Starting phenix.real_space_refine on Mon Jul 28 21:48:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jc2_61340/07_2025/9jc2_61340_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jc2_61340/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jc2_61340/07_2025/9jc2_61340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jc2_61340/07_2025/9jc2_61340.map" model { file = "/net/cci-nas-00/data/ceres_data/9jc2_61340/07_2025/9jc2_61340_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jc2_61340/07_2025/9jc2_61340_neut.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 8, 'GLU:plan': 4, 'ARG:plan': 5} 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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 4, 'ARG:plan': 5} 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: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 9, 'GLU:plan': 4, 'ARG:plan': 5} 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: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 10} 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: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 2, 'ARG:plan': 1, 'HIS: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: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 5} 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: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} 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: {'GLN:plan1': 6, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 5} 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: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} 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: {'GLN:plan1': 6, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 5} 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: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} 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: {'PHE:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, '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: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG: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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG: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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLU:plan': 2, '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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} 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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'PHE:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 10.04, per 1000 atoms: 0.93 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: 3.22 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.04 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: 3.93 Time building geometry restraints manager: 3.79 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: 95.800 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.580 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.210 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.35 (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 TRP 0.037 0.003 TRP A 54 HIS 0.002 0.001 HIS A 190 PHE 0.042 0.002 PHE B 209 TYR 0.007 0.001 TYR D 45 ARG 0.006 0.001 ARG M 41 Details of bonding type rmsd hydrogen bonds : bond 0.07665 ( 1308) hydrogen bonds : angle 3.59047 ( 3921) covalent geometry : bond 0.00293 (10884) covalent geometry : angle 0.61993 (14993) *********************** 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 : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 GLN cc_start: 0.9123 (mt0) cc_final: 0.8861 (mt0) 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: 0.6984 (tpp) REVERT: E 67 PHE cc_start: 0.7440 (m-80) cc_final: 0.7092 (t80) REVERT: M 23 ASN cc_start: 0.8601 (m-40) cc_final: 0.8344 (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: 0.8242 (m-80) outliers start: 3 outliers final: 0 residues processed: 345 average time/residue: 0.1749 time to fit residues: 93.8097 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 : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 0.0070 chunk 105 optimal weight: 80.0000 chunk 164 optimal weight: 0.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.072855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.048532 restraints weight = 77175.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.049423 restraints weight = 54076.