Starting phenix.real_space_refine on Wed Sep 17 19:21:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jc2_61340/09_2025/9jc2_61340_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jc2_61340/09_2025/9jc2_61340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jc2_61340/09_2025/9jc2_61340_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jc2_61340/09_2025/9jc2_61340_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jc2_61340/09_2025/9jc2_61340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jc2_61340/09_2025/9jc2_61340.map" } resolution = 3.96 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 6732 2.51 5 N 2001 2.21 5 O 2066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10815 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 918 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PTRANS': 3, 'TRANS': 162} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 511 Unresolved non-hydrogen dihedrals: 320 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'PHE:plan': 8, 'ASN:plan1': 5, 'ASP:plan': 2, 'ARG:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 4, 'HIS:plan': 2, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 169 Chain: "B" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 932 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 3, 'TRANS': 162} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 490 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'PHE:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 2, 'ARG:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 4, 'HIS:plan': 2, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 160 Chain: "C" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 899 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 3, 'TRANS': 163} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 426 Unresolved non-hydrogen angles: 553 Unresolved non-hydrogen dihedrals: 351 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'PHE:plan': 9, 'ASN:plan1': 4, 'ASP:plan': 3, 'ARG:plan': 5, 'GLN:plan1': 4, 'GLU:plan': 4, 'TRP:plan': 2, 'HIS:plan': 3, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 193 Chain: "D" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1595 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 10, 'TRANS': 228} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 311 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 7, 'GLU:plan': 12, 'TYR:plan': 3, 'GLN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 180 Chain: "E" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 482 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 66} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 317 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 6, 'PHE:plan': 2, 'ARG:plan': 5, 'TRP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 9, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "G" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 275 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 52} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 5, 'PHE:plan': 2, 'ARG:plan': 4, 'TRP:plan': 1, 'GLU:plan': 7, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "H" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 320 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 1, 'TRANS': 62} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 6, 'PHE:plan': 2, 'ARG:plan': 5, 'TRP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 9, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "I" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 274 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 1, 'TRANS': 51} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 5, 'PHE:plan': 2, 'ARG:plan': 4, 'TRP:plan': 1, 'GLU:plan': 7, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "J" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 325 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 1, 'TRANS': 62} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 6, 'PHE:plan': 2, 'ARG:plan': 5, 'TRP:plan': 1, 'GLU:plan': 9, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "K" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 286 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 1, 'TRANS': 55} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 5, 'PHE:plan': 2, 'ARG:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 7, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "L" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 398 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "M" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 415 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "N" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 428 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "O" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 438 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "P" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 423 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "Q" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 437 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "R" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 414 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "S" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 412 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "T" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 421 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "U" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 406 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 2, 'PHE:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 2.78, per 1000 atoms: 0.26 Number of scatterers: 10815 At special positions: 0 Unit cell: (115.5, 116.25, 146.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 2066 8.00 N 2001 7.00 C 6732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 605.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3414 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 3 sheets defined 86.8% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 16 through 38 Processing helix chain 'A' and resid 47 through 66 Processing helix chain 'A' and resid 75 through 93 removed outlier: 3.562A pdb=" N GLY A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 131 removed outlier: 3.923A pdb=" N GLY A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 191 removed outlier: 3.788A pdb=" N THR A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 232 Processing helix chain 'B' and resid 16 through 38 Processing helix chain 'B' and resid 47 through 66 Processing helix chain 'B' and resid 75 through 93 Processing helix chain 'B' and resid 115 through 131 removed outlier: 4.080A pdb=" N GLY B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 191 Processing helix chain 'B' and resid 199 through 232 Processing helix chain 'C' and resid 16 through 38 Processing helix chain 'C' and resid 47 through 66 Processing helix chain 'C' and resid 75 through 93 removed outlier: 3.887A pdb=" N GLY C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 131 removed outlier: 3.776A pdb=" N GLY C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 191 Processing helix chain 'C' and resid 200 through 232 Processing helix chain 'D' and resid 11 through 42 removed outlier: 3.599A pdb=" N GLN D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 57 removed outlier: 3.951A pdb=" N MET D 46 " --> pdb=" O PHE D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 69 removed outlier: 3.724A pdb=" N LEU D 68 " --> pdb=" O HIS D 65 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL D 69 " --> pdb=" O PRO D 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 69' Processing helix chain 'D' and resid 90 through 107 removed outlier: 4.319A pdb=" N VAL D 95 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU D 96 " --> pdb=" O ASN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 146 through 163 removed outlier: 4.505A pdb=" N GLU D 151 " --> pdb=" O ALA D 147 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 255 Proline residue: D 218 - end of helix removed outlier: 4.327A pdb=" N TYR D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLY D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU