 142606.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.041070 restraints weight = 103173.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.041254 restraints weight = 87513.170| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35562 Z= 0.161 Angle : 0.682 11.071 48439 Z= 0.356 Chirality : 0.045 0.283 5858 Planarity : 0.005 0.077 6483 Dihedral : 7.016 114.338 5483 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.77 % Favored : 93.19 % Rotamer: Outliers : 0.21 % Allowed : 6.18 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.08 % 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: -1.87 (0.11), residues: 5123 helix: -0.04 (0.09), residues: 2876 sheet: -3.60 (0.20), residues: 434 loop : -2.52 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 277 TYR 0.042 0.002 TYR E 298 PHE 0.026 0.002 PHE F 343 TRP 0.014 0.003 TRP e 15 HIS 0.007 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (35558) covalent geometry : angle 0.68182 / 0.36 (48437) SS BOND : bond 0.00246 / 0.13 ( 1) SS BOND : angle 1.15160 / 0.64 ( 2) hydrogen bonds : bond 0.04600 / 3.08 ( 2444) hydrogen bonds : angle 5.25332 / 3.69 ( 7218) Misc. bond : bond 0.00262 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 348 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8268 (mpp) cc_final: 0.7689 (mpp) REVERT: A 154 ILE cc_start: 0.9512 (mm) cc_final: 0.9260 (mm) REVERT: A 164 GLN cc_start: 0.8257 (tt0) cc_final: 0.7676 (tp40) REVERT: A 213 PHE cc_start: 0.8693 (p90) cc_final: 0.8247 (p90) REVERT: A 223 ILE cc_start: 0.9183 (mp) cc_final: 0.8589 (mt) REVERT: A 266 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8811 (mmmm) REVERT: A 285 GLU cc_start: 0.8705 (tt0) cc_final: 0.8229 (tp30) REVERT: A 292 PHE cc_start: 0.8423 (t80) cc_final: 0.7986 (t80) REVERT: A 295 HIS cc_start: 0.9015 (m170) cc_final: 0.8757 (m-70) REVERT: A 344 PHE cc_start: 0.8703 (t80) cc_final: 0.8064 (t80) REVERT: A 376 MET cc_start: 0.8584 (tpt) cc_final: 0.8336 (tpp) REVERT: A 436 MET cc_start: 0.9162 (ptp) cc_final: 0.8900 (ptp) REVERT: B 196 TYR cc_start: 0.7106 (t80) cc_final: 0.6862 (t80) REVERT: B 223 ILE cc_start: 0.8715 (mt) cc_final: 0.8500 (mt) REVERT: B 263 ASP cc_start: 0.7444 (m-30) cc_final: 0.6861 (m-30) REVERT: B 274 MET cc_start: 0.9278 (ptm) cc_final: 0.8253 (ppp) REVERT: C 37 ASP cc_start: 0.7116 (t0) cc_final: 0.6863 (t0) REVERT: C 49 MET cc_start: 0.6684 (tpt) cc_final: 0.6351 (tpt) REVERT: C 295 HIS cc_start: 0.8915 (m90) cc_final: 0.8435 (m90) REVERT: D 199 PHE cc_start: 0.8875 (t80) cc_final: 0.8668 (t80) REVERT: D 214 MET cc_start: 0.9422 (mtt) cc_final: 0.8996 (mmm) REVERT: D 374 MET cc_start: 0.8296 (mmp) cc_final: 0.7758 (mmm) REVERT: D 416 GLU cc_start: 0.8998 (pm20) cc_final: 0.8651 (pm20) REVERT: E 247 MET cc_start: 0.7578 (ppp) cc_final: 0.7330 (ppp) REVERT: E 374 MET cc_start: 0.6846 (tpp) cc_final: 0.6069 (tpp) REVERT: F 42 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8511 (m110) REVERT: F 79 MET cc_start: 0.8670 (mmm) cc_final: 0.8339 (mmm) REVERT: F 247 MET cc_start: 0.8793 (ttp) cc_final: 0.8488 (ttp) REVERT: F 256 MET cc_start: 0.8882 (mmp) cc_final: 0.8646 (mmm) REVERT: F 270 LEU cc_start: 0.9242 (tp) cc_final: 0.9013 (tp) REVERT: F 285 VAL cc_start: 0.9143 (p) cc_final: 0.8940 (p) REVERT: F 369 ASP cc_start: 0.8521 (t70) cc_final: 0.8190 (t70) REVERT: F 374 MET cc_start: 0.8241 (mmm) cc_final: 0.7922 (mmm) REVERT: F 390 ARG cc_start: 0.8595 (ttp-170) cc_final: 0.8346 (ttp-170) REVERT: F 428 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8860 (tm-30) REVERT: F 429 ARG cc_start: 0.8925 (mpt-90) cc_final: 0.8485 (mpt-90) REVERT: F 488 MET cc_start: 0.8280 (tpt) cc_final: 0.7881 (tpt) REVERT: d 115 PHE cc_start: 0.8885 (m-10) cc_final: 0.8679 (m-10) REVERT: d 145 PHE cc_start: 0.9053 (t80) cc_final: 0.8775 (t80) REVERT: d 154 ARG cc_start: 0.9299 (mmm-85) cc_final: 0.9011 (mmm-85) REVERT: d 224 ARG cc_start: 0.9366 (ttm-80) cc_final: 0.8495 (ttp80) REVERT: g 94 TYR cc_start: 0.9247 (t80) cc_final: 0.8789 (t80) REVERT: g 121 MET cc_start: 0.8789 (tpt) cc_final: 0.8282 (tpp) REVERT: g 136 MET cc_start: 0.8547 (tmm) cc_final: 0.8198 (tmm) REVERT: g 180 PHE cc_start: 0.7889 (t80) cc_final: 0.7680 (t80) REVERT: g 199 PHE cc_start: 0.8393 (t80) cc_final: 0.8171 (t80) REVERT: g 304 ILE cc_start: 0.8736 (tp) cc_final: 0.8419 (tp) REVERT: g 340 ASN cc_start: 0.9498 (t0) cc_final: 0.9150 (m-40) REVERT: g 352 GLU cc_start: 0.8713 (tt0) cc_final: 0.8363 (tt0) REVERT: X 41 ARG cc_start: 0.8620 (mtm110) cc_final: 0.8259 (ttp80) outliers start: 6 outliers final: 1 residues processed: 354 average time/residue: 0.2132 time to fit residues: 124.4104 Evaluate side-chains 251 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 249 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 357 optimal weight: 5.9990 chunk 360 optimal weight: 6.9990 chunk 355 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 64 optimal weight: 0.0050 chunk 442 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 47 optimal weight: 0.1980 chunk 483 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 3.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN B 497 GLN C 410 GLN D 299 GLN E 120 ASN ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN F 141 GLN F 187 ASN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 199 GLN ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 30 GLN e 93 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.046856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.038531 restraints weight = 369721.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.039592 restraints weight = 230194.