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.050056 restraints weight = 41102.418| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1627 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= 0.142 Angle : 0.632 11.409 14993 Z= 0.320 Chirality : 0.044 0.246 1998 Planarity : 0.004 0.038 2023 Dihedral : 3.297 24.883 1879 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.50 % Favored : 98.45 % Rotamer: Outliers : 5.62 % Allowed : 38.39 % Favored : 55.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.34 (0.19), residues: 1805 helix: 3.49 (0.12), residues: 1582 sheet: -2.26 (0.82), residues: 36 loop : -2.44 (0.37), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 54 HIS 0.002 0.001 HIS D 65 PHE 0.039 0.002 PHE O 49 TYR 0.017 0.001 TYR C 175 ARG 0.008 0.001 ARG L 41 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 1308) hydrogen bonds : angle 3.42494 ( 3921) covalent geometry : bond 0.00279 (10884) covalent geometry : angle 0.63230 (14993) *********************** 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 334 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 304 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 GLN cc_start: 0.9013 (mt0) cc_final: 0.8790 (mt0) REVERT: D 45 TYR cc_start: 0.8278 (t80) cc_final: 0.7921 (t80) REVERT: D 185 GLU cc_start: 0.9521 (pt0) cc_final: 0.9063 (pp20) REVERT: D 244 MET cc_start: 0.7955 (tpp) cc_final: 0.7177 (tpp) REVERT: E 26 LYS cc_start: 0.9249 (tptp) cc_final: 0.8953 (tptp) REVERT: L 44 LEU cc_start: 0.9839 (mt) cc_final: 0.9597 (pp) REVERT: L 45 GLN cc_start: 0.9679 (tp40) cc_final: 0.9115 (tp-100) REVERT: L 49 PHE cc_start: 0.8912 (m-80) cc_final: 0.7874 (m-10) REVERT: M 23 ASN cc_start: 0.9613 (m110) cc_final: 0.9104 (p0) REVERT: N 27 VAL cc_start: 0.9743 (m) cc_final: 0.9489 (p) REVERT: N 41 ARG cc_start: 0.9165 (ttp80) cc_final: 0.8890 (ttp80) REVERT: O 17 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9178 (mm) REVERT: O 44 LEU cc_start: 0.9575 (mt) cc_final: 0.9033 (pp) REVERT: O 45 GLN cc_start: 0.9627 (mm-40) cc_final: 0.9129 (tp-100) REVERT: O 48 MET cc_start: 0.9343 (mmm) cc_final: 0.8944 (mmm) REVERT: P 27 VAL cc_start: 0.9748 (t) cc_final: 0.9524 (p) REVERT: Q 48 MET cc_start: 0.9505 (ppp) cc_final: 0.9236 (ppp) REVERT: Q 49 PHE cc_start: 0.9355 (m-80) cc_final: 0.8844 (m-80) REVERT: S 49 PHE cc_start: 0.9143 (m-80) cc_final: 0.8888 (m-80) REVERT: T 49 PHE cc_start: 0.9198 (m-80) cc_final: 0.8953 (m-80) outliers start: 30 outliers final: 13 residues processed: 315 average time/residue: 0.1567 time to fit residues: 77.2875 Evaluate side-chains 296 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 282 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 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 M residue 45 GLN Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain U residue 25 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 135 optimal weight: 0.4980 chunk 128 optimal weight: 3.9990 chunk 26 optimal weight: 30.0000 chunk 117 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 102 optimal weight: 50.0000 chunk 108 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 23 ASN ** S 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.096934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.077191 restraints weight = 80268.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.078501 restraints weight = 38048.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.079304 restraints weight = 21985.386| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10884 Z= 0.136 Angle : 0.628 10.942 14993 Z= 0.316 Chirality : 0.043 0.216 1998 Planarity : 0.004 0.040 2023 Dihedral : 3.315 24.451 1879 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.39 % Favored : 98.56 % Rotamer: Outliers : 5.81 % Allowed : 37.45 % Favored : 56.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.41 (0.19), residues: 1805 helix: 3.53 (0.12), residues: 1582 sheet: -2.34 (0.77), residues: 36 loop : -2.27 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 54 HIS 0.001 0.001 HIS D 65 PHE 0.040 0.002 PHE A 219 TYR 0.017 0.001 TYR B 85 ARG 0.005 0.001 ARG L 41 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 1308) hydrogen bonds : angle 3.37265 ( 3921) covalent geometry : bond 0.00279 (10884) covalent geometry : angle 0.62808 (14993) *********************** 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 328 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 297 time to evaluate : 1.333 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: 0.8956 (mt0) cc_final: 0.8720 (mt0) REVERT: D 45 TYR cc_start: 0.8289 (t80) cc_final: 0.7863 (t80) REVERT: D 185 GLU