D 230 " --> pdb=" O TYR D 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 70 removed outlier: 3.962A pdb=" N LYS F 27 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE F 28 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLN F 31 " --> pdb=" O LYS F 27 " (cutoff:3.500A) Proline residue: F 32 - end of helix Processing helix chain 'G' and resid 11 through 63 removed outlier: 5.302A pdb=" N GLN G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) Proline residue: G 32 - end of helix Processing helix chain 'H' and resid 8 through 70 removed outlier: 3.634A pdb=" N PHE H 28 " --> pdb=" O LEU H 24 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLN H 31 " --> pdb=" O LYS H 27 " (cutoff:3.500A) Proline residue: H 32 - end of helix removed outlier: 3.574A pdb=" N ALA H 51 " --> pdb=" O GLU H 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 23 Processing helix chain 'I' and resid 23 through 63 Proline residue: I 32 - end of helix removed outlier: 3.781A pdb=" N ASN I 35 " --> pdb=" O GLN I 31 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE I 36 " --> pdb=" O PRO I 32 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN I 39 " --> pdb=" O ASN I 35 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE I 44 " --> pdb=" O ARG I 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 70 removed outlier: 6.306A pdb=" N GLN J 31 " --> pdb=" O LYS J 27 " (cutoff:3.500A) Proline residue: J 32 - end of helix removed outlier: 3.504A pdb=" N ILE J 36 " --> pdb=" O PRO J 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 63 removed outlier: 5.545A pdb=" N GLN K 31 " --> pdb=" O LYS K 27 " (cutoff:3.500A) Proline residue: K 32 - end of helix Processing helix chain 'L' and resid 3 through 37 removed outlier: 4.399A pdb=" N ARG L 29 " --> pdb=" O LEU L 25 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N THR L 30 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE L 31 " --> pdb=" O VAL L 27 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU L 32 " --> pdb=" O SER L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 50 Processing helix chain 'L' and resid 51 through 72 removed outlier: 4.375A pdb=" N LEU L 58 " --> pdb=" O LEU L 54 " (cutoff:3.500A) Proline residue: L 59 - end of helix Processing helix chain 'M' and resid 3 through 37 Processing helix chain 'M' and resid 40 through 72 removed outlier: 4.571A pdb=" N LEU M 58 " --> pdb=" O LEU M 54 " (cutoff:3.500A) Proline residue: M 59 - end of helix Processing helix chain 'N' and resid 3 through 37 Processing helix chain 'N' and resid 40 through 56 Processing helix chain 'N' and resid 57 through 72 Processing helix chain 'O' and resid 3 through 37 Processing helix chain 'O' and resid 40 through 72 removed outlier: 4.021A pdb=" N LEU O 44 " --> pdb=" O LEU O 40 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE O 49 " --> pdb=" O GLN O 45 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE O 50 " --> pdb=" O THR O 46 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LEU O 58 " --> pdb=" O LEU O 54 " (cutoff:3.500A) Proline residue: O 59 - end of helix Processing helix chain 'P' and resid 3 through 37 removed outlier: 3.592A pdb=" N GLU P 32 " --> pdb=" O SER P 28 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN P 37 " --> pdb=" O GLY P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 72 removed outlier: 4.471A pdb=" N LEU P 58 " --> pdb=" O LEU P 54 " (cutoff:3.500A) Proline residue: P 59 - end of helix Processing helix chain 'Q' and resid 3 through 37 Processing helix chain 'Q' and resid 40 through 72 removed outlier: 3.612A pdb=" N ALA Q 53 " --> pdb=" O PHE Q 49 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU Q 58 " --> pdb=" O LEU Q 54 " (cutoff:3.500A) Proline residue: Q 59 - end of helix Processing helix chain 'R' and resid 3 through 37 removed outlier: 3.841A pdb=" N ILE R 21 " --> pdb=" O LEU R 17 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG R 29 " --> pdb=" O LEU R 25 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR R 30 " --> pdb=" O ILE R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 56 Processing helix chain 'R' and resid 57 through 72 Processing helix chain 'S' and resid 3 through 37 Processing helix chain 'S' and resid 40 through 72 removed outlier: 4.510A pdb=" N LEU S 58 " --> pdb=" O LEU S 54 " (cutoff:3.500A) Proline residue: S 59 - end of helix Processing helix chain 'T' and resid 3 through 37 removed outlier: 4.154A pdb=" N ALA T 7 " --> pdb=" O LEU T 3 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 56 Processing helix chain 'T' and resid 57 through 72 Processing helix chain 'U' and resid 3 through 37 removed outlier: 3.502A pdb=" N VAL U 12 " --> pdb=" O ALA U 8 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY U 15 " --> pdb=" O ALA U 11 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU U 25 " --> pdb=" O ILE U 21 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE U 26 " --> pdb=" O GLY U 22 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER U 28 " --> pdb=" O GLY U 24 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG U 29 " --> pdb=" O LEU U 25 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR U 30 " --> pdb=" O ILE U 26 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE U 31 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU U 32 " --> pdb=" O SER U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 56 removed outlier: 3.504A pdb=" N THR U 47 " --> pdb=" O VAL U 43 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA U 53 " --> pdb=" O PHE U 49 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU U 54 " --> pdb=" O ILE U 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 removed outlier: 3.518A pdb=" N VAL U 64 " --> pdb=" O ILE U 60 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 133 through 136 removed outlier: 8.714A pdb=" N ILE D 115 " --> pdb=" O ILE D 134 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ASP D 136 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL D 117 " --> pdb=" O ASP D 136 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TYR D 78 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR D 169 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET D 170 " --> pdb=" O ARG D 186 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR D 172 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU D 182 " --> pdb=" O HIS D 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 204 through 205 removed outlier: 6.696A pdb=" N GLU D 204 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU E 41 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E 70 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY E 66 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU E 69 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR E 76 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL E 9 " --> pdb=" O ILE E 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 31 through 34 removed outlier: 3.501A pdb=" N VAL E 23 " --> pdb=" O ILE E 34 " (cutoff:3.500A) 1308 hydrogen bonds defined for protein. 