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.040271 restraints weight = 144481.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.040450 restraints weight = 105148.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.040650 restraints weight = 91750.895| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35562 Z= 0.200 Angle : 0.668 10.789 48439 Z= 0.352 Chirality : 0.044 0.308 5858 Planarity : 0.005 0.078 6483 Dihedral : 6.775 114.579 5483 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.18 % Favored : 92.80 % Rotamer: Outliers : 0.14 % Allowed : 6.94 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.06 % 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: -1.15 (0.12), residues: 5123 helix: 0.63 (0.09), residues: 2872 sheet: -3.45 (0.21), residues: 427 loop : -2.33 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 277 TYR 0.025 0.002 TYR E 298 PHE 0.038 0.002 PHE F 343 TRP 0.013 0.002 TRP e 15 HIS 0.010 0.002 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.20 (35558) covalent geometry : angle 0.66811 / 0.35 (48437) SS BOND : bond 0.00384 / 0.20 ( 1) SS BOND : angle 1.19984 / 0.68 ( 2) hydrogen bonds : bond 0.04538 / 3.04 ( 2444) hydrogen bonds : angle 5.02519 / 3.52 ( 7218) Misc. bond : bond 0.00156 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 316 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 77 MET cc_start: 0.8439 (mpp) cc_final: 0.7987 (mpp) REVERT: A 154 ILE cc_start: 0.9472 (mm) cc_final: 0.9266 (mm) REVERT: A 164 GLN cc_start: 0.8376 (tt0) cc_final: 0.7771 (tp40) REVERT: A 213 PHE cc_start: 0.8826 (p90) cc_final: 0.8362 (p90) REVERT: A 223 ILE cc_start: 0.9242 (mp) cc_final: 0.8609 (mt) REVERT: A 285 GLU cc_start: 0.8653 (tt0) cc_final: 0.8119 (tp30) REVERT: A 314 MET cc_start: 0.8794 (tpt) cc_final: 0.8112 (tpt) REVERT: A 344 PHE cc_start: 0.8823 (t80) cc_final: 0.8168 (t80) REVERT: A 376 MET cc_start: 0.8620 (tpt) cc_final: 0.8224 (tpp) REVERT: B 196 TYR cc_start: 0.7176 (t80) cc_final: 0.6827 (t80) REVERT: B 248 GLU cc_start: 0.8714 (tt0) cc_final: 0.8462 (tt0) REVERT: B 263 ASP cc_start: 0.7463 (m-30) cc_final: 0.6937 (m-30) REVERT: B 274 MET cc_start: 0.9333 (ptm) cc_final: 0.8414 (ppp) REVERT: C 49 MET cc_start: 0.6819 (tpt) cc_final: 0.6453 (tpt) REVERT: C 251 MET cc_start: 0.8197 (ttp) cc_final: 0.7606 (tmm) REVERT: C 485 GLU cc_start: 0.8885 (mp0) cc_final: 0.8046 (mp0) REVERT: D 183 MET cc_start: 0.9362 (mmm) cc_final: 0.9131 (mmm) REVERT: D 199 PHE cc_start: 0.8971 (t80) cc_final: 0.8739 (t80) REVERT: E 247 MET cc_start: 0.7665 (ppp) cc_final: 0.7359 (ppp) REVERT: F 79 MET cc_start: 0.8477 (mmm) cc_final: 0.8134 (mmm) REVERT: F 254 LEU cc_start: 0.9088 (tp) cc_final: 0.8885 (tt) REVERT: F 369 ASP cc_start: 0.8616 (t70) cc_final: 0.8283 (t70) REVERT: F 374 MET cc_start: 0.8276 (mmm) cc_final: 0.7930 (mmm) REVERT: F 402 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8573 (tm-30) REVERT: F 428 GLU cc_start: 0.9367 (tm-30) cc_final: 0.8814 (tm-30) REVERT: d 115 PHE cc_start: 0.8923 (m-10) cc_final: 0.8722 (m-10) REVERT: d 224 ARG cc_start: 0.9462 (ttm-80) cc_final: 0.8698 (ttp80) REVERT: g 94 TYR cc_start: 0.9259 (t80) cc_final: 0.8788 (t80) REVERT: g 121 MET cc_start: 0.8847 (tpt) cc_final: 0.8381 (tpp) REVERT: g 136 MET cc_start: 0.8522 (tmm) cc_final: 0.8173 (tmm) REVERT: g 199 PHE cc_start: 0.8461 (t80) cc_final: 0.8260 (t80) REVERT: g 260 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8745 (mmmt) REVERT: g 355 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8258 (pp20) REVERT: X 41 ARG cc_start: 0.8526 (mtm110) cc_final: 0.8251 (ttp80) outliers start: 4 outliers final: 0 residues processed: 319 average time/residue: 0.2218 time to fit residues: 118.2663 Evaluate side-chains 248 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 127 optimal weight: 0.0370 chunk 438 optimal weight: 8.9990 chunk 327 optimal weight: 9.9990 chunk 345 optimal weight: 10.0000 chunk 342 optimal weight: 9.9990 chunk 474 optimal weight: 30.0000 chunk 154 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 495 optimal weight: 20.0000 overall best weight: 4.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A 273 GLN A 323 GLN A 334 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN D 299 GLN D 396 GLN E 120 ASN ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.045932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.037780 restraints weight = 375923.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.038789 restraints weight = 244089.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.039393 restraints weight = 154477.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.039673 restraints weight = 112622.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.039846 restraints weight = 95823.959| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 35562 Z= 0.264 Angle : 0.720 10.406 48439 Z= 0.381 Chirality : 0.045 0.339 5858 Planarity : 0.005 0.071 6483 Dihedral : 6.816 114.739 5483 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 21.