cc_start: 0.9524 (pt0) cc_final: 0.9206 (pp20) REVERT: D 244 MET cc_start: 0.7700 (tpp) cc_final: 0.6973 (tpp) REVERT: E 32 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8150 (mm) REVERT: L 45 GLN cc_start: 0.9754 (tp40) cc_final: 0.8925 (tp-100) REVERT: L 48 MET cc_start: 0.8969 (mmt) cc_final: 0.8528 (mmm) REVERT: L 49 PHE cc_start: 0.8987 (m-80) cc_final: 0.7966 (m-80) REVERT: M 23 ASN cc_start: 0.9706 (m110) cc_final: 0.9242 (p0) REVERT: M 48 MET cc_start: 0.9631 (tmm) cc_final: 0.9354 (ptt) REVERT: N 27 VAL cc_start: 0.9686 (m) cc_final: 0.9477 (p) REVERT: O 17 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9263 (mm) REVERT: O 45 GLN cc_start: 0.9684 (mm-40) cc_final: 0.9195 (tp-100) REVERT: O 48 MET cc_start: 0.9558 (mmm) cc_final: 0.9129 (mmm) REVERT: P 27 VAL cc_start: 0.9670 (t) cc_final: 0.9348 (p) REVERT: Q 48 MET cc_start: 0.9542 (ppp) cc_final: 0.9325 (ppp) REVERT: Q 49 PHE cc_start: 0.9404 (m-80) cc_final: 0.8942 (m-80) REVERT: S 49 PHE cc_start: 0.9262 (m-80) cc_final: 0.8908 (m-80) REVERT: T 29 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8216 (mmt-90) REVERT: T 49 PHE cc_start: 0.9251 (m-80) cc_final: 0.9002 (m-80) outliers start: 31 outliers final: 13 residues processed: 313 average time/residue: 0.1651 time to fit residues: 81.9042 Evaluate side-chains 295 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 279 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 123 LEU Chi-restraints excluded: chain D residue 145 SER 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 32 LEU 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 50 ILE Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain T residue 29 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 121 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 50.0000 chunk 55 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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** T 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.093877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.074070 restraints weight = 81348.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.075369 restraints weight = 38488.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.076165 restraints weight = 22247.733| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10884 Z= 0.166 Angle : 0.639 11.230 14993 Z= 0.330 Chirality : 0.045 0.308 1998 Planarity : 0.004 0.057 2023 Dihedral : 3.368 24.201 1879 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.55 % Favored : 98.39 % Rotamer: Outliers : 8.05 % Allowed : 41.01 % Favored : 50.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.32 (0.19), residues: 1805 helix: 3.46 (0.12), residues: 1582 sheet: -2.22 (0.64), residues: 46 loop : -2.18 (0.41), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 54 HIS 0.002 0.001 HIS D 65 PHE 0.039 0.002 PHE M 49 TYR 0.013 0.001 TYR B 85 ARG 0.013 0.001 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 1308) hydrogen bonds : angle 3.51010 ( 3921) covalent geometry : bond 0.00332 (10884) covalent geometry : angle 0.63948 (14993) *********************** 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 339 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 296 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 GLN cc_start: 0.8963 (mt0) cc_final: 0.8734 (mt0) REVERT: D 45 TYR cc_start: 0.8430 (t80) cc_final: 0.8013 (t80) REVERT: D 117 VAL cc_start: 0.9276 (t) cc_final: 0.9074 (p) REVERT: D 185 GLU cc_start: 0.9461 (pt0) cc_final: 0.9224 (pp20) REVERT: D 244 MET cc_start: 0.7722 (tpp) cc_final: 0.6974 (tpp) REVERT: E 22 MET cc_start: 0.8445 (tpp) cc_final: 0.8230 (tpp) REVERT: L 45 GLN cc_start: 0.9763 (tp40) cc_final: 0.9037 (tp-100) REVERT: L 48 MET cc_start: 0.9146 (mmt) cc_final: 0.8651 (mmm) REVERT: L 49 PHE cc_start: 0.9042 (m-80) cc_final: 0.8016 (m-80) REVERT: M 23 ASN cc_start: 0.9768 (m110) cc_final: 0.9403 (p0) REVERT: N 27 VAL cc_start: 0.9655 (m) cc_final: 0.9421 (p) REVERT: N 49 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8802 (m-80) REVERT: O 17 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9252 (mm) REVERT: O 45 GLN cc_start: 0.9680 (mm-40) cc_final: 0.9166 (tp-100) REVERT: O 48 MET cc_start: 0.9576 (mmm) cc_final: 0.9148 (mmm) REVERT: O 49 PHE cc_start: 0.9466 (m-80) cc_final: 0.9127 (m-10) REVERT: Q 48 MET cc_start: 0.9593 (ppp) cc_final: 0.9313 (ppp) REVERT: Q 49 PHE cc_start: 0.9430 (m-80) cc_final: 0.8947 (m-80) REVERT: S 48 MET cc_start: 0.9734 (ttp) cc_final: 0.9242 (mmm) REVERT: S 49 PHE cc_start: 