3921 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: 1.83 Time building geometry restraints manager: 1.35 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: 2280 1.33 - 1.45: 2103 1.45 - 1.57: 6469 1.57 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 10884 Sorted by residual: bond pdb=" CG1 ILE Q 26 " pdb=" CD1 ILE Q 26 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" CG1 ILE O 26 " pdb=" CD1 ILE O 26 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.64e+00 bond pdb=" CG1 ILE N 50 " pdb=" CD1 ILE N 50 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.53e+00 bond pdb=" C ARG L 41 " pdb=" N PRO L 42 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.30e-02 5.92e+03 1.49e+00 bond pdb=" CG1 ILE P 26 " pdb=" CD1 ILE P 26 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.39e+00 ... (remaining 10879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 14633 1.66 - 3.32: 252 3.32 - 4.98: 77 4.98 - 6.63: 20 6.63 - 8.29: 11 Bond angle restraints: 14993 Sorted by residual: angle pdb=" C ALA B 208 " pdb=" N PHE B 209 " pdb=" CA PHE B 209 " ideal model delta sigma weight residual 121.14 115.18 5.96 1.75e+00 3.27e-01 1.16e+01 angle pdb=" C ILE N 26 " pdb=" N VAL N 27 " pdb=" CA VAL N 27 " ideal model delta sigma weight residual 120.64 115.48 5.16 1.64e+00 3.72e-01 9.90e+00 angle pdb=" CA GLN L 37 " pdb=" CB GLN L 37 " pdb=" CG GLN L 37 " ideal model delta sigma weight residual 114.10 120.37 -6.27 2.00e+00 2.50e-01 9.82e+00 angle pdb=" CA LYS E 26 " pdb=" CB LYS E 26 " pdb=" CG LYS E 26 " ideal model delta sigma weight residual 114.10 120.32 -6.22 2.00e+00 2.50e-01 9.67e+00 angle pdb=" C GLY O 22 " pdb=" N ASN O 23 " pdb=" CA ASN O 23 " ideal model delta sigma weight residual 120.31 115.92 4.39 1.52e+00 4.33e-01 8.34e+00 ... (remaining 14988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 5885 16.96 - 33.92: 351 33.92 - 50.87: 74 50.87 - 67.83: 9 67.83 - 84.79: 3 Dihedral angle restraints: 6322 sinusoidal: 1053 harmonic: 5269 Sorted by residual: dihedral pdb=" CA ALA I 23 " pdb=" C ALA I 23 " pdb=" N LEU I 24 " pdb=" CA LEU I 24 " ideal model delta harmonic sigma weight residual 180.00 154.05 25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA MET O 48 " pdb=" C MET O 48 " pdb=" N PHE O 49 " pdb=" CA PHE O 49 " ideal model delta harmonic sigma weight residual -180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA THR L 47 " pdb=" C THR L 47 " pdb=" N MET L 48 " pdb=" CA MET L 48 " ideal model delta harmonic sigma weight residual 180.00 163.72 16.28 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 6319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1559 0.054 - 0.108: 402 0.108 - 0.163: 32 0.163 - 0.217: 2 0.217 - 0.271: 3 Chirality restraints: 1998 Sorted by residual: chirality pdb=" CB VAL E 6 " pdb=" CA VAL E 6 " pdb=" CG1 VAL E 6 " pdb=" CG2 VAL E 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CG LEU N 44 " pdb=" CB LEU N 44 " pdb=" CD1 LEU N 44 " pdb=" CD2 LEU N 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL O 27 " pdb=" CA VAL O 27 " pdb=" CG1 VAL O 27 " pdb=" CG2 VAL O 27 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1995 not shown) Planarity restraints: 2023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA I 23 " -0.019 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C ALA I 23 " 0.068 2.00e-02 2.50e+03 pdb=" O ALA I 23 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU I 24 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 209 " 0.019 2.00e-02 2.50e+03 1.83e-02 5.88e+00 pdb=" CG PHE B 209 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 209 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 209 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B 209 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 209 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 209 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 54 " -0.014 2.00e-02 2.50e+03 1.37e-02 4.69e+00 pdb=" CG TRP A 54 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 54 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 54 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 54 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 54 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 54 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 54 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 54 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 54 " 0.000 2.00e-02 2.50e+03 ... (remaining 2020 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1031 2.74 - 3.28: 11618 3.28 - 3.82: 20183 3.82 - 4.36: 16582 4.36 - 4.90: 31718 Nonbonded interactions: 81132 Sorted by model distance: nonbonded pdb=" O GLY M 24 " pdb=" OG SER M 28 " model vdw 2.199 3.040 nonbonded pdb=" O ALA M 19 " pdb=" ND2 ASN M 23 " model vdw 2.215 3.120 nonbonded pdb=" O VAL U 27 " pdb=" OG1 THR U 30 " model vdw 2.242 3.040 nonbonded pdb=" O VAL L 43 " pdb=" OG1 THR L 46 " model vdw 2.263 3.040 nonbonded pdb=" OE1 GLU P 32 " pdb=" NH1 ARG Q 29 " model vdw 2.275 3.120 ... (remaining 81127 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 15 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 through 57 or (resid 58 and (name N or nam \ e CA or name C or name O or name CB )) or resid 59 through 81 or (resid 82 throu \ gh 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throu \ gh 86 or (resid 87 through 89 and (name N or name CA or name C or name O or name \ CB )) or resid 90 through 95 or resid 114 through 173 or (resid 174 and (name N \ or name CA or name C or name O or name CB )) or resid 175 through 189 or (resid \ 190 through 191 and (name N or name CA or name C or name O or name CB )) or res \ id 199 through 206 or (resid 207 through 208 and (name N or name CA or name C or \ name O or name CB )) or resid 209 through 218 or (resid 219 through 226 and (na \ me N or name CA or name C or name O or name CB )) or resid 227 through 232)) selection = (chain 'B' and (resid 15 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 through 57 or (resid 58 and (name N or nam \ e CA or name C or name O or name CB )) or resid 59 through 66 or (resid 74 throu \ gh 76 and (name N or name CA or name C or name O or name CB )) or resid 77 throu \ gh 81 or (resid 82 through 84 and (name N or name CA or name C or name O or name \ CB )) or resid 85 through 91 or (resid 92 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 93 through 166 and (name N or name CA or name C or \ name O or name CB )) or resid 167 through 173 or (resid 174 and (name N or name \ CA or name C or name O or name CB )) or resid 175 through 189 or (resid 190 thr \ ough 191 and (name N or name CA or name C or name O or name CB )) or resid 199 t \ hrough 206 or (resid 207 through 208 and (name N or name CA or name C or name O \ or name CB )) or resid 209 through 211 or (resid 212 through 213 and (name N or \ name CA or name C or name O or name CB )) or resid 214 through 218 or (resid 219 \ through 226 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 27 through 232)) selection = (chain 'C' and (resid 15 through 66 or (resid 74 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 91 or (resid 92 and (na \ me N or name CA or name C or name O or name CB )) or resid 93 through 95 or (res \ id 114 through 166 and (name N or name CA or name C or name O or name CB )) or r \ esid 167 through 211 or (resid 212 through 213 and (name N or name CA or name C \ or name O or name CB )) or resid 214 through 232)) } ncs_group { reference = (chain 'F' and (resid 11 through 63 and (name N or name CA or name C or name O o \ r name CB ))) selection = (chain 'G' and (resid 11 through 63 and (name N or name CA or name C or name O o \ r name CB ))) selection = (chain 'H' and (resid 11 through 63 and (name N or name CA or name C or name O o \ r name CB ))) selection = (chain 'I' and (name N or name CA or name C or name O or name CB )) selection = (chain 'J' and (resid 11 through 63 and (name N or name CA or name C or name O o \ r name CB ))) selection = (chain 'K' and (resid 11 through 63 and (name N or name CA or name C or name O o \ r name CB ))) } ncs_group { reference = (chain 'L' and (resid 2 through 33 or (resid 34 through 37 and (name N or name C \ A or name C or name O or name CB )) or resid 38 through 40 or (resid 41 and (nam \ e N or name CA or name C or name O or name CB )) or resid 42 or (resid 43 throug \ h 46 and (name N or name CA or name C or name O or name CB )) or resid 47 throug \ h 48 or (resid 49 through 50 and (name N or name CA or name C or name O or name \ CB )) or (resid 51 through 70 and (name N or name CA or name C or name O or name \ CB )) or resid 71 through 72)) selection = (chain 'M' and ((resid 2 through 23 and (name N or name CA or name C or name O o \ r name CB )) or (resid 24 through 26 and (name N or name CA or name C or name O \ or name CB )) or resid 27 or (resid 28 and (name N or name CA or name C or name \ O or name CB )) or resid 29 through 33 or (resid 34 through 37 and (name N or na \ me CA or name C or name O or name CB )) or resid 38 through 40 or (resid 41 and \ (name N or name CA or name C or name O or name CB )) or resid 42 or (resid 43 th \ rough 46 and (name N or name CA or name C or name O or name CB )) or resid 47 th \ rough 48 or (resid 49 through 50 and (name N or name CA or name C