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.10 % Favored : 91.88 % Rotamer: Outliers : 0.07 % Allowed : 6.05 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.06 % 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: -0.91 (0.12), residues: 5123 helix: 0.85 (0.09), residues: 2881 sheet: -3.40 (0.21), residues: 421 loop : -2.28 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 397 TYR 0.022 0.002 TYR A 439 PHE 0.034 0.002 PHE D 343 TRP 0.016 0.003 TRP e 15 HIS 0.010 0.002 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.26 (35558) covalent geometry : angle 0.72041 / 0.38 (48437) SS BOND : bond 0.00530 / 0.28 ( 1) SS BOND : angle 1.46991 / 0.84 ( 2) hydrogen bonds : bond 0.04744 / 3.18 ( 2444) hydrogen bonds : angle 5.08379 / 3.55 ( 7218) Misc. bond : bond 0.00111 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 294 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.7969 (ptt) cc_final: 0.7655 (ptt) REVERT: A 77 MET cc_start: 0.8738 (mpp) cc_final: 0.8374 (mpp) REVERT: A 154 ILE cc_start: 0.9480 (mm) cc_final: 0.9259 (mm) REVERT: A 157 MET cc_start: 0.7898 (tpt) cc_final: 0.7685 (tpp) REVERT: A 213 PHE cc_start: 0.8762 (p90) cc_final: 0.8399 (p90) REVERT: A 223 ILE cc_start: 0.9169 (mp) cc_final: 0.8645 (mt) REVERT: A 266 LYS cc_start: 0.9066 (mmtt) cc_final: 0.8827 (mmmm) REVERT: A 285 GLU cc_start: 0.8571 (tt0) cc_final: 0.8074 (tp30) REVERT: A 314 MET cc_start: 0.8932 (tpt) cc_final: 0.8215 (tpt) REVERT: A 344 PHE cc_start: 0.8881 (t80) cc_final: 0.8230 (t80) REVERT: A 376 MET cc_start: 0.8566 (tpt) cc_final: 0.8174 (tpp) REVERT: B 196 TYR cc_start: 0.7221 (t80) cc_final: 0.6839 (t80) REVERT: B 223 ILE cc_start: 0.8688 (mt) cc_final: 0.8466 (mt) REVERT: B 263 ASP cc_start: 0.7458 (m-30) cc_final: 0.7172 (m-30) REVERT: B 274 MET cc_start: 0.9274 (ptm) cc_final: 0.8337 (ppp) REVERT: C 37 ASP cc_start: 0.7400 (t0) cc_final: 0.7155 (t0) REVERT: C 49 MET cc_start: 0.7051 (tpt) cc_final: 0.6596 (tpt) REVERT: D 183 MET cc_start: 0.9278 (mmm) cc_final: 0.9010 (mmm) REVERT: D 199 PHE cc_start: 0.9025 (t80) cc_final: 0.8783 (t80) REVERT: D 214 MET cc_start: 0.9381 (mtt) cc_final: 0.9073 (mmm) REVERT: D 325 GLN cc_start: 0.8368 (pt0) cc_final: 0.8160 (pm20) REVERT: D 416 GLU cc_start: 0.8866 (pm20) cc_final: 0.8539 (pm20) REVERT: E 247 MET cc_start: 0.7487 (ppp) cc_final: 0.7214 (ppp) REVERT: E 292 MET cc_start: 0.7339 (mmm) cc_final: 0.7119 (mmm) REVERT: E 374 MET cc_start: 0.7167 (tpp) cc_final: 0.6127 (tpp) REVERT: F 183 MET cc_start: 0.8817 (mtm) cc_final: 0.8350 (mtt) REVERT: F 369 ASP cc_start: 0.8646 (t70) cc_final: 0.8405 (t70) REVERT: F 402 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8587 (tm-30) REVERT: F 428 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8825 (tm-30) REVERT: F 488 MET cc_start: 0.8459 (tpt) cc_final: 0.8226 (tpt) REVERT: F 492 MET cc_start: 0.7979 (mmm) cc_final: 0.7701 (mmp) REVERT: d 115 PHE cc_start: 0.8849 (m-10) cc_final: 0.8524 (m-10) REVERT: d 129 LEU cc_start: 0.9527 (mt) cc_final: 0.9220 (tp) REVERT: d 210 LYS cc_start: 0.9341 (tptp) cc_final: 0.9105 (tppt) REVERT: d 224 ARG cc_start: 0.9439 (ttm-80) cc_final: 0.8711 (ttp80) REVERT: g 94 TYR cc_start: 0.9217 (t80) cc_final: 0.8776 (t80) REVERT: g 121 MET cc_start: 0.8887 (tpt) cc_final: 0.8412 (tpp) REVERT: g 136 MET cc_start: 0.8525 (tmm) cc_final: 0.8163 (tmm) REVERT: g 260 LYS cc_start: 0.9009 (mmmt) cc_final: 0.8785 (mmmt) REVERT: g 340 ASN cc_start: 0.9512 (t0) cc_final: 0.9183 (m-40) REVERT: g 355 GLU cc_start: 0.8549 (pm20) cc_final: 0.8334 (pm20) REVERT: e 4 ASN cc_start: 0.8158 (t0) cc_final: 0.7702 (p0) REVERT: X 41 ARG cc_start: 0.8537 (mtm110) cc_final: 0.8234 (ttp80) outliers start: 2 outliers final: 0 residues processed: 296 average time/residue: 0.2113 time to fit residues: 104.7851 Evaluate side-chains 245 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 182 optimal weight: 7.9990 chunk 379 optimal weight: 10.0000 chunk 489 optimal weight: 30.0000 chunk 389 optimal weight: 40.0000 chunk 155 optimal weight: 20.0000 chunk 122 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 373 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 334 ASN ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 267 GLN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN C 410 GLN D 299 GLN ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN E 210 ASN ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.045862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.037545 restraints weight = 376478.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.038474 restraints weight = 230945.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.039150 restraints weight = 158573.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.039634 restraints weight = 118259.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.039937 restraints weight = 93708.134| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 35562 Z= 0.254 Angle : 0.715 9.956 48439 Z= 0.377 Chirality : 0.045 0.275 5858 Planarity : 0.005 0.093 6483 Dihedral : 6.862 117.757 5483 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.94 % Favored : 92.04 % Rotamer: Outliers : 0.07 % Allowed : 5.53 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.06 % 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: -0.73 (0.12), residues: 5123 helix: 1.02 (0.09), residues: 2878 sheet: -3.38 (0.21), residues: 432 loop : -2.23 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG d 208 TYR 0.023 0.002 TYR g 341 PHE 0.028 0.002 PHE F 343 TRP 0.017 0.003 TRP e 15 HIS 0.009 0.002 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.25 (35558) covalent geometry : angle 0.71465 / 0.38 (48437) SS BOND : bond 0.00513 / 0.27 ( 1) SS BOND : angle 1.47682 / 0.85 ( 2) hydrogen bonds : bond 0.04686 / 3.14 ( 2444) hydrogen bonds : angle 5.03578 / 3.51 ( 7218) Misc. bond : bond 0.00100 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 280 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8012 (ptt) cc_final: 0.7675 (ptt) REVERT: A 157 MET cc_start: 0.7859 (tpt) cc_final: 0.7635 (tpp) REVERT: A 213 PHE cc_start: 0.8890 (p90) cc_final: 0.8474 (p90) REVERT: A 223 ILE cc_start: 0.9218 (mp) cc_final: 0.8669 (mt) REVERT: A 266 