0.9326 (m-80) cc_final: 0.8902 (m-80) REVERT: T 49 PHE cc_start: 0.9297 (m-80) cc_final: 0.8982 (m-80) outliers start: 43 outliers final: 25 residues processed: 313 average time/residue: 0.1517 time to fit residues: 74.7666 Evaluate side-chains 305 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 37 GLN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 197 ASN 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 N residue 49 PHE 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 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 S residue 30 THR Chi-restraints excluded: chain U residue 54 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 130 optimal weight: 10.0000 chunk 32 optimal weight: 80.0000 chunk 99 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- 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** T 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.066884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.043807 restraints weight = 82371.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.044575 restraints weight = 57815.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.045176 restraints weight = 44180.785| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10884 Z= 0.267 Angle : 0.701 11.585 14993 Z= 0.388 Chirality : 0.045 0.369 1998 Planarity : 0.005 0.048 2023 Dihedral : 3.776 23.966 1879 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.11 % Favored : 97.84 % Rotamer: Outliers : 8.99 % Allowed : 42.51 % Favored : 48.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.63 (0.19), residues: 1805 helix: 2.98 (0.12), residues: 1582 sheet: -2.74 (0.69), residues: 36 loop : -2.25 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 54 HIS 0.004 0.001 HIS D 65 PHE 0.041 0.003 PHE M 49 TYR 0.016 0.002 TYR D 172 ARG 0.008 0.001 ARG P 29 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 1308) hydrogen bonds : angle 4.05142 ( 3921) covalent geometry : bond 0.00492 (10884) covalent geometry : angle 0.70113 (14993) *********************** 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 321 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 273 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 GLN cc_start: 0.9050 (mt0) cc_final: 0.8846 (mt0) REVERT: D 126 PHE cc_start: 0.9105 (m-80) cc_final: 0.8780 (m-10) REVERT: D 244 MET cc_start: 0.8049 (tpp) cc_final: 0.7044 (tpp) REVERT: E 22 MET cc_start: 0.8401 (tpp) cc_final: 0.8127 (tpp) REVERT: L 45 GLN cc_start: 0.9793 (tp40) cc_final: 0.8852 (tp-100) REVERT: L 48 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.9051 (tpt) REVERT: L 49 PHE cc_start: 0.9121 (m-80) cc_final: 0.8081 (m-80) REVERT: N 49 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8662 (m-80) REVERT: O 17 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9175 (mm) REVERT: O 45 GLN cc_start: 0.9671 (mm-40) cc_final: 0.9159 (tp-100) REVERT: O 48 MET cc_start: 0.9447 (mmm) cc_final: 0.9073 (mmm) REVERT: Q 48 MET cc_start: 0.9569 (ppp) cc_final: 0.9181 (ppp) REVERT: Q 49 PHE cc_start: 0.9443 (m-80) cc_final: 0.8812 (m-80) REVERT: S 48 MET cc_start: 0.9593 (ttp) cc_final: 0.9281 (mmm) REVERT: S 49 PHE cc_start: 0.9291 (m-80) cc_final: 0.8836 (m-80) REVERT: T 49 PHE cc_start: 0.9286 (m-80) cc_final: 0.8975 (m-80) outliers start: 48 outliers final: 37 residues processed: 294 average time/residue: 0.1427 time to fit residues: 68.9385 Evaluate side-chains 300 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 260 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 212 PHE 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 91 TYR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 145 SER 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 42 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 49 PHE Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain O residue 17 LEU 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 10 ILE 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 R residue 58 LEU Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 27 VAL 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 157 optimal weight: 7.9990 chunk 16 optimal weight: 110.0000 chunk 76 optimal weight: 10.0000 chunk 105 optimal weight: 50.0000 chunk 85 optimal weight: 50.0000 chunk 33 optimal weight: 50.0000 chunk 63 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 12 optimal weight: 50.0000 chunk 19 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.063543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.041393 restraints weight = 87739.