or name O or n \ ame CB )) or resid 51 or (resid 52 through 61 and (name N or name CA or name C o \ r name O or name CB )) or (resid 62 through 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 72)) selection = (chain 'N' and ((resid 2 through 17 and (name N or name CA or name C or name O o \ r name CB )) or (resid 18 through 21 and (name N or name CA or name C or name O \ or name CB )) or resid 22 or (resid 23 and (name N or name CA or name C or name \ O or name CB )) or resid 24 or (resid 25 through 26 and (name N or name CA or na \ me C or name O or name CB )) or resid 27 or (resid 28 and (name N or name CA or \ name C or name O or name CB )) or resid 29 through 33 or (resid 34 through 37 an \ d (name N or name CA or name C or name O or name CB )) or resid 38 through 39 or \ (resid 40 through 41 and (name N or name CA or name C or name O or name CB )) o \ r resid 42 or (resid 43 through 46 and (name N or name CA or name C or name O or \ name CB )) or resid 47 through 48 or (resid 49 through 50 and (name N or name C \ A or name C or name O or name CB )) or (resid 51 through 61 and (name N or name \ CA or name C or name O or name CB )) or resid 62 through 72)) selection = (chain 'O' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 or (resid 5 through 12 and (name N or name CA or name C o \ r name O or name CB )) or resid 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or (resid 15 through 17 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 or (resid 25 through 26 and (name N or \ name CA or name C or name O or name CB )) or resid 27 or (resid 28 and (name N o \ r name CA or name C or name O or name CB )) or resid 29 through 31 or (resid 32 \ and (name N or name CA or name C or name O or name CB )) or resid 33 or (resid 3 \ 4 through 37 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 8 through 40 or (resid 41 and (name N or name CA or name C or name O or name CB \ )) or resid 42 or (resid 43 through 46 and (name N or name CA or name C or name \ O or name CB )) or resid 47 through 48 or (resid 49 through 50 and (name N or na \ me CA or name C or name O or name CB )) or resid 51 or (resid 52 through 61 and \ (name N or name CA or name C or name O or name CB )) or resid 62 through 72)) selection = (chain 'P' and ((resid 2 through 26 and (name N or name CA or name C or name O o \ r name CB )) or resid 27 or (resid 28 and (name N or name CA or name C or name O \ or name CB )) or resid 29 through 31 or (resid 32 and (name N or name CA or nam \ e C or name O or name CB )) or resid 33 or (resid 34 through 37 and (name N or n \ ame CA or name C or name O or name CB )) or resid 38 through 39 or (resid 40 thr \ ough 41 and (name N or name CA or name C or name O or name CB )) or resid 42 thr \ ough 43 or (resid 44 through 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 48 or (resid 49 through 50 and (name N or name CA o \ r name C or name O or name CB )) or resid 51 or (resid 52 through 61 and (name N \ or name CA or name C or name O or name CB )) or resid 62 through 72)) selection = (chain 'Q' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 or (resid 5 through 12 and (name N or name CA or name C o \ r name O or name CB )) or resid 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or (resid 15 through 17 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 or (resid 25 through 26 and (name N or \ name CA or name C or name O or name CB )) or resid 27 or (resid 28 and (name N o \ r name CA or name C or name O or name CB )) or resid 29 through 33 or (resid 34 \ through 37 and (name N or name CA or name C or name O or name CB )) or resid 38 \ through 40 or (resid 41 and (name N or name CA or name C or name O or name CB )) \ or resid 42 or (resid 43 through 46 and (name N or name CA or name C or name O \ or name CB )) or resid 47 through 48 or (resid 49 through 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 or (resid 52 through 61 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 62 through 70 and ( \ name N or name CA or name C or name O or name CB )) or resid 71 through 72)) selection = (chain 'R' and ((resid 2 through 12 and (name N or name CA or name C or name O o \ r name CB )) or (resid 13 through 21 and (name N or name CA or name C or name O \ or name CB )) or resid 22 or (resid 23 and (name N or name CA or name C or name \ O or name CB )) or resid 24 or (resid 25 through 26 and (name N or name CA or na \ me C or name O or name CB )) or resid 27 or (resid 28 and (name N or name CA or \ name C or name O or name CB )) or resid 29 through 33 or (resid 34 through 37 an \ d (name N or name CA or name C or name O or name CB )) or resid 38 through 42 or \ (resid 43 through 46 and (name N or name CA or name C or name O or name CB )) o \ r resid 47 through 48 or (resid 49 through 50 and (name N or name CA or name C o \ r name O or name CB )) or resid 51 or (resid 52 through 61 and (name N or name C \ A or name C or name O or name CB )) or (resid 62 through 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 72)) selection = (chain 'S' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or (resid 4 through 21 and (name N or name CA or name C or name O or \ name CB )) or resid 22 or (resid 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 or (resid 25 through 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 or (resid 28 and (name N or name CA or na \ me C or name O or name CB )) or resid 29 through 33 or (resid 34 through 37 and \ (name N or name CA or name C or name O or name CB )) or resid 38 through 40 or ( \ resid 41 and (name N or name CA or name C or name O or name CB )) or resid 42 or \ (resid 43 through 46 and (name N or name CA or name C or name O or name CB )) o \ r resid 47 through 48 or (resid 49 through 50 and (name N or name CA or name C o \ r name O or name CB )) or resid 51 or (resid 52 through 61 and (name N or name C \ A or name C or name O or name CB )) or resid 62 or (resid 63 through 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 72)) selection = (chain 'T' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 or (resid 5 through 12 and (name N or name CA or name C o \ r name O or name CB )) or (resid 13 through 17 and (name N or name CA or name C \ or name O or name CB )) or (resid 18 through 21 and (name N or name CA or name C \ or name O or name CB )) or (resid 22 through 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 or (resid 28 and (name N or name CA or nam \ e C or name O or name CB )) or resid 29 through 39 or (resid 40 through 41 and ( \ name N or name CA or name C or name O or name CB )) or resid 42 or (resid 43 thr \ ough 46 and (name N or name CA or name C or name O or name CB )) or resid 47 thr \ ough 48 or (resid 49 through 50 and (name N or name CA or name C or name O or na \ me CB )) or (resid 51 through 61 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 62 through 70 and (name N or name CA or name C or name O or \ name CB )) or resid 71 through 72)) selection = (chain 'U' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 or (resid 5 through 12 and (name N or name CA or name C o \ r name O or name CB )) or resid 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or (resid 15 through 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 or (resid 25 through 26 and (name N or nam \ e CA or name C or name O or name CB )) or resid 27 or (resid 28 and (name N or n \ ame CA or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and \ (name N or name CA or name C or name O or name CB )) or resid 33 or (resid 34 t \ hrough 37 and (name N or name CA or name C or name O or name CB )) or resid 38 t \ hrough 42 or (resid 43 through 46 and (name N or name CA or name C or name O or \ name CB )) or resid 47 through 51 or (resid 52 through 61 and (name N or name CA \ or name C or name O or name CB )) or resid 62 or (resid 63 through 70 and (name \ N or name CA or name C or name O or name CB )) or resid 71 through 72)) } 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: 6.