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8889 (mmmm) REVERT: A 285 GLU cc_start: 0.8607 (tt0) cc_final: 0.8094 (tp30) REVERT: A 295 HIS cc_start: 0.8864 (m-70) cc_final: 0.8645 (m-70) REVERT: A 314 MET cc_start: 0.8966 (tpt) cc_final: 0.8310 (tpt) REVERT: A 344 PHE cc_start: 0.8957 (t80) cc_final: 0.8194 (t80) REVERT: A 376 MET cc_start: 0.8533 (tpt) cc_final: 0.8089 (tpp) REVERT: B 196 TYR cc_start: 0.7206 (t80) cc_final: 0.6832 (t80) REVERT: B 223 ILE cc_start: 0.8758 (mt) cc_final: 0.8534 (mt) REVERT: B 263 ASP cc_start: 0.7545 (m-30) cc_final: 0.7268 (m-30) REVERT: B 274 MET cc_start: 0.9364 (ptm) cc_final: 0.8480 (ppp) REVERT: C 37 ASP cc_start: 0.7345 (t0) cc_final: 0.7078 (t0) REVERT: C 49 MET cc_start: 0.6864 (tpt) cc_final: 0.6397 (tpt) REVERT: D 183 MET cc_start: 0.9296 (mmm) cc_final: 0.8989 (mmm) REVERT: D 199 PHE cc_start: 0.9111 (t80) cc_final: 0.8866 (t80) REVERT: D 214 MET cc_start: 0.9413 (mtt) cc_final: 0.9116 (mmm) REVERT: D 325 GLN cc_start: 0.8433 (pt0) cc_final: 0.8230 (pm20) REVERT: D 416 GLU cc_start: 0.8842 (pm20) cc_final: 0.8503 (pm20) REVERT: E 247 MET cc_start: 0.7727 (ppp) cc_final: 0.7459 (ppp) REVERT: E 374 MET cc_start: 0.6911 (tpp) cc_final: 0.6165 (tpp) REVERT: F 79 MET cc_start: 0.8039 (mmp) cc_final: 0.7716 (mmt) REVERT: F 183 MET cc_start: 0.8855 (mtm) cc_final: 0.8443 (mtt) REVERT: F 254 LEU cc_start: 0.8965 (tp) cc_final: 0.8680 (tp) REVERT: F 345 HIS cc_start: 0.8031 (m90) cc_final: 0.7819 (m-70) REVERT: F 369 ASP cc_start: 0.8696 (t70) cc_final: 0.8423 (t70) REVERT: F 374 MET cc_start: 0.8290 (mmm) cc_final: 0.7966 (mmm) REVERT: F 402 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8763 (tm-30) REVERT: F 428 GLU cc_start: 0.9360 (tm-30) cc_final: 0.8913 (tm-30) REVERT: F 488 MET cc_start: 0.8438 (tpt) cc_final: 0.8157 (tpt) REVERT: F 492 MET cc_start: 0.8076 (mmm) cc_final: 0.7778 (mmp) REVERT: d 115 PHE cc_start: 0.8902 (m-10) cc_final: 0.8545 (m-10) REVERT: d 129 LEU cc_start: 0.9524 (mt) cc_final: 0.9239 (tp) REVERT: d 224 ARG cc_start: 0.9465 (ttm-80) cc_final: 0.8712 (ttp80) REVERT: g 94 TYR cc_start: 0.9202 (t80) cc_final: 0.8743 (t80) REVERT: g 121 MET cc_start: 0.8851 (tpt) cc_final: 0.8476 (tpp) REVERT: g 136 MET cc_start: 0.8519 (tmm) cc_final: 0.8159 (tmm) REVERT: g 199 PHE cc_start: 0.8467 (t80) cc_final: 0.8211 (t80) REVERT: g 212 MET cc_start: 0.8785 (tmm) cc_final: 0.8541 (tmm) REVERT: g 260 LYS cc_start: 0.9030 (mmmt) cc_final: 0.8791 (mmmt) REVERT: e 4 ASN cc_start: 0.8146 (t0) cc_final: 0.7699 (p0) outliers start: 2 outliers final: 0 residues processed: 282 average time/residue: 0.2187 time to fit residues: 104.0470 Evaluate side-chains 238 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 166 optimal weight: 4.9990 chunk 250 optimal weight: 10.0000 chunk 255 optimal weight: 1.9990 chunk 343 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 324 optimal weight: 10.0000 chunk 476 optimal weight: 0.7980 chunk 349 optimal weight: 10.0000 chunk 313 optimal weight: 0.4980 chunk 477 optimal weight: 6.9990 chunk 291 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A 334 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN C 71 ASN C 186 ASN ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN E 238 GLN ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.047789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.039318 restraints weight = 362027.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.040538 restraints weight = 232461.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.041116 restraints weight = 138110.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.041350 restraints weight = 106205.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.041483 restraints weight = 92575.411| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35562 Z= 0.139 Angle : 0.659 11.908 48439 Z= 0.338 Chirality : 0.044 0.279 5858 Planarity : 0.004 0.060 6483 Dihedral : 6.531 118.981 5483 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.46 % Favored : 93.52 % Rotamer: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.04 % 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: -0.24 (0.12), residues: 5123 helix: 1.41 (0.10), residues: 2887 sheet: -3.22 (0.21), residues: 443 loop : -1.98 (0.15), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 165 TYR 0.023 0.002 TYR B 271 PHE 0.023 0.002 PHE F 474 TRP 0.015 0.002 TRP e 15 HIS 0.006 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (35558) covalent geometry : angle 0.65926 / 0.34 (48437) SS BOND : bond 0.00318 / 0.17 ( 1) SS BOND : angle 1.24668 / 0.72 ( 2) hydrogen bonds : bond 0.04130 / 2.75 ( 2444) hydrogen bonds : angle 4.69961 / 3.28 ( 7218) Misc. bond : bond 0.00477 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8389 (mpp) cc_final: 0.7828 (mmt) REVERT: A 213 PHE cc_start: 0.8702 (p90) cc_final: 0.8276 (p90) REVERT: A 223 ILE cc_start: 0.9140 (mp) cc_final: 0.8490 (mt) REVERT: A 266 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8783 (mmmm) REVERT: A 285 GLU cc_start: 0.8546 (tt0) cc_final: 0.8001 (tp30) REVERT: A 314 MET cc_start: 0.8779 (tpt) cc_final: 0.8208 (tpp) REVERT: A 344 PHE cc_start: 0.8789 (t80) cc_final: 0.8099 (t80) REVERT: A 376 MET cc_start: 0.8392 (tpt) cc_final: 0.7977 (tpp) REVERT: A 392 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8397 (mp0) REVERT: B 196 TYR cc_start: 0.7084 (t80) cc_final: 0.6800 (t80) REVERT: B 223 ILE cc_start: 0.8611 (mt) cc_final: 0.8384 (mt) REVERT: B 274 MET cc_start: 0.9338 (ptm) cc_final: 0.8494 (ppp) REVERT: D 183 MET cc_start: 0.9289 (mmm) cc_final: 0.8955 (mmm) REVERT: E 374 MET cc_start: 0.6645 (tpp) cc_final: 0.6078 (tpp) REVERT: F 254 LEU cc_start: 0.8868 (tp) cc_final: 0.8576 (tp) REVERT: F 342 THR cc_start: 0.9046 (p) cc_final: 0.8664 (p) REVERT: F 374 MET cc_start: 0.8145 (mmm) cc_final: 0.7811 (mmm) REVERT: F 402 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8723 (tm-30) REVERT: F 428 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8741 (tm-30) REVERT: F 488 MET cc_start: 0.8311 (tpt) cc_final: 0.7881 (tpp) REVERT: F 492 MET cc_start: 0.8012 (mmm) cc_final: 0.7723 (mmp) REVERT: d 145 PHE cc_start: 0.9032 (t80) cc_final: 0.8800 (t80) REVERT: d 224 ARG cc_start: 0.9361 (ttm-80) cc_final: 0.8458 (ttp80) REVERT: g 94 TYR cc_start: 0.9194 (t80) cc_final: 0.8740 (t80) REVERT: g 121 MET cc_start: 0.8766 (tpt) cc_final: 0.8512 (tpp) REVERT: g 136 MET cc_start: 0.8565 (tmm) cc_final: 0.8194 (tmm) REVERT: g 199 PHE cc_start: 0.8480 (t80) cc_final: 0.8231 (t80) REVERT: e 4 ASN cc_start: 0.8163 (t0) cc_final: 0.7665 (p0) outliers start: 1 outliers final: 0 residues processed: 330 average time/residue: 0.2160 time to fit residues: 118.5152 Evaluate side-chains 259 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 88 optimal weight: 1.9990 chunk 453 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 415 optimal weight: 6.9990 chunk 436 optimal weight: 20.0000 chunk 293 optimal weight: 0.9980 chunk 331 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 387 optimal weight: 10.0000 chunk 319 optimal weight: 0.7980 chunk 164 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A 334 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN C 186 ASN ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN D 396 GLN D 479 ASN ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN E 210 ASN ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 ASN ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.047824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.039506 restraints weight = 364850.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.040682 restraints weight = 220248.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.041226 restraints weight = 139091.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.041681 restraints weight = 100023.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.041753 restraints weight = 86003.616| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35562 Z= 0.141 Angle : 0.655 11.089 48439 Z= 0.337 Chirality : 0.044 0.285 5858 Planarity : 0.004 0.078 6483 Dihedral : 6.328 119.934 5483 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.07 % Allowed : 2.10 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.04 % 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: -0.01 (0.12), residues: 5123 helix: 1.59 (0.10), residues: 2897 sheet: -3.19 (0.22), residues: 450 loop : -1.85 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 165 TYR 0.023 0.002 TYR B 271 PHE 0.031 0.002 PHE g 168 TRP 0.015 0.002 TRP e 15 HIS 0.007 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (35558) covalent geometry : angle 0.65522 / 0.34 (48437) SS BOND : bond 0.00117 / 0.06 ( 1) SS BOND : angle 1.38809 / 0.82 ( 2) hydrogen bonds : bond 0.04008 / 2.67 ( 2444) hydrogen bonds : angle 4.59772 / 3.20 ( 7218) Misc. bond : bond 0.00511 / 0.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 327 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8393 (mpp) cc_final: 0.7794 (mmt) REVERT: A 213 PHE cc_start: 0.8754 (p90) cc_final: 0.8348 (p90) REVERT: A 223 ILE cc_start: 0.9208 (mp) cc_final: 0.8631 (mt) REVERT: A 264 LEU cc_start: 0.9351 (tt) cc_final: 0.8941 (tt) REVERT: A 266 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8808 (mmmm) REVERT: A 285 GLU cc_start: 0.8682 (tt0) cc_final: 0.7935 (tp30) REVERT: A 295 HIS cc_start: 0.8699 (m-70) cc_final: 0.8477 (m-70) REVERT: A 314 MET cc_start: 0.8842 (tpt) cc_final: 0.8367 (tpp) REVERT: A 344 PHE cc_start: 0.8875 (t80) cc_final: 0.8204 (t80) REVERT: A 376 MET cc_start: 0.8433 (tpt) cc_final: 0.7980 (tpp) REVERT: A 392 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8334 (mp0) REVERT: B 56 PHE cc_start: 0.8450 (m-80) cc_final: 0.8081 (m-80) REVERT: B 196 TYR cc_start: 0.7176 (t80) cc_final: 0.6901 (t80) REVERT: B 223 ILE cc_start: 0.8634 (mt) cc_final: 0.8434 (mt) REVERT: B 274 MET cc_start: 0.9283 (ptm) cc_final: 0.8487 (ppp) REVERT: B 436 MET cc_start: 0.8899 (ppp) cc_final: 0.8679 (ppp) REVERT: C 49 MET cc_start: 0.6807 (tpt) cc_final: 0.6433 (tpt) REVERT: C 138 MET cc_start: 0.8838 (ppp) cc_final: 0.8588 (ppp) REVERT: C 157 MET cc_start: 0.8260 (tpt) cc_final: 0.8040 (tpt) REVERT: C 300 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6460 (mt-10) REVERT: D 183 MET cc_start: 0.9359 (mmm) cc_final: 0.8984 (mmm) REVERT: D 416 GLU cc_start: 0.8931 (pm20) cc_final: 0.8727 (pm20) REVERT: E 69 LEU cc_start: 0.8337 (mm) cc_final: 0.8099 (tp) REVERT: E 171 PHE cc_start: 0.8477 (m-10) cc_final: 0.8036 (m-10) REVERT: E 292 MET cc_start: 0.7549 (mmm) cc_final: 0.7209 (mmm) REVERT: E 374 MET cc_start: 0.6770 (tpp) cc_final: 0.6064 (tpp) REVERT: F 79 MET cc_start: 0.8248 (mpp) cc_final: 0.7890 (mpp) REVERT: F 215 GLU cc_start: 0.8786 (tp30) cc_final: 0.8519 (tm-30) REVERT: F 254 LEU cc_start: 0.8749 (tp) cc_final: 0.8406 (tp) REVERT: F 306 MET cc_start: 0.9183 (mmm) cc_final: 0.8891 (mmm) REVERT: F 369 ASP cc_start: 0.8476 (t70) cc_final: 0.8166 (t70) REVERT: F 402 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8791 (tm-30) REVERT: F 428 GLU cc_start: 0.9385 (tm-30) cc_final: 0.8781 (tm-30) REVERT: F 488 MET cc_start: 0.8289 (tpt) cc_final: 0.7843 (tpp) REVERT: F 492 MET cc_start: 0.8070 (mmm) cc_final: 0.7737 (mmp) REVERT: d 115 PHE cc_start: 