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.042119 restraints weight = 60538.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.042686 restraints weight = 46077.486| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 10884 Z= 0.388 Angle : 0.826 17.237 14993 Z= 0.476 Chirality : 0.049 0.406 1998 Planarity : 0.006 0.046 2023 Dihedral : 4.419 23.984 1879 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 12.36 % Allowed : 41.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.19), residues: 1805 helix: 1.90 (0.12), residues: 1571 sheet: -2.71 (0.68), residues: 36 loop : -2.51 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 54 HIS 0.008 0.002 HIS D 174 PHE 0.039 0.003 PHE A 219 TYR 0.027 0.002 TYR D 172 ARG 0.005 0.001 ARG M 41 Details of bonding type rmsd hydrogen bonds : bond 0.05356 ( 1308) hydrogen bonds : angle 4.82861 ( 3921) covalent geometry : bond 0.00696 (10884) covalent geometry : angle 0.82641 (14993) *********************** 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 323 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 257 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 180 GLN cc_start: 0.9598 (OUTLIER) cc_final: 0.9297 (tp-100) REVERT: D 244 MET cc_start: 0.8183 (tpp) cc_final: 0.7204 (tpp) REVERT: E 22 MET cc_start: 0.8540 (tpp) cc_final: 0.8312 (tpt) REVERT: L 45 GLN cc_start: 0.9769 (tp40) cc_final: 0.9170 (tp-100) REVERT: L 49 PHE cc_start: 0.9201 (m-80) cc_final: 0.8502 (m-80) REVERT: N 45 GLN cc_start: 0.9514 (pt0) cc_final: 0.9250 (pt0) REVERT: N 49 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8687 (m-80) REVERT: O 17 LEU cc_start: 0.9482 (mm) cc_final: 0.9163 (mm) REVERT: O 45 GLN cc_start: 0.9684 (mm-40) cc_final: 0.9251 (tp-100) REVERT: O 48 MET cc_start: 0.9462 (mmm) cc_final: 0.9080 (mmm) REVERT: Q 48 MET cc_start: 0.9568 (ppp) cc_final: 0.9166 (ppp) REVERT: Q 49 PHE cc_start: 0.9452 (m-80) cc_final: 0.8749 (m-80) REVERT: R 34 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9171 (mm) REVERT: S 48 MET cc_start: 0.9566 (ttp) cc_final: 0.9339 (tpt) REVERT: S 49 PHE cc_start: 0.9358 (m-80) cc_final: 0.8886 (m-80) REVERT: T 49 PHE cc_start: 0.9307 (m-80) cc_final: 0.9004 (m-80) outliers start: 66 outliers final: 52 residues processed: 288 average time/residue: 0.1477 time to fit residues: 69.4578 Evaluate side-chains 305 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 250 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 219 PHE 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 C residue 162 ASN Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 180 GLN 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 35 LEU 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 49 PHE Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain P residue 48 MET Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 58 LEU Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 VAL Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain S residue 21 ILE Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 40 LEU Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 63 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 41 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 107 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 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 = 0.3526 r_free = 0.3526 target = 0.068494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.044844 restraints weight = 80912.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.045696 restraints weight = 55393.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046338 restraints weight = 41608.402| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10884 Z= 0.149 Angle : 0.745 15.921 14993 Z= 0.364 Chirality : 0.047 0.393 1998 Planarity : 0.004 0.049 2023 Dihedral : 3.761 23.602 1879 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.50 % Favored : 98.45 % Rotamer: Outliers : 5.99 % Allowed : 48.13 % Favored : 45.