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.640 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 : 0.003 0.050 10884 Z= 0.139 Angle : 0.620 8.292 14993 Z= 0.321 Chirality : 0.043 0.271 1998 Planarity : 0.004 0.040 2023 Dihedral : 12.385 84.789 2908 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.61 % Favored : 98.34 % Rotamer: Outliers : 0.56 % Allowed : 47.19 % Favored : 52.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.35 (0.19), residues: 1805 helix: 3.48 (0.12), residues: 1583 sheet: -1.26 (0.76), residues: 51 loop : -2.53 (0.39), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 41 TYR 0.007 0.001 TYR D 45 PHE 0.042 0.002 PHE B 209 TRP 0.037 0.003 TRP A 54 HIS 0.002 0.001 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00293 (10884) covalent geometry : angle 0.61993 (14993) hydrogen bonds : bond 0.07665 ( 1308) hydrogen bonds : angle 3.59047 ( 3921) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 344 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 GLN cc_start: 0.9123 (mt0) cc_final: 0.8861 (mt0) REVERT: B 227 VAL cc_start: 0.9277 (t) cc_final: 0.9063 (p) REVERT: C 227 VAL cc_start: 0.9422 (t) cc_final: 0.9196 (t) REVERT: D 244 MET cc_start: 0.7383 (tpp) cc_final: 0.6889 (tpp) REVERT: E 67 PHE cc_start: 0.7440 (m-80) cc_final: 0.7093 (t80) REVERT: L 49 PHE cc_start: 0.8278 (m-80) cc_final: 0.7666 (m-10) REVERT: M 23 ASN cc_start: 0.8601 (m-40) cc_final: 0.8343 (p0) REVERT: M 49 PHE cc_start: 0.8939 (m-80) cc_final: 0.8251 (m-80) REVERT: O 45 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8137 (tp-100) REVERT: Q 29 ARG cc_start: 0.8223 (mmt180) cc_final: 0.7955 (mmt-90) REVERT: Q 49 PHE cc_start: 0.8949 (m-80) cc_final: 0.8244 (m-80) outliers start: 3 outliers final: 0 residues processed: 345 average time/residue: 0.0673 time to fit residues: 36.1862 Evaluate side-chains 289 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 120.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 50.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN L 45 GLN M 23 ASN ** O 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 GLN T 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.068566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.045316 restraints weight = 81327.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.046090 restraints weight = 57713.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.046671 restraints weight = 44518.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.047059 restraints weight = 36231.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.047392 restraints weight = 31170.832| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10884 Z= 0.243 Angle : 0.670 11.414 14993 Z= 0.368 Chirality : 0.044 0.229 1998 Planarity : 0.004 0.036 2023 Dihedral : 3.599 25.008 1879 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.11 % Favored : 97.78 % Rotamer: Outliers : 8.99 % Allowed : 38.76 % Favored : 52.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.94 (0.19), residues: 1805 helix: 3.21 (0.12), residues: 1583 sheet: -2.42 (0.79), residues: 36 loop : -2.42 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 41 TYR 0.015 0.002 TYR C 175 PHE 0.034 0.003 PHE B 219 TRP 0.019 0.001 TRP A 54 HIS 0.004 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00446 (10884) covalent geometry : angle 0.66956 (14993) hydrogen bonds : bond 0.04207 ( 1308) hydrogen bonds : angle 3.88955 ( 3921) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 294 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 GLN cc_start: 0.9026 (mt0) cc_final: 0.8806 (mt0) REVERT: B 227 VAL cc_start: 0.9412 (t) cc_final: 0.9132 (t) REVERT: D 45 TYR cc_start: 0.8467 (t80) cc_final: 0.8102 (t80) REVERT: D 126 PHE cc_start: 0.9092 (m-80) cc_final: 0.8693 (m-80) REVERT: D 185 GLU cc_start: 0.9482 (pt0) cc_final: 0.9234 (pp20) REVERT: D 244 MET cc_start: 0.7945 (tpp) cc_final: 0.6976 (tpp) REVERT: E 22 MET cc_start: 0.8503 (tpp) cc_final: 0.8254 (tpp) REVERT: L 45 GLN cc_start: 0.9739 (tp40) cc_final: 0.8704 (tp-100) REVERT: L 48 MET cc_start: 0.9164 (tpp) cc_final: 0.8683 (mtt) REVERT: L 49 PHE cc_start: 0.9118 (m-80) cc_final: 0.7963 (m-10) REVERT: M 23 ASN cc_start: 0.9748 (OUTLIER) cc_final: 0.9242 (p0) REVERT: N 27 VAL cc_start: 0.9762 (m) cc_final: 0.9540 (p) REVERT: O 17 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9187 (mm) REVERT: O 45 GLN cc_start: 0.9701 (mm-40) cc_final: 0.9154 (tp-100) REVERT: O 48 MET cc_start: 0.9469 (mmm) cc_final: 0.9059 (mmm) REVERT: Q 29 ARG cc_start: 0.9181 (mmt180) cc_final: 0.8961 (mmt-90) REVERT: Q 48 MET cc_start: 0.9561 (ppp) cc_final: 0.9313 (ppp) REVERT: Q 49 PHE cc_start: 0.9416 (m-80) cc_final: 0.8905 (m-80) REVERT: S 49 PHE cc_start: 0.9263 (m-80) cc_final: 0.8999 (m-80) outliers start: 48 outliers final: 29 residues processed: 310 average time/residue: 0.0616 time to fit residues: 30.9418 Evaluate side-chains 306 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 275 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain M residue 23 ASN Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain U residue 25 LEU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 2 optimal weight: 0.4980 chunk 93 optimal weight: 50.0000 chunk 115 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 12 optimal weight: 50.0000 chunk 70 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 51 optimal weight: 0.0020 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 45 GLN O 23 ASN ** S 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.096242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.076616 restraints weight = 80415.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.077928 restraints weight = 37797.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.078741 restraints weight = 21741.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.079236 restraints weight = 14435.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.079534 restraints weight = 10906.389| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10884 Z= 0.134 Angle : 0.642 11.765 14993 Z= 0.317 Chirality : 0.044 0.264 1998 Planarity : 0.004 0.040 2023 Dihedral : 3.414 24.623 1879 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.22 % Favored : 98.73 % Rotamer: Outliers : 6.37 % Allowed : 38.58 % Favored : 55.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.25 (0.19), residues: 1805 helix: 3.42 (0.12), residues: 1583 sheet: -1.79 (0.72), residues: 46 loop : -2.51 (0.39), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 41 TYR 0.014 0.001 TYR D 220 PHE 0.041 0.002 PHE T 49 TRP 0.015 0.001 TRP A 54 HIS 0.001 0.000 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00261 (10884) covalent geometry : angle 0.64238 (14993) hydrogen bonds : bond 0.03994 ( 1308) hydrogen bonds : angle 3.37654 ( 3921) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 297 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8074 (p0) cc_final: 0.7843 (p0) REVERT: B 207 GLN cc_start: 0.8968 (mt0) cc_final: 0.8738 (mt0) REVERT: D 45 TYR cc_start: 0.8338 (t80) cc_final: 0.7900 (t80) REVERT: D 126 PHE cc_start: 0.9071 (m-80) cc_final: 0.8661 (m-10) REVERT: D 185 GLU cc_start: 0.9471 (pt0) cc_final: 0.9262 (pp20) REVERT: D 244 MET cc_start: 0.7648 (tpp) cc_final: 0.6881 (tpp) REVERT: E 22 MET cc_start: 0.8586 (tpp) cc_final: 0.8277 (tpp) REVERT: L 44 LEU cc_start: 0.9838 (mt) cc_final: 0.9611 (pp) REVERT: L 45 GLN cc_start: 0.9766 (tp40) cc_final: 0.9355 (tp-100) REVERT: L 49 PHE cc_start: 0.9003 (m-80) cc_final: 0.8088 (m-10) REVERT: M 23 ASN cc_start: 0.9622 (m-40) cc_final: 0.9282 (p0) REVERT: M 48 MET cc_start: 0.9523 (tmm) cc_final: 0.9274 (ptt) REVERT: M 49 PHE cc_start: 0.9543 (m-80) cc_final: 0.9286 (m-80) REVERT: O 17 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9268 (mm) REVERT: O 44 LEU cc_start: 0.9603 (mt) cc_final: 0.8930 (pp) REVERT: O 45 GLN cc_start: 0.9682 (mm-40) cc_final: 0.9244 (tp-100) REVERT: O 48 MET cc_start: 0.9558 (mmm) cc_final: 0.9078 (mmm) REVERT: P 48 MET cc_start: 0.9797 (ttt) cc_final: 0.9494 (tmm) REVERT: Q 48 MET cc_start: 0.9563 (ppp) cc_final: 0.9299 (ppp) REVERT: Q 49 PHE cc_start: 0.9419 (m-80) cc_final: 0.8923 (m-80) REVERT: S 49 PHE cc_start: 0.9289 (m-80) cc_final: 0.8920 (m-80) REVERT: T 49 PHE cc_start: 0.9221 (m-80) cc_final: 0.9020 (m-80) outliers start: 34 outliers final: 14 residues processed: 314 average time/residue: 0.0658 time to fit residues: 32.7539 Evaluate side-chains 295 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 280 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain S residue 30 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 130 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 1 optimal weight: 0.0270 chunk 7 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 12 optimal weight: 50.0000 chunk 108 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 97 optimal weight: 40.0000 overall best weight: 1.6244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 45 GLN ** S 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.095669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.076778 restraints weight = 81469.