0.8772 (m-10) cc_final: 0.8500 (m-10) REVERT: d 129 LEU cc_start: 0.9536 (mt) cc_final: 0.9242 (tp) REVERT: d 224 ARG cc_start: 0.9430 (ttm-80) cc_final: 0.8493 (ttp80) REVERT: g 94 TYR cc_start: 0.9187 (t80) cc_final: 0.8772 (t80) REVERT: g 121 MET cc_start: 0.8764 (tpt) cc_final: 0.8493 (tpp) REVERT: g 199 PHE cc_start: 0.8537 (t80) cc_final: 0.8274 (t80) REVERT: g 260 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8787 (mmmt) REVERT: g 334 LYS cc_start: 0.8437 (ptpt) cc_final: 0.8061 (ptmm) REVERT: e 4 ASN cc_start: 0.8142 (t0) cc_final: 0.7649 (p0) outliers start: 2 outliers final: 0 residues processed: 329 average time/residue: 0.2028 time to fit residues: 112.7060 Evaluate side-chains 262 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 306 optimal weight: 3.9990 chunk 308 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 489 optimal weight: 40.0000 chunk 424 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 334 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN E 210 ASN E 299 GLN ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS ** g 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 346 GLN e 56 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.046350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.038042 restraints weight = 375698.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.039282 restraints weight = 253656.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.039720 restraints weight = 149490.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.040133 restraints weight = 111950.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.040262 restraints weight = 92731.502| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 35562 Z= 0.229 Angle : 0.700 11.501 48439 Z= 0.367 Chirality : 0.045 0.281 5858 Planarity : 0.005 0.054 6483 Dihedral : 6.483 119.563 5483 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.06 % 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: 0.00 (0.12), residues: 5123 helix: 1.59 (0.10), residues: 2902 sheet: -3.20 (0.22), residues: 459 loop : -1.82 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG g 73 TYR 0.022 0.002 TYR B 20 PHE 0.029 0.002 PHE F 343 TRP 0.018 0.003 TRP e 15 HIS 0.009 0.002 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.23 (35558) covalent geometry : angle 0.69986 / 0.37 (48437) SS BOND : bond 0.00401 / 0.21 ( 1) SS BOND : angle 1.48083 / 0.86 ( 2) hydrogen bonds : bond 0.04360 / 2.92 ( 2444) hydrogen bonds : angle 4.73559 / 3.30 ( 7218) Misc. bond : bond 0.00256 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 297 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8690 (pmm) cc_final: 0.8387 (pmm) REVERT: A 213 PHE cc_start: 0.8762 (p90) cc_final: 0.8342 (p90) REVERT: A 223 ILE cc_start: 0.9239 (mp) cc_final: 0.8659 (mt) REVERT: A 266 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8881 (mmmm) REVERT: A 285 GLU cc_start: 0.8617 (tt0) cc_final: 0.7920 (tp30) REVERT: A 295 HIS cc_start: 0.8807 (m-70) cc_final: 0.8574 (m-70) REVERT: A 314 MET cc_start: 0.8900 (tpt) cc_final: 0.8284 (tpt) REVERT: A 344 PHE cc_start: 0.9042 (t80) cc_final: 0.8309 (t80) REVERT: A 376 MET cc_start: 0.8531 (tpt) cc_final: 0.8103 (tpp) REVERT: A 392 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8370 (mp0) REVERT: B 196 TYR cc_start: 0.7248 (t80) cc_final: 0.6911 (t80) REVERT: B 223 ILE cc_start: 0.8732 (mt) cc_final: 0.8527 (mt) REVERT: B 263 ASP cc_start: 0.7272 (m-30) cc_final: 0.7068 (m-30) REVERT: B 274 MET cc_start: 0.9323 (ptm) cc_final: 0.8576 (ppp) REVERT: B 376 MET cc_start: 0.8589 (mtm) cc_final: 0.8384 (mtp) REVERT: B 436 MET cc_start: 0.8917 (ppp) cc_final: 0.8707 (ppp) REVERT: C 49 MET cc_start: 0.7087 (tpt) cc_final: 0.6806 (tpt) REVERT: C 172 ARG cc_start: 0.6338 (mpp-170) cc_final: 0.5812 (mpt180) REVERT: C 462 ARG cc_start: 0.8841 (ptm-80) cc_final: 0.8562 (ttp-110) REVERT: D 183 MET cc_start: 0.9348 (mmm) cc_final: 0.8891 (mmm) REVERT: D 199 PHE cc_start: 0.9074 (t80) cc_final: 0.8765 (t80) REVERT: D 214 MET cc_start: 0.9359 (mmt) cc_final: 0.8969 (mmm) REVERT: D 416 GLU cc_start: 0.8872 (pm20) cc_final: 0.8643 (pm20) REVERT: E 69 LEU cc_start: 0.8298 (mm) cc_final: 0.8024 (tp) REVERT: E 170 LEU cc_start: 0.9569 (mm) cc_final: 0.9308 (mm) REVERT: E 403 ASP cc_start: 0.9112 (t70) cc_final: 0.8893 (t0) REVERT: F 369 ASP cc_start: 0.8406 (t70) cc_final: 0.8182 (t70) REVERT: F 374 MET cc_start: 0.8212 (mmm) cc_final: 0.7860 (mmm) REVERT: F 402 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8709 (tm-30) REVERT: F 428 GLU cc_start: 0.9378 (tm-30) cc_final: 0.8827 (tm-30) REVERT: F 488 MET cc_start: 0.8363 (tpt) cc_final: 0.7839 (tpp) REVERT: F 492 MET cc_start: 0.8101 (mmm) cc_final: 0.7766 (mmp) REVERT: d 224 ARG cc_start: 0.9464 (ttm-80) cc_final: 0.8571 (ttp80) REVERT: g 94 TYR cc_start: 0.9154 (t80) cc_final: 0.8742 (t80) REVERT: g 121 MET cc_start: 0.8817 (tpt) cc_final: 0.8523 (tpt) REVERT: g 199 PHE cc_start: 0.8544 (t80) cc_final: 0.8271 (t80) REVERT: e 4 ASN cc_start: 0.8218 (t0) cc_final: 0.7641 (p0) outliers start: 2 outliers final: 0 residues processed: 299 average time/residue: 0.2138 time to fit residues: 108.4012 Evaluate side-chains 243 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 388 optimal weight: 5.9990 chunk 357 optimal weight: 9.9990 chunk 112 optimal weight: 0.0470 chunk 478 optimal weight: 9.9990 chunk 265 optimal weight: 0.0050 chunk 134 optimal weight: 0.5980 chunk 295 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 449 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 274 optimal weight: 2.9990 overall best weight: 0.5294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 201 GLN ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN g 58 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.048095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.039718 restraints weight = 362266.