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.19), residues: 1805 helix: 2.99 (0.12), residues: 1582 sheet: -2.26 (0.65), residues: 46 loop : -2.43 (0.42), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 54 HIS 0.002 0.000 HIS D 65 PHE 0.039 0.002 PHE A 219 TYR 0.016 0.001 TYR D 45 ARG 0.004 0.001 ARG Q 41 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 1308) hydrogen bonds : angle 3.77001 ( 3921) covalent geometry : bond 0.00309 (10884) covalent geometry : angle 0.74544 (14993) *********************** 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 : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 126 PHE cc_start: 0.9132 (m-80) cc_final: 0.8888 (m-80) REVERT: D 244 MET cc_start: 0.8015 (tpp) cc_final: 0.7308 (tpp) REVERT: E 22 MET cc_start: 0.8458 (tpp) cc_final: 0.8214 (tpp) REVERT: L 44 LEU cc_start: 0.9877 (mt) cc_final: 0.9637 (pp) REVERT: L 45 GLN cc_start: 0.9743 (tp40) cc_final: 0.9223 (tp-100) REVERT: L 49 PHE cc_start: 0.8972 (m-80) cc_final: 0.8139 (m-80) REVERT: M 23 ASN cc_start: 0.9749 (m110) cc_final: 0.9407 (p0) REVERT: N 27 VAL cc_start: 0.9742 (m) cc_final: 0.9526 (p) REVERT: O 17 LEU cc_start: 0.9488 (mm) cc_final: 0.9157 (mm) REVERT: O 45 GLN cc_start: 0.9642 (mm-40) cc_final: 0.9182 (tp-100) REVERT: O 48 MET cc_start: 0.9406 (mmm) cc_final: 0.9044 (mmm) REVERT: Q 48 MET cc_start: 0.9532 (ppp) cc_final: 0.9139 (ppp) REVERT: Q 49 PHE cc_start: 0.9460 (m-80) cc_final: 0.8718 (m-80) REVERT: R 23 ASN cc_start: 0.9677 (OUTLIER) cc_final: 0.9197 (p0) REVERT: S 48 MET cc_start: 0.9570 (ttp) cc_final: 0.9238 (mmm) REVERT: S 49 PHE cc_start: 0.9359 (m-80) cc_final: 0.8823 (m-80) REVERT: T 49 PHE cc_start: 0.9312 (m-80) cc_final: 0.8973 (m-80) outliers start: 32 outliers final: 22 residues processed: 301 average time/residue: 0.1671 time to fit residues: 81.1338 Evaluate side-chains 288 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 265 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASN 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 95 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 159 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 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 50 ILE Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain S residue 21 ILE Chi-restraints excluded: chain T residue 43 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 88 optimal weight: 40.0000 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 32 optimal weight: 80.0000 chunk 67 optimal weight: 20.0000 chunk 160 optimal weight: 20.0000 chunk 177 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 40.0000 chunk 104 optimal weight: 50.0000 overall best weight: 3.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.067536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.044326 restraints weight = 80840.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.045145 restraints weight = 56209.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.045687 restraints weight = 42638.580| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10884 Z= 0.173 Angle : 0.751 14.839 14993 Z= 0.376 Chirality : 0.048 0.362 1998 Planarity : 0.005 0.070 2023 Dihedral : 3.702 23.032 1879 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.99 % Favored : 97.95 % Rotamer: Outliers : 5.24 % Allowed : 47.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.19), residues: 1805 helix: 3.04 (0.12), residues: 1582 sheet: -2.37 (0.69), residues: 36 loop : -2.34 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 54 HIS 0.003 0.001 HIS D 174 PHE 0.042 0.002 PHE A 219 TYR 0.020 0.001 TYR D 172 ARG 0.013 0.001 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 1308) hydrogen bonds : angle 3.88953 ( 3921) covalent geometry : bond 0.00356 (10884) covalent geometry : angle 0.75126 (14993) *********************** 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 297 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 269 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 126 PHE cc_start: 0.9160 (m-80) cc_final: 0.8884 (m-10) REVERT: D 244 MET cc_start: 0.8071 (tpp) cc_final: 0.7310 (tpp) REVERT: E 22 MET cc_start: 0.8407 (tpp) cc_final: 0.8199 (tpt) REVERT: L 45 GLN cc_start: 0.9763 (tp40) cc_final: 0.9089 (tp-100) REVERT: L 49 PHE cc_start: 0.9002 (m-80) cc_final: 0.8202 (m-80) REVERT: M 23 ASN cc_start: 0.9729 (m110) cc_final: 0.9451 (p0) REVERT: N 27 VAL cc_start: 0.9743 (m) cc_final: 0.9543 (p) REVERT: O 17 LEU cc_start: 0.9473 (mm) cc_final: 0.9140 (mm) REVERT: O 45 GLN cc_start: 0.9647 (mm-40) cc_final: 0.9147 (tp-100) REVERT: O 48 MET cc_start: 0.9415 (mmm) cc_final: 0.9059 (mmm) REVERT: Q 48 MET cc_start: 0.9536 (ppp) cc_final: 0.9154 (ppp) REVERT: Q 49 PHE cc_start: 0.9445 (m-80) cc_final: 0.8694 (m-80) REVERT: S 48 MET cc_start: 0.9563 (ttp) cc_final: 0.9231 (mmm) REVERT: S 49 PHE cc_start: 0.9366 (m-80) cc_final: 0.8850 (m-80) REVERT: T 49 PHE cc_start: 0.9339 (m-80) cc_final: 0.8996 (m-80) outliers start: 28 outliers final: 24 residues processed: 286 average time/residue: 0.1503 time to fit residues: 70.6952 Evaluate