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.077612 restraints weight = 43192.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.078933 restraints weight = 22037.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.078815 restraints weight = 12947.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.078897 restraints weight = 12273.174| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10884 Z= 0.129 Angle : 0.653 12.029 14993 Z= 0.320 Chirality : 0.045 0.333 1998 Planarity : 0.004 0.053 2023 Dihedral : 3.366 24.077 1879 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.33 % Favored : 98.61 % Rotamer: Outliers : 4.31 % Allowed : 41.20 % Favored : 54.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.31 (0.19), residues: 1805 helix: 3.46 (0.12), residues: 1583 sheet: -2.07 (0.68), residues: 46 loop : -2.33 (0.41), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 139 TYR 0.018 0.001 TYR B 85 PHE 0.035 0.002 PHE T 49 TRP 0.014 0.001 TRP A 54 HIS 0.001 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00268 (10884) covalent geometry : angle 0.65318 (14993) hydrogen bonds : bond 0.03768 ( 1308) hydrogen bonds : angle 3.35391 ( 3921) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 296 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 GLN cc_start: 0.9021 (mt0) cc_final: 0.8784 (mt0) REVERT: D 45 TYR cc_start: 0.8512 (t80) cc_final: 0.8003 (t80) REVERT: D 126 PHE cc_start: 0.9027 (m-80) cc_final: 0.8751 (m-80) REVERT: D 244 MET cc_start: 0.7733 (tpp) cc_final: 0.7027 (tpp) REVERT: E 22 MET cc_start: 0.8385 (tpp) cc_final: 0.8103 (tpp) REVERT: L 45 GLN cc_start: 0.9690 (tp40) cc_final: 0.9155 (tp-100) REVERT: L 49 PHE cc_start: 0.8868 (m-80) cc_final: 0.8101 (m-10) REVERT: M 49 PHE cc_start: 0.9393 (m-80) cc_final: 0.9115 (m-80) REVERT: O 17 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9256 (mm) REVERT: O 45 GLN cc_start: 0.9591 (mm-40) cc_final: 0.8734 (tp-100) REVERT: O 48 MET cc_start: 0.9412 (mmm) cc_final: 0.9005 (mmm) REVERT: O 49 PHE cc_start: 0.9382 (m-80) cc_final: 0.8682 (m-80) REVERT: P 48 MET cc_start: 0.9713 (ttt) cc_final: 0.9403 (tmm) REVERT: Q 48 MET cc_start: 0.9486 (ppp) cc_final: 0.9190 (ppp) REVERT: Q 49 PHE cc_start: 0.9403 (m-80) cc_final: 0.8761 (m-80) REVERT: S 49 PHE cc_start: 0.9208 (m-80) cc_final: 0.8813 (m-80) REVERT: T 49 PHE cc_start: 0.9153 (m-80) cc_final: 0.8872 (m-80) outliers start: 23 outliers final: 14 residues processed: 306 average time/residue: 0.0669 time to fit residues: 32.7829 Evaluate side-chains 296 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 281 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain Q residue 5 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 118 optimal weight: 20.0000 chunk 78 optimal weight: 50.0000 chunk 14 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 45 optimal weight: 0.0060 chunk 30 optimal weight: 9.9990 chunk 104 optimal weight: 50.0000 chunk 110 optimal weight: 6.9990 chunk 7 optimal weight: 40.0000 chunk 21 optimal weight: 0.0170 overall best weight: 4.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.069366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.045806 restraints weight = 80234.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046642 restraints weight = 56351.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.047252 restraints weight = 42947.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.047702 restraints weight = 34777.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.048067 restraints weight = 29491.591| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10884 Z= 0.175 Angle : 0.666 12.218 14993 Z= 0.345 Chirality : 0.045 0.393 1998 Planarity : 0.004 0.043 2023 Dihedral : 3.452 23.759 1879 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.50 % Favored : 98.45 % Rotamer: Outliers : 6.55 % Allowed : 43.07 % Favored : 50.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.21 (0.20), residues: 1805 helix: 3.39 (0.12), residues: 1582 sheet: -2.32 (0.78), residues: 36 loop : -2.28 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 41 TYR 0.015 0.001 TYR B 85 PHE 0.041 0.002 PHE R 49 TRP 0.023 0.002 TRP A 54 HIS 0.003 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00339 (10884) covalent geometry : angle 0.66582 (14993) hydrogen bonds : bond 0.03865 ( 1308) hydrogen bonds : angle 3.58428 ( 3921) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 GLN cc_start: 0.9024 (mt0) cc_final: 0.8801 (mt0) REVERT: D 126 PHE cc_start: 0.9215 (m-80) cc_final: 0.8802 (m-10) REVERT: D 170 MET cc_start: 0.9410 (mpp) cc_final: 0.8926 (pmm) REVERT: D 244 MET cc_start: 0.7921 (tpp) cc_final: 0.7066 (tpp) REVERT: L 45 GLN cc_start: 0.9749 (tp40) cc_final: 0.8826 (tp-100) REVERT: L 48 MET cc_start: 0.9181 (mmt) cc_final: 0.8721 (mmm) REVERT: L 49 PHE cc_start: 0.9002 (m-80) cc_final: 0.7990 (m-80) REVERT: M 23 ASN cc_start: 0.9724 (m110) cc_final: 0.9323 (p0) REVERT: M 48 MET cc_start: 0.9285 (ptt) cc_final: 0.8849 (ptt) REVERT: M 49 PHE cc_start: 0.9555 (m-80) cc_final: 0.9241 (m-80) REVERT: O 45 GLN cc_start: 0.9630 (mm-40) cc_final: 0.8867 (tp-100) REVERT: O 48 MET cc_start: 0.9448 (mmm) cc_final: 0.9080 (mmm) REVERT: O 49 PHE cc_start: 0.9408 (m-80) cc_final: 0.8685 (m-80) REVERT: P 48 MET cc_start: 0.9749 (ttt) cc_final: 0.9429 (tmm) REVERT: Q 48 MET cc_start: 0.9542 (ppp) cc_final: 0.9195 (ppp) REVERT: Q 49 PHE cc_start: 0.9430 (m-80) cc_final: 0.8811 (m-80) REVERT: R 49 PHE cc_start: 0.8936 (m-80) cc_final: 0.8717 (m-80) REVERT: S 48 MET cc_start: 0.9571 (ttp) cc_final: 0.9212 (mmm) REVERT: S 49 PHE cc_start: 0.9258 (m-80) cc_final: 0.8810 (m-80) REVERT: T 49 PHE cc_start: 0.9235 (m-80) cc_final: 0.8937 (m-80) outliers start: 35 outliers final: 26 residues processed: 299 average time/residue: 0.0605 time to fit residues: 29.9832 Evaluate side-chains 298 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 272 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 25 LEU Chi-restraints excluded: chain U residue 54 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 170 optimal weight: 8.9990 chunk 39 optimal weight: 0.0370 chunk 43 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 94 optimal weight: 50.0000 chunk 92 optimal weight: 6.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 35 ASN ** S 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.094162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.074534 restraints weight = 81435.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.075827 restraints weight = 38342.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.076620 restraints weight = 22100.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.077130 restraints weight = 14791.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.077412 restraints weight = 11172.241| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10884 Z= 0.135 Angle : 0.711 14.673 14993 Z= 0.343 Chirality : 0.046 0.336 1998 Planarity : 0.004 0.046 2023 Dihedral : 3.400 22.927 1879 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.27 % Favored : 98.67 % Rotamer: Outliers : 5.06 % Allowed : 46.07 % Favored : 48.