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.040872 restraints weight = 220194.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.041420 restraints weight = 141968.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.041705 restraints weight = 103613.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.041864 restraints weight = 90320.424| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35562 Z= 0.132 Angle : 0.659 12.421 48439 Z= 0.336 Chirality : 0.044 0.295 5858 Planarity : 0.004 0.072 6483 Dihedral : 6.249 123.835 5483 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.03 % Allowed : 1.31 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.04 % 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: 0.23 (0.12), residues: 5123 helix: 1.79 (0.10), residues: 2898 sheet: -3.12 (0.22), residues: 477 loop : -1.70 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 312 TYR 0.053 0.002 TYR B 293 PHE 0.022 0.002 PHE A 213 TRP 0.016 0.002 TRP e 15 HIS 0.006 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (35558) covalent geometry : angle 0.65865 / 0.34 (48437) SS BOND : bond 0.00076 / 0.04 ( 1) SS BOND : angle 1.14842 / 0.67 ( 2) hydrogen bonds : bond 0.03916 / 2.61 ( 2444) hydrogen bonds : angle 4.51391 / 3.14 ( 7218) Misc. bond : bond 0.00190 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8662 (pmm) cc_final: 0.8377 (pmm) REVERT: A 213 PHE cc_start: 0.8644 (p90) cc_final: 0.8270 (p90) REVERT: A 223 ILE cc_start: 0.9225 (mp) cc_final: 0.8618 (mt) REVERT: A 264 LEU cc_start: 0.9316 (tt) cc_final: 0.8877 (tt) REVERT: A 266 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8822 (mmmm) REVERT: A 285 GLU cc_start: 0.8689 (tt0) cc_final: 0.7943 (tp30) REVERT: A 295 HIS cc_start: 0.8739 (m-70) cc_final: 0.8366 (m-70) REVERT: A 314 MET cc_start: 0.8655 (tpt) cc_final: 0.8185 (tpp) REVERT: A 344 PHE cc_start: 0.8954 (t80) cc_final: 0.8262 (t80) REVERT: A 376 MET cc_start: 0.8430 (tpt) cc_final: 0.7952 (tpp) REVERT: A 392 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8350 (mp0) REVERT: B 56 PHE cc_start: 0.8464 (m-80) cc_final: 0.8156 (m-80) REVERT: B 82 MET cc_start: 0.8903 (mpp) cc_final: 0.8663 (mpp) REVERT: B 196 TYR cc_start: 0.7178 (t80) cc_final: 0.6870 (t80) REVERT: B 263 ASP cc_start: 0.7454 (m-30) cc_final: 0.7236 (m-30) REVERT: B 274 MET cc_start: 0.9326 (ptm) cc_final: 0.8371 (ppp) REVERT: B 436 MET cc_start: 0.8937 (ppp) cc_final: 0.8701 (ppp) REVERT: C 37 ASP cc_start: 0.7456 (t0) cc_final: 0.7179 (t0) REVERT: C 49 MET cc_start: 0.6988 (tpt) cc_final: 0.6357 (tpt) REVERT: C 138 MET cc_start: 0.8794 (ppp) cc_final: 0.8545 (ppp) REVERT: C 172 ARG cc_start: 0.5908 (mpp-170) cc_final: 0.5675 (mpt180) REVERT: C 274 MET cc_start: 0.8878 (mmp) cc_final: 0.8645 (mmp) REVERT: D 183 MET cc_start: 0.9366 (mmm) cc_final: 0.9028 (mmm) REVERT: D 214 MET cc_start: 0.9360 (mmt) cc_final: 0.9003 (mmm) REVERT: D 374 MET cc_start: 0.8264 (mmp) cc_final: 0.7887 (mmp) REVERT: D 382 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8733 (tm-30) REVERT: E 69 LEU cc_start: 0.8286 (mm) cc_final: 0.8058 (tp) REVERT: E 170 LEU cc_start: 0.9622 (mm) cc_final: 0.9409 (mm) REVERT: E 335 THR cc_start: 0.8475 (t) cc_final: 0.7949 (m) REVERT: E 403 ASP cc_start: 0.8990 (t70) cc_final: 0.8758 (t0) REVERT: F 79 MET cc_start: 0.8265 (mpp) cc_final: 0.7983 (mpp) REVERT: F 215 GLU cc_start: 0.8757 (tp30) cc_final: 0.8484 (tm-30) REVERT: F 247 MET cc_start: 0.8962 (ttp) cc_final: 0.8610 (ppp) REVERT: F 254 LEU cc_start: 0.9006 (tp) cc_final: 0.8785 (tp) REVERT: F 369 ASP cc_start: 0.8330 (t70) cc_final: 0.8097 (t70) REVERT: F 402 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8729 (tm-30) REVERT: F 428 GLU cc_start: 0.9370 (tm-30) cc_final: 0.8830 (tm-30) REVERT: d 112 TYR cc_start: 0.8413 (t80) cc_final: 0.7412 (t80) REVERT: d 115 PHE cc_start: 0.8762 (m-10) cc_final: 0.8486 (m-10) REVERT: d 129 LEU cc_start: 0.9549 (mt) cc_final: 0.9265 (tp) REVERT: d 224 ARG cc_start: 0.9493 (ttm-80) cc_final: 0.8535 (ttp80) REVERT: g 94 TYR cc_start: 0.9138 (t80) cc_final: 0.8728 (t80) REVERT: g 121 MET cc_start: 0.8772 (tpt) cc_final: 0.8551 (tpp) REVERT: g 199 PHE cc_start: 0.8538 (t80) cc_final: 0.8253 (t80) REVERT: g 334 LYS cc_start: 0.8322 (ptmt) cc_final: 0.8015 (ptmm) REVERT: e 4 ASN cc_start: 0.8154 (t0) cc_final: 0.7720 (p0) outliers start: 1 outliers final: 0 residues processed: 330 average time/residue: 0.2017 time to fit residues: 113.0010 Evaluate side-chains 259 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 392 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 448 optimal weight: 20.0000 chunk 303 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 246 optimal weight: 8.9990 chunk 216 optimal weight: 0.6980 chunk 499 optimal weight: 5.9990 chunk 287 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN E 133 HIS ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 GLN g 346 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.047234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.039066 restraints weight = 370956.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.040141 restraints weight = 228004.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.040699 restraints weight = 149468.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.041009 restraints weight = 106891.