side-chains 289 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 265 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TRP 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 95 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 159 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 77 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain O residue 50 ILE 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 T residue 43 VAL Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 54 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 5 optimal weight: 30.0000 chunk 27 optimal weight: 20.0000 chunk 88 optimal weight: 40.0000 chunk 147 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 89 optimal weight: 90.0000 chunk 67 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 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 = 0.3530 r_free = 0.3530 target = 0.068659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.045226 restraints weight = 81305.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.046069 restraints weight = 56250.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.046706 restraints weight = 42486.230| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10884 Z= 0.149 Angle : 0.775 16.107 14993 Z= 0.377 Chirality : 0.049 0.399 1998 Planarity : 0.004 0.050 2023 Dihedral : 3.579 22.739 1879 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.61 % Favored : 98.34 % Rotamer: Outliers : 3.93 % Allowed : 48.31 % Favored : 47.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.19), residues: 1805 helix: 3.15 (0.12), residues: 1582 sheet: -2.04 (0.66), residues: 46 loop : -2.43 (0.42), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 54 HIS 0.001 0.001 HIS D 174 PHE 0.041 0.002 PHE A 219 TYR 0.017 0.001 TYR D 45 ARG 0.005 0.001 ARG O 41 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 1308) hydrogen bonds : angle 3.75913 ( 3921) covalent geometry : bond 0.00311 (10884) covalent geometry : angle 0.77509 (14993) *********************** 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 294 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 273 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 TYR cc_start: 0.9244 (t80) cc_final: 0.8962 (t80) REVERT: D 67 MET cc_start: 0.9661 (ptp) cc_final: 0.8750 (ppp) REVERT: D 126 PHE cc_start: 0.9127 (m-80) cc_final: 0.8839 (m-80) REVERT: D 244 MET cc_start: 0.8064 (tpp) cc_final: 0.7343 (tpp) REVERT: E 22 MET cc_start: 0.8385 (tpp) cc_final: 0.8157 (tpp) REVERT: L 44 LEU cc_start: 0.9893 (mt) cc_final: 0.9644 (pp) REVERT: L 45 GLN cc_start: 0.9760 (tp40) cc_final: 0.9125 (tp-100) REVERT: L 49 PHE cc_start: 0.8920 (m-80) cc_final: 0.7821 (m-80) REVERT: M 23 ASN cc_start: 0.9722 (m110) cc_final: 0.9490 (p0) REVERT: N 27 VAL cc_start: 0.9714 (m) cc_final: 0.9497 (p) REVERT: O 17 LEU cc_start: 0.9496 (mm) cc_final: 0.9167 (mm) REVERT: O 45 GLN cc_start: 0.9641 (mm-40) cc_final: 0.9057 (tp-100) REVERT: O 48 MET cc_start: 0.9416 (mmm) cc_final: 0.9071 (mmm) REVERT: O 49 PHE cc_start: 0.9432 (m-80) cc_final: 0.8854 (m-10) REVERT: Q 48 MET cc_start: 0.9526 (ppp) cc_final: 0.9130 (ppp) REVERT: Q 49 PHE cc_start: 0.9460 (m-80) cc_final: 0.8707 (m-80) REVERT: R 23 ASN cc_start: 0.9685 (OUTLIER) cc_final: 0.9232 (p0) REVERT: R 49 PHE cc_start: 0.9221 (m-80) cc_final: 0.8975 (t80) REVERT: S 48 MET cc_start: 0.9559 (ttp) cc_final: 0.9208 (mmm) REVERT: S 49 PHE cc_start: 0.9374 (m-80) cc_final: 0.8862 (m-80) REVERT: T 49 PHE cc_start: 0.9362 (m-80) cc_final: 0.9011 (m-80) outliers start: 21 outliers final: 17 residues processed: 287 average time/residue: 0.1549 time to fit residues: 71.6283 Evaluate side-chains 285 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 267 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 95 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 159 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 77 ILE Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain O residue 50 ILE 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 T residue 43 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 42 optimal weight: 40.0000 chunk 37 optimal weight: 9.9990 chunk 156 optimal weight: 0.3980 chunk 0 optimal weight: 90.0000 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.091339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.071705 restraints weight = 82532.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.072995 restraints weight = 38824.