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.30 (0.19), residues: 1805 helix: 3.44 (0.12), residues: 1582 sheet: -1.55 (0.69), residues: 51 loop : -2.39 (0.42), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 41 TYR 0.012 0.001 TYR D 45 PHE 0.041 0.002 PHE R 49 TRP 0.015 0.001 TRP A 54 HIS 0.002 0.000 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00278 (10884) covalent geometry : angle 0.71094 (14993) hydrogen bonds : bond 0.03804 ( 1308) hydrogen bonds : angle 3.46482 ( 3921) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 284 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 GLN cc_start: 0.8966 (mt0) cc_final: 0.8749 (mt0) REVERT: D 126 PHE cc_start: 0.9259 (m-80) cc_final: 0.8880 (m-10) REVERT: D 170 MET cc_start: 0.9295 (mpp) cc_final: 0.8893 (pmm) REVERT: D 244 MET cc_start: 0.7699 (tpp) cc_final: 0.6893 (tpp) REVERT: L 45 GLN cc_start: 0.9787 (tp40) cc_final: 0.9063 (tp-100) REVERT: L 48 MET cc_start: 0.9180 (mmt) cc_final: 0.8727 (mmm) REVERT: L 49 PHE cc_start: 0.9029 (m-80) cc_final: 0.8001 (m-80) REVERT: M 23 ASN cc_start: 0.9779 (m110) cc_final: 0.9427 (p0) REVERT: M 48 MET cc_start: 0.9248 (ptt) cc_final: 0.8740 (ptt) REVERT: M 49 PHE cc_start: 0.9626 (m-80) cc_final: 0.9328 (m-80) REVERT: N 21 ILE cc_start: 0.9582 (mm) cc_final: 0.9270 (pt) REVERT: O 44 LEU cc_start: 0.9635 (mt) cc_final: 0.8964 (pp) REVERT: O 45 GLN cc_start: 0.9646 (mm-40) cc_final: 0.9177 (tp-100) REVERT: O 48 MET cc_start: 0.9630 (mmm) cc_final: 0.9197 (mmm) REVERT: O 49 PHE cc_start: 0.9370 (m-80) cc_final: 0.8752 (m-10) REVERT: P 48 MET cc_start: 0.9794 (ttt) cc_final: 0.9469 (tmm) REVERT: Q 48 MET cc_start: 0.9580 (ppp) cc_final: 0.9297 (ppp) REVERT: Q 49 PHE cc_start: 0.9425 (m-80) cc_final: 0.8913 (m-80) REVERT: R 58 LEU cc_start: 0.9764 (mm) cc_final: 0.9472 (pp) REVERT: S 49 PHE cc_start: 0.9388 (m-80) cc_final: 0.8970 (m-80) REVERT: T 49 PHE cc_start: 0.9326 (m-80) cc_final: 0.8997 (m-80) outliers start: 27 outliers final: 22 residues processed: 298 average time/residue: 0.0617 time to fit residues: 30.0239 Evaluate side-chains 296 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 274 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 14 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 177 optimal weight: 8.9990 chunk 101 optimal weight: 50.0000 chunk 128 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.069160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.045683 restraints weight = 80891.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.046516 restraints weight = 56793.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.047144 restraints weight = 43315.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.047603 restraints weight = 34999.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.047930 restraints weight = 29614.327| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10884 Z= 0.169 Angle : 0.721 14.541 14993 Z= 0.358 Chirality : 0.046 0.357 1998 Planarity : 0.004 0.075 2023 Dihedral : 3.480 22.609 1879 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.66 % Favored : 98.28 % Rotamer: Outliers : 5.99 % Allowed : 46.63 % Favored : 47.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.24 (0.19), residues: 1805 helix: 3.40 (0.12), residues: 1582 sheet: -2.00 (0.76), residues: 36 loop : -2.24 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 139 TYR 0.015 0.001 TYR D 45 PHE 0.053 0.002 PHE R 49 TRP 0.013 0.001 TRP A 54 HIS 0.003 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00342 (10884) covalent geometry : angle 0.72145 (14993) hydrogen bonds : bond 0.03859 ( 1308) hydrogen bonds : angle 3.63344 ( 3921) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 283 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 207 GLN cc_start: 0.9006 (mt0) cc_final: 0.8779 (mt0) REVERT: D 126 PHE cc_start: 0.9253 (m-80) cc_final: 0.8906 (m-80) REVERT: D 244 MET cc_start: 0.7961 (tpp) cc_final: 0.7096 (tpp) REVERT: E 22 MET cc_start: 0.8590 (mpp) cc_final: 0.8111 (tpt) REVERT: L 45 GLN cc_start: 0.9775 (tp40) cc_final: 0.8788 (tp-100) REVERT: L 49 PHE cc_start: 0.9003 (m-80) cc_final: 0.7941 (m-80) REVERT: M 48 MET cc_start: 0.9256 (ptt) cc_final: 0.8710 (ptt) REVERT: M 49 PHE cc_start: 0.9560 (m-80) cc_final: 0.9265 (m-80) REVERT: O 45 GLN cc_start: 0.9624 (mm-40) cc_final: 0.9164 (tp-100) REVERT: O 48 MET cc_start: 0.9494 (mmm) cc_final: 0.9160 (mmm) REVERT: P 48 MET cc_start: 0.9758 (OUTLIER) cc_final: 0.9416 (tmm) REVERT: Q 48 MET cc_start: 0.9540 (ppp) cc_final: 0.9207 (ppp) REVERT: Q 49 PHE cc_start: 0.9435 (m-80) cc_final: 0.8746 (m-80) REVERT: S 48 MET cc_start: 0.9570 (ttp) cc_final: 0.9198 (mmm) REVERT: S 49 PHE cc_start: 0.9295 (m-80) cc_final: 0.8813 (m-80) REVERT: T 49 PHE cc_start: 0.9286 (m-80) cc_final: 0.8933 (m-80) outliers start: 32 outliers final: 26 residues processed: 300 average time/residue: 0.0627 time to fit residues: 30.6519 Evaluate side-chains 300 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 273 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain P residue 48 MET Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 54 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 132 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.070354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.046634 restraints weight = 79568.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.047509 restraints weight = 55684.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.048142 restraints weight = 42215.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.048631 restraints weight = 34151.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.049005 restraints weight = 28850.977| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10884 Z= 0.138 Angle : 0.757 16.376 14993 Z= 0.359 Chirality : 0.047 0.351 1998 Planarity : 0.004 0.049 2023 Dihedral : 3.445 22.190 1879 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.27 % Favored : 98.67 % Rotamer: Outliers : 5.62 % Allowed : 47.19 % Favored : 47.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.30 (0.19), residues: 1805 helix: 3.42 (0.12), residues: 1582 sheet: -1.00 (0.71), residues: 49 loop : -2.30 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 41 TYR 0.009 0.001 TYR D 45 PHE 0.033 0.002 PHE B 209 TRP 0.012 0.001 TRP A 54 HIS 0.001 0.000 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00291 (10884) covalent geometry : angle 0.75686 (14993) hydrogen bonds : bond 0.03815 ( 1308) hydrogen bonds : angle 3.52311 ( 3921) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 279 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 GLN cc_start: 0.8926 (mt0) cc_final: 0.8719 (mt0) REVERT: D 126 PHE cc_start: 0.9301 (m-80) cc_final: 0.8909 (m-10) REVERT: D 244 MET cc_start: 0.7931 (tpp) cc_final: 0.7063 (tpp) REVERT: L 45 GLN cc_start: 0.9804 (tp40) cc_final: 0.9209 (tp-100) REVERT: L 49 PHE cc_start: 0.9000 (m-80) cc_final: 0.8190 (m-80) REVERT: M 23 ASN cc_start: 0.9785 (m110) cc_final: 0.9461 (p0) REVERT: M 48 MET cc_start: 0.9222 (ptt) cc_final: 0.8693 (ptt) REVERT: M 49 PHE cc_start: 0.9628 (m-80) cc_final: 0.9326 (m-80) REVERT: N 17 LEU cc_start: 0.9711 (mm) cc_final: 0.9501 (mm) REVERT: N 21 ILE cc_start: 0.9482 (mm) cc_final: 0.9119 (pt) REVERT: O 17 LEU cc_start: 0.9372 (pp) cc_final: 0.8937 (tt) REVERT: O 41 ARG cc_start: 0.8669 (ttp80) cc_final: 0.8437 (ttp80) REVERT: O 44 LEU cc_start: 0.9641 (mt) cc_final: 0.8977 (pp) REVERT: O 45 GLN cc_start: 0.9759 (mm-40) cc_final: 0.9350 (tp-100) REVERT: O 48 MET cc_start: 0.9614 (mmm) cc_final: 0.9227 (mmm) REVERT: P 48 MET cc_start: 0.9787 (ttt) cc_final: 0.9539 (tmm) REVERT: Q 48 MET cc_start: 0.9570 (ppp) cc_final: 0.9281 (ppp) REVERT: Q 49 PHE cc_start: 0.9430 (m-80) cc_final: 0.8839 (m-80) REVERT: R 58 LEU cc_start: 0.9734 (mm) cc_final: 0.9435 (pp) REVERT: S 49 PHE cc_start: 0.9419 (m-80) cc_final: 0.8982 (m-80) REVERT: T 49 PHE cc_start: 0.9391 (m-80) cc_final: 0.9062 (m-80) outliers start: 30 outliers final: 23 residues processed: 295 average time/residue: 0.0604 time to fit residues: 29.6420 Evaluate side-chains 298 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 275 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 14 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 164 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 176 optimal weight: 0.0050 chunk 58 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 32 optimal weight: 80.0000 chunk 90 optimal weight: 30.0000 chunk 131 optimal weight: 20.0000 chunk 95 optimal weight: 50.0000 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.091110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.071374 restraints weight = 82324.