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.041118 restraints weight = 93083.584| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35562 Z= 0.184 Angle : 0.683 11.260 48439 Z= 0.352 Chirality : 0.045 0.320 5858 Planarity : 0.004 0.068 6483 Dihedral : 6.280 122.741 5483 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.03 % Allowed : 0.55 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.06 % 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: 0.29 (0.12), residues: 5123 helix: 1.81 (0.10), residues: 2905 sheet: -3.09 (0.22), residues: 465 loop : -1.67 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 312 TYR 0.032 0.002 TYR d 112 PHE 0.027 0.002 PHE F 343 TRP 0.017 0.002 TRP e 15 HIS 0.006 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (35558) covalent geometry : angle 0.68341 / 0.35 (48437) SS BOND : bond 0.00243 / 0.13 ( 1) SS BOND : angle 1.35118 / 0.79 ( 2) hydrogen bonds : bond 0.04067 / 2.71 ( 2444) hydrogen bonds : angle 4.56513 / 3.17 ( 7218) Misc. bond : bond 0.00217 / 0.10 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8642 (pmm) cc_final: 0.8353 (pmm) REVERT: A 213 PHE cc_start: 0.8660 (p90) cc_final: 0.8282 (p90) REVERT: A 223 ILE cc_start: 0.9203 (mp) cc_final: 0.8587 (mt) REVERT: A 264 LEU cc_start: 0.9360 (tt) cc_final: 0.8818 (tp) REVERT: A 266 LYS cc_start: 0.9138 (mmtt) cc_final: 0.8832 (mmmm) REVERT: A 285 GLU cc_start: 0.8638 (tt0) cc_final: 0.7919 (tp30) REVERT: A 295 HIS cc_start: 0.8822 (m-70) cc_final: 0.8455 (m170) REVERT: A 314 MET cc_start: 0.8654 (tpt) cc_final: 0.8079 (tpt) REVERT: A 344 PHE cc_start: 0.9019 (t80) cc_final: 0.8282 (t80) REVERT: A 376 MET cc_start: 0.8434 (tpt) cc_final: 0.7941 (tpp) REVERT: A 392 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8369 (mp0) REVERT: B 196 TYR cc_start: 0.7162 (t80) cc_final: 0.6831 (t80) REVERT: B 223 ILE cc_start: 0.8725 (mt) cc_final: 0.8515 (mt) REVERT: B 274 MET cc_start: 0.9325 (ptm) cc_final: 0.8518 (ppp) REVERT: B 376 MET cc_start: 0.8602 (mtm) cc_final: 0.8375 (mtp) REVERT: B 436 MET cc_start: 0.8928 (ppp) cc_final: 0.8661 (ppp) REVERT: C 49 MET cc_start: 0.7206 (tpt) cc_final: 0.6732 (tpt) REVERT: C 138 MET cc_start: 0.8819 (ppp) cc_final: 0.8589 (ppp) REVERT: C 172 ARG cc_start: 0.6013 (mpp-170) cc_final: 0.5705 (mpt180) REVERT: C 274 MET cc_start: 0.8956 (mmp) cc_final: 0.8736 (mmp) REVERT: D 183 MET cc_start: 0.9376 (mmm) cc_final: 0.8864 (mmm) REVERT: D 214 MET cc_start: 0.9323 (mmt) cc_final: 0.8961 (mmm) REVERT: D 374 MET cc_start: 0.8303 (mmp) cc_final: 0.7869 (mmm) REVERT: E 69 LEU cc_start: 0.8315 (mm) cc_final: 0.8046 (tp) REVERT: E 170 LEU cc_start: 0.9579 (mm) cc_final: 0.9350 (mm) REVERT: E 403 ASP cc_start: 0.8985 (t70) cc_final: 0.8766 (t0) REVERT: F 254 LEU cc_start: 0.9062 (tp) cc_final: 0.8773 (tp) REVERT: F 342 THR cc_start: 0.9089 (p) cc_final: 0.8771 (p) REVERT: F 369 ASP cc_start: 0.8373 (t70) cc_final: 0.8143 (t70) REVERT: F 402 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8755 (tm-30) REVERT: F 428 GLU cc_start: 0.9366 (tm-30) cc_final: 0.8818 (tm-30) REVERT: d 112 TYR cc_start: 0.8367 (t80) cc_final: 0.7902 (t80) REVERT: d 224 ARG cc_start: 0.9456 (ttm-80) cc_final: 0.8560 (ttp80) REVERT: g 94 TYR cc_start: 0.9136 (t80) cc_final: 0.8721 (t80) REVERT: g 121 MET cc_start: 0.8778 (tpt) cc_final: 0.8480 (tpt) REVERT: g 199 PHE cc_start: 0.8492 (t80) cc_final: 0.8171 (t80) REVERT: g 334 LYS cc_start: 0.8370 (ptmt) cc_final: 0.8084 (ptmm) REVERT: e 4 ASN cc_start: 0.8187 (t0) cc_final: 0.7579 (p0) outliers start: 1 outliers final: 0 residues processed: 297 average time/residue: 0.2039 time to fit residues: 103.7362 Evaluate side-chains 247 residues out of total 4083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 474 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 471 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 183 optimal weight: 0.2980 chunk 10 optimal weight: 5.9990 chunk 372 optimal weight: 20.0000 chunk 274 optimal weight: 0.9980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** E 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.047499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.039006 restraints weight = 366120.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.039982 restraints weight = 227394.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.040646 restraints weight = 156559.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.041146 restraints weight = 117185.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.041484 restraints weight = 92854.653| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35562 Z= 0.163 Angle : 0.670 11.619 48439 Z= 0.345 Chirality : 0.044 0.309 5858 Planarity : 0.004 0.077 6483 Dihedral : 6.265 122.668 5483 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.03 % Allowed : 0.58 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.14 % Twisted Proline : 0.49 % Twisted General : 0.06 % 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: 0.29 (0.12), residues: 5123 helix: 1.81 (0.10), residues: 2885 sheet: -3.02 (0.22), residues: 465 loop : -1.64 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 462 TYR 0.026 0.002 TYR B 293 PHE 0.027 0.002 PHE E 343 TRP 0.017 0.002 TRP e 15 HIS 0.007 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (35558) covalent geometry : angle 0.66952 / 0.34 (48437) SS BOND : bond 0.00171 / 0.09 ( 1) SS BOND : angle 1.40580 / 0.83 ( 2) hydrogen bonds : bond 0.03991 / 2.66 ( 2444) hydrogen bonds : angle 4.52900 / 3.15 ( 7218) Misc. bond : bond 0.00197 / 0.09 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5168.55 seconds wall clock time: 90 minutes 45.93 seconds (5445.93 seconds total)