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.073793 restraints weight = 22418.842| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4155 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= 0.153 Angle : 0.784 17.573 14993 Z= 0.381 Chirality : 0.049 0.398 1998 Planarity : 0.004 0.050 2023 Dihedral : 3.535 22.152 1879 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.83 % Favored : 98.12 % Rotamer: Outliers : 4.31 % Allowed : 48.13 % Favored : 47.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.19), residues: 1805 helix: 3.19 (0.12), residues: 1582 sheet: -1.60 (0.63), residues: 53 loop : -2.48 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 54 HIS 0.002 0.001 HIS D 174 PHE 0.044 0.002 PHE A 219 TYR 0.018 0.001 TYR D 172 ARG 0.007 0.001 ARG O 41 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 1308) hydrogen bonds : angle 3.75779 ( 3921) covalent geometry : bond 0.00323 (10884) covalent geometry : angle 0.78390 (14993) ********************** 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 297 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 274 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 ASN cc_start: 0.9577 (m110) cc_final: 0.9187 (p0) REVERT: D 45 TYR cc_start: 0.9357 (t80) cc_final: 0.8993 (t80) REVERT: D 67 MET cc_start: 0.9666 (ptp) cc_final: 0.8820 (ppp) REVERT: D 126 PHE cc_start: 0.9196 (m-80) cc_final: 0.8897 (m-80) REVERT: D 244 MET cc_start: 0.7981 (tpp) cc_final: 0.7243 (tpp) REVERT: E 22 MET cc_start: 0.8492 (tpp) cc_final: 0.8245 (tpp) REVERT: L 44 LEU cc_start: 0.9897 (mt) cc_final: 0.9633 (pp) REVERT: L 45 GLN cc_start: 0.9769 (tp40) cc_final: 0.9200 (tp-100) REVERT: L 48 MET cc_start: 0.9161 (tpt) cc_final: 0.8838 (tpt) REVERT: L 49 PHE cc_start: 0.8975 (m-80) cc_final: 0.7873 (m-80) REVERT: M 23 ASN cc_start: 0.9742 (m110) cc_final: 0.9504 (p0) REVERT: N 21 ILE cc_start: 0.9744 (mm) cc_final: 0.9434 (pt) REVERT: O 17 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9178 (mm) REVERT: O 45 GLN cc_start: 0.9665 (mm-40) cc_final: 0.9099 (tp-100) REVERT: O 48 MET cc_start: 0.9523 (mmm) cc_final: 0.9139 (mmm) REVERT: O 49 PHE cc_start: 0.9412 (m-80) cc_final: 0.8824 (m-10) REVERT: Q 48 MET cc_start: 0.9553 (ppp) cc_final: 0.9190 (ppp) REVERT: Q 49 PHE cc_start: 0.9451 (m-80) cc_final: 0.8744 (m-80) REVERT: R 48 MET cc_start: 0.9447 (ptp) cc_final: 0.9234 (ptm) REVERT: S 48 MET cc_start: 0.9706 (ttp) cc_final: 0.9255 (mmm) REVERT: S 49 PHE cc_start: 0.9461 (m-80) cc_final: 0.8963 (m-80) REVERT: T 49 PHE cc_start: 0.9428 (m-80) cc_final: 0.9055 (m-80) outliers start: 23 outliers final: 19 residues processed: 288 average time/residue: 0.1592 time to fit residues: 73.4362 Evaluate side-chains 288 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 268 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 43 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 159 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 77 ILE Chi-restraints excluded: chain I residue 35 ASN 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 R residue 21 ILE Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain T residue 43 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 170 optimal weight: 9.9990 chunk 3 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 80 optimal weight: 40.0000 chunk 114 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.066136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.043319 restraints weight = 83016.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.044072 restraints weight = 57833.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.044672 restraints weight = 44230.027| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10884 Z= 0.244 Angle : 0.795 15.272 14993 Z= 0.418 Chirality : 0.049 0.373 1998 Planarity : 0.005 0.047 2023 Dihedral : 3.822 22.145 1879 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.45 % Rotamer: Outliers : 4.68 % Allowed : 48.88 % Favored : 46.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.19), residues: 1805 helix: 2.92 (0.12), residues: 1582 sheet: -1.68 (0.66), residues: 53 loop : -2.59 (0.42), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 54 HIS 0.005 0.002 HIS D 174 PHE 0.065 0.003 PHE R 49 TYR 0.016 0.001 TYR D 45 ARG 0.006 0.001 ARG O 41 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 1308) hydrogen bonds : angle 4.14763 ( 3921) covalent geometry : bond 0.00468 (10884) covalent geometry : angle 0.79523 (14993) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4829.40 seconds wall clock time: 87 minutes 3.65 seconds (5223.65 seconds total)