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.072660 restraints weight = 38601.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.073458 restraints weight = 22331.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.073949 restraints weight = 14944.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 69)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.074222 restraints weight = 11365.334| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10884 Z= 0.174 Angle : 0.756 15.629 14993 Z= 0.373 Chirality : 0.047 0.379 1998 Planarity : 0.004 0.048 2023 Dihedral : 3.514 21.930 1879 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.72 % Favored : 98.23 % Rotamer: Outliers : 5.62 % Allowed : 47.19 % Favored : 47.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.17 (0.19), residues: 1805 helix: 3.34 (0.12), residues: 1582 sheet: -1.58 (0.75), residues: 36 loop : -2.22 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 41 TYR 0.019 0.001 TYR D 172 PHE 0.022 0.002 PHE D 165 TRP 0.011 0.001 TRP A 54 HIS 0.003 0.001 HIS D 174 Details of bonding type rmsd covalent geometry : bond 0.00355 (10884) covalent geometry : angle 0.75570 (14993) hydrogen bonds : bond 0.03936 ( 1308) hydrogen bonds : angle 3.71745 ( 3921) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 272 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 207 GLN cc_start: 0.8959 (mt0) cc_final: 0.8732 (mt0) REVERT: D 126 PHE cc_start: 0.9353 (m-80) cc_final: 0.9016 (m-80) REVERT: D 165 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8225 (t80) REVERT: D 244 MET cc_start: 0.7775 (tpp) cc_final: 0.6963 (tpp) REVERT: L 45 GLN cc_start: 0.9815 (tp40) cc_final: 0.9193 (tp-100) REVERT: L 49 PHE cc_start: 0.9033 (m-80) cc_final: 0.8199 (m-80) REVERT: M 23 ASN cc_start: 0.9779 (m110) cc_final: 0.9471 (p0) REVERT: M 48 MET cc_start: 0.9243 (ptt) cc_final: 0.8713 (ptt) REVERT: M 49 PHE cc_start: 0.9621 (m-80) cc_final: 0.9321 (m-80) REVERT: N 21 ILE cc_start: 0.9550 (mm) cc_final: 0.9205 (pt) REVERT: O 17 LEU cc_start: 0.9406 (pp) cc_final: 0.9024 (tt) REVERT: O 45 GLN cc_start: 0.9734 (mm-40) cc_final: 0.9230 (tp-100) REVERT: O 48 MET cc_start: 0.9624 (mmm) cc_final: 0.9301 (mmm) REVERT: P 48 MET cc_start: 0.9810 (OUTLIER) cc_final: 0.9498 (tmm) REVERT: Q 48 MET cc_start: 0.9578 (ppp) cc_final: 0.9296 (ppp) REVERT: Q 49 PHE cc_start: 0.9422 (m-80) cc_final: 0.8823 (m-80) REVERT: S 48 MET cc_start: 0.9762 (ttp) cc_final: 0.9254 (mmm) REVERT: S 49 PHE cc_start: 0.9452 (m-80) cc_final: 0.9004 (m-80) REVERT: T 49 PHE cc_start: 0.9415 (m-80) cc_final: 0.9080 (m-80) outliers start: 30 outliers final: 25 residues processed: 287 average time/residue: 0.0561 time to fit residues: 27.0643 Evaluate side-chains 296 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 269 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain P residue 48 MET Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 14 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 121 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 158 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 163 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.094617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.075333 restraints weight = 81058.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.076636 restraints weight = 38341.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.077457 restraints weight = 22207.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.077932 restraints weight = 14905.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.078184 restraints weight = 11334.534| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10884 Z= 0.137 Angle : 0.806 17.434 14993 Z= 0.374 Chirality : 0.049 0.404 1998 Planarity : 0.004 0.052 2023 Dihedral : 3.407 21.276 1879 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.22 % Favored : 98.73 % Rotamer: Outliers : 3.93 % Allowed : 49.25 % Favored : 46.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.24 (0.19), residues: 1805 helix: 3.36 (0.12), residues: 1582 sheet: -0.96 (0.69), residues: 46 loop : -2.19 (0.44), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 41 TYR 0.008 0.001 TYR D 226 PHE 0.032 0.001 PHE B 209 TRP 0.012 0.001 TRP A 54 HIS 0.000 0.000 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00281 (10884) covalent geometry : angle 0.80551 (14993) hydrogen bonds : bond 0.03782 ( 1308) hydrogen bonds : angle 3.51731 ( 3921) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 282 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 GLN cc_start: 0.8935 (mt0) cc_final: 0.8697 (mt0) REVERT: D 67 MET cc_start: 0.9641 (ptp) cc_final: 0.8683 (ppp) REVERT: D 126 PHE cc_start: 0.9298 (m-80) cc_final: 0.8946 (m-80) REVERT: D 165 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.7966 (t80) REVERT: D 244 MET cc_start: 0.7731 (tpp) cc_final: 0.6956 (tpp) REVERT: L 45 GLN cc_start: 0.9795 (tp40) cc_final: 0.9162 (tp-100) REVERT: L 49 PHE cc_start: 0.8951 (m-80) cc_final: 0.8142 (m-80) REVERT: M 23 ASN cc_start: 0.9744 (m110) cc_final: 0.9463 (p0) REVERT: M 48 MET cc_start: 0.9206 (ptt) cc_final: 0.8702 (ptt) REVERT: M 49 PHE cc_start: 0.9634 (m-80) cc_final: 0.9327 (m-80) REVERT: N 21 ILE cc_start: 0.9489 (mm) cc_final: 0.9143 (pt) REVERT: O 41 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8435 (ttp80) REVERT: O 44 LEU cc_start: 0.9651 (mt) cc_final: 0.9003 (pp) REVERT: O 45 GLN cc_start: 0.9719 (mm-40) cc_final: 0.9313 (tp-100) REVERT: O 48 MET cc_start: 0.9632 (mmm) cc_final: 0.9273 (mmm) REVERT: P 48 MET cc_start: 0.9788 (OUTLIER) cc_final: 0.9538 (tmm) REVERT: Q 48 MET cc_start: 0.9548 (ppp) cc_final: 0.9271 (ppp) REVERT: Q 49 PHE cc_start: 0.9412 (m-80) cc_final: 0.8831 (m-80) REVERT: R 58 LEU cc_start: 0.9736 (mm) cc_final: 0.9422 (pp) REVERT: S 49 PHE cc_start: 0.9463 (m-80) cc_final: 0.9032 (m-80) REVERT: T 49 PHE cc_start: 0.9416 (m-80) cc_final: 0.9076 (m-80) outliers start: 21 outliers final: 16 residues processed: 295 average time/residue: 0.0594 time to fit residues: 28.7344 Evaluate side-chains 295 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 277 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 165 PHE Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain P residue 48 MET Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 14 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 172 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 144 optimal weight: 0.0870 chunk 56 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 32 optimal weight: 80.0000 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.071204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.047526 restraints weight = 80061.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.048419 restraints weight = 55814.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.049094 restraints weight = 42225.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.049603 restraints weight = 33996.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.049982 restraints weight = 28671.497| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10884 Z= 0.134 Angle : 0.800 17.173 14993 Z= 0.372 Chirality : 0.049 0.393 1998 Planarity : 0.004 0.051 2023 Dihedral : 3.335 20.802 1879 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.44 % Favored : 98.50 % Rotamer: Outliers : 3.37 % Allowed : 50.37 % Favored : 46.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.28 (0.19), residues: 1805 helix: 3.39 (0.12), residues: 1577 sheet: -0.90 (0.62), residues: 56 loop : -2.06 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 139 TYR 0.017 0.001 TYR D 172 PHE 0.026 0.002 PHE D 205 TRP 0.012 0.001 TRP A 54 HIS 0.001 0.000 HIS D 174 Details of bonding type rmsd covalent geometry : bond 0.00279 (10884) covalent geometry : angle 0.79980 (14993) hydrogen bonds : bond 0.03633 ( 1308) hydrogen bonds : angle 3.49939 ( 3921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2258.07 seconds wall clock time: 39 minutes 21.20 seconds (2361.20 seconds total)