Starting phenix.real_space_refine on Sat Aug 8 20:04:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bd6_15976/08_2026/8bd6_15976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bd6_15976/08_2026/8bd6_15976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8bd6_15976/08_2026/8bd6_15976.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bd6_15976/08_2026/8bd6_15976.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bd6_15976/08_2026/8bd6_15976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bd6_15976/08_2026/8bd6_15976.map" model { file = "/net/cci-nas-00/data/ceres_data/8bd6_15976/08_2026/8bd6_15976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bd6_15976/08_2026/8bd6_15976.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 338 5.49 5 Mg 9 5.21 5 S 85 5.16 5 C 17646 2.51 5 N 5416 2.21 5 O 6457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29951 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4542 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 17, 'TRANS': 542} Chain breaks: 2 Chain: "B" Number of atoms: 4961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 4961 Classifications: {'RNAv2': 233} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 16, 'rna3p_pur': 102, 'rna3p_pyr': 97} Link IDs: {'rna2p': 34, 'rna3p': 198} Chain breaks: 1 Chain: "C" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 356 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 206 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "R" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2056 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "T" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "U" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "V" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "W" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "X" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Z" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2056 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "c" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 533 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "d" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 533 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.22, per 1000 atoms: 0.21 Number of scatterers: 29951 At special positions: 0 Unit cell: (149.5, 133.9, 198.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 85 16.00 P 338 15.00 Mg 9 11.99 O 6457 8.00 N 5416 7.00 C 17646 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: 2.59 Conformation dependent library (CDL) restraints added in 760.2 milliseconds 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5454 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 11 sheets defined 62.5% alpha, 6.7% beta 101 base pairs and 206 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 13 through 26 removed outlier: 3.830A pdb=" N LEU A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.534A pdb=" N LEU A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 51 removed outlier: 3.621A pdb=" N LYS A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 63 through 68 removed outlier: 4.307A pdb=" N THR A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 115 Processing helix chain 'A' and resid 117 through 125 Processing helix chain 'A' and resid 128 through 141 removed outlier: 3.655A pdb=" N ILE A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 187 through 200 Processing helix chain 'A' and resid 211 through 231 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 318 through 338 removed outlier: 4.400A pdb=" N HIS A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N TRP A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 407 removed outlier: 3.669A pdb=" N ILE A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 430 removed outlier: 3.584A pdb=" N GLN A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 484 through 506 removed outlier: 3.507A pdb=" N GLN A 506 " --> pdb=" O ARG A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 538 removed outlier: 3.662A pdb=" N ALA A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 551 Processing helix chain 'A' and resid 552 through 567 Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 618 through 636 removed outlier: 3.830A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 30 Processing helix chain 'R' and resid 36 through 52 removed outlier: 3.524A pdb=" N ALA R 52 " --> pdb=" O GLY R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 77 removed outlier: 3.657A pdb=" N ALA R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS R 77 " --> pdb=" O TYR R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 113 Processing helix chain 'R' and resid 121 through 136 Processing helix chain 'R' and resid 150 through 165 removed outlier: 3.682A pdb=" N PHE R 154 " --> pdb=" O LYS R 150 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA R 155 " --> pdb=" O PRO R 151 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASP R 156 " --> pdb=" O GLU R 152 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 182 removed outlier: 3.697A pdb=" N ALA R 178 " --> pdb=" O ASP R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 190 removed outlier: 3.665A pdb=" N GLU R 188 " --> pdb=" O GLU R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 215 Processing helix chain 'R' and resid 226 through 238 removed outlier: 3.537A pdb=" N GLU R 238 " --> pdb=" O THR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 240 through 258 Processing helix chain 'R' and resid 264 through 274 removed outlier: 3.637A pdb=" N LEU R 268 " --> pdb=" O ASP R 264 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 30 Processing helix chain 'S' and resid 36 through 52 removed outlier: 3.522A pdb=" N ALA S 52 " --> pdb=" O GLY S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 77 removed outlier: 3.659A pdb=" N ALA S 69 " --> pdb=" O GLY S 65 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS S 77 " --> pdb=" O TYR S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 113 Processing helix chain 'S' and resid 121 through 136 Processing helix chain 'S' and resid 150 through 165 removed outlier: 3.681A pdb=" N PHE S 154 " --> pdb=" O LYS S 150 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA S 155 " --> pdb=" O PRO S 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP S 156 " --> pdb=" O GLU S 152 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY S 165 " --> pdb=" O ALA S 161 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 182 removed outlier: 3.698A pdb=" N ALA S 178 " --> pdb=" O ASP S 174 " (cutoff:3.500A) Processing helix chain 'S' and resid 184 through 190 removed outlier: 3.664A pdb=" N GLU S 188 " --> pdb=" O GLU S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 201 through 215 Processing helix chain 'S' and resid 226 through 238 removed outlier: 3.537A pdb=" N GLU S 238 " --> pdb=" O THR S 234 " (cutoff:3.500A) Processing helix chain 'S' and resid 240 through 258 Processing helix chain 'S' and resid 264 through 274 removed outlier: 3.637A pdb=" N LEU S 268 " --> pdb=" O ASP S 264 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 30 Processing helix chain 'T' and resid 36 through 52 removed outlier: 3.523A pdb=" N ALA T 52 " --> pdb=" O GLY T 48 " (cutoff:3.500A) Processing helix chain 'T' and resid 65 through 77 removed outlier: 3.658A pdb=" N ALA T 69 " --> pdb=" O GLY T 65 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS T 77 " --> pdb=" O TYR T 73 " (cutoff:3.500A) Processing helix chain 'T' and resid 101 through 113 Processing helix chain 'T' and resid 121 through 136 Processing helix chain 'T' and resid 150 through 165 removed outlier: 3.681A pdb=" N PHE T 154 " --> pdb=" O LYS T 150 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA T 155 " --> pdb=" O PRO T 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP T 156 " --> pdb=" O GLU T 152 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY T 165 " --> pdb=" O ALA T 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 174 through 182 removed outlier: 3.699A pdb=" N ALA T 178 " --> pdb=" O ASP T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 184 through 190 removed outlier: 3.664A pdb=" N GLU T 188 " --> pdb=" O GLU T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 201 through 215 Processing helix chain 'T' and resid 226 through 238 removed outlier: 3.535A pdb=" N GLU T 238 " --> pdb=" O THR T 234 " (cutoff:3.500A) Processing helix chain 'T' and resid 240 through 258 Processing helix chain 'T' and resid 264 through 274 removed outlier: 3.637A pdb=" N LEU T 268 " --> pdb=" O ASP T 264 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 30 Processing helix chain 'U' and resid 36 through 52 removed outlier: 3.523A pdb=" N ALA U 52 " --> pdb=" O GLY U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 77 removed outlier: 3.657A pdb=" N ALA U 69 " --> pdb=" O GLY U 65 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS U 77 " --> pdb=" O TYR U 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 101 through 113 Processing helix chain 'U' and resid 121 through 136 Processing helix chain 'U' and resid 150 through 165 removed outlier: 3.682A pdb=" N PHE U 154 " --> pdb=" O LYS U 150 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA U 155 " --> pdb=" O PRO U 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP U 156 " --> pdb=" O GLU U 152 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY U 165 " --> pdb=" O ALA U 161 " (cutoff:3.500A) Processing helix chain 'U' and resid 174 through 182 removed outlier: 3.698A pdb=" N ALA U 178 " --> pdb=" O ASP U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 184 through 190 removed outlier: 3.666A pdb=" N GLU U 188 " --> pdb=" O GLU U 184 " (cutoff:3.500A) Processing helix chain 'U' and resid 201 through 215 Processing helix chain 'U' and resid 226 through 238 removed outlier: 3.538A pdb=" N GLU U 238 " --> pdb=" O THR U 234 " (cutoff:3.500A) Processing helix chain 'U' and resid 240 through 258 removed outlier: 3.864A pdb=" N GLU U 246 " --> pdb=" O GLY U 242 " (cutoff:3.500A) Processing helix chain 'U' and resid 264 through 274 removed outlier: 3.636A pdb=" N LEU U 268 " --> pdb=" O ASP U 264 " (cutoff:3.500A) Processing helix chain 'V' and resid 18 through 30 Processing helix chain 'V' and resid 36 through 52 removed outlier: 3.522A pdb=" N ALA V 52 " --> pdb=" O GLY V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 65 through 77 removed outlier: 3.658A pdb=" N ALA V 69 " --> pdb=" O GLY V 65 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS V 77 " --> pdb=" O TYR V 73 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 113 Processing helix chain 'V' and resid 121 through 136 Processing helix chain 'V' and resid 150 through 165 removed outlier: 3.682A pdb=" N PHE V 154 " --> pdb=" O LYS V 150 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA V 155 " --> pdb=" O PRO V 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP V 156 " --> pdb=" O GLU V 152 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY V 165 " --> pdb=" O ALA V 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 174 through 182 removed outlier: 3.698A pdb=" N ALA V 178 " --> pdb=" O ASP V 174 " (cutoff:3.500A) Processing helix chain 'V' and resid 184 through 190 removed outlier: 3.666A pdb=" N GLU V 188 " --> pdb=" O GLU V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 201 through 215 Processing helix chain 'V' and resid 226 through 238 removed outlier: 3.538A pdb=" N GLU V 238 " --> pdb=" O THR V 234 " (cutoff:3.500A) Processing helix chain 'V' and resid 240 through 258 Processing helix chain 'V' and resid 264 through 274 removed outlier: 3.636A pdb=" N LEU V 268 " --> pdb=" O ASP V 264 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 30 Processing helix chain 'W' and resid 36 through 52 removed outlier: 3.523A pdb=" N ALA W 52 " --> pdb=" O GLY W 48 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 77 removed outlier: 3.658A pdb=" N ALA W 69 " --> pdb=" O GLY W 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS W 77 " --> pdb=" O TYR W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 101 through 113 Processing helix chain 'W' and resid 121 through 136 Processing helix chain 'W' and resid 150 through 165 removed outlier: 3.681A pdb=" N PHE W 154 " --> pdb=" O LYS W 150 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA W 155 " --> pdb=" O PRO W 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP W 156 " --> pdb=" O GLU W 152 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY W 165 " --> pdb=" O ALA W 161 " (cutoff:3.500A) Processing helix chain 'W' and resid 174 through 182 removed outlier: 3.697A pdb=" N ALA W 178 " --> pdb=" O ASP W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 190 removed outlier: 3.665A pdb=" N GLU W 188 " --> pdb=" O GLU W 184 " (cutoff:3.500A) Processing helix chain 'W' and resid 201 through 215 Processing helix chain 'W' and resid 226 through 238 removed outlier: 3.536A pdb=" N GLU W 238 " --> pdb=" O THR W 234 " (cutoff:3.500A) Processing helix chain 'W' and resid 240 through 258 Processing helix chain 'W' and resid 264 through 274 removed outlier: 3.636A pdb=" N LEU W 268 " --> pdb=" O ASP W 264 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 30 Processing helix chain 'X' and resid 36 through 52 removed outlier: 3.522A pdb=" N ALA X 52 " --> pdb=" O GLY X 48 " (cutoff:3.500A) Processing helix chain 'X' and resid 65 through 77 removed outlier: 3.658A pdb=" N ALA X 69 " --> pdb=" O GLY X 65 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS X 77 " --> pdb=" O TYR X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 113 Processing helix chain 'X' and resid 121 through 136 Processing helix chain 'X' and resid 150 through 165 removed outlier: 3.681A pdb=" N PHE X 154 " --> pdb=" O LYS X 150 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA X 155 " --> pdb=" O PRO X 151 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP X 156 " --> pdb=" O GLU X 152 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY X 165 " --> pdb=" O ALA X 161 " (cutoff:3.500A) Processing helix chain 'X' and resid 174 through 182 removed outlier: 3.700A pdb=" N ALA X 178 " --> pdb=" O ASP X 174 " (cutoff:3.500A) Processing helix chain 'X' and resid 184 through 190 removed outlier: 3.664A pdb=" N GLU X 188 " --> pdb=" O GLU X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 201 through 215 Processing helix chain 'X' and resid 226 through 238 removed outlier: 3.537A pdb=" N GLU X 238 " --> pdb=" O THR X 234 " (cutoff:3.500A) Processing helix chain 'X' and resid 240 through 258 Processing helix chain 'X' and resid 264 through 274 removed outlier: 3.635A pdb=" N LEU X 268 " --> pdb=" O ASP X 264 " (cutoff:3.500A) Processing helix chain 'Y' and resid 18 through 30 Processing helix chain 'Y' and resid 36 through 52 removed outlier: 3.523A pdb=" N ALA Y 52 " --> pdb=" O GLY Y 48 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 77 removed outlier: 3.659A pdb=" N ALA Y 69 " --> pdb=" O GLY Y 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS Y 77 " --> pdb=" O TYR Y 73 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 113 Processing helix chain 'Y' and resid 121 through 136 Processing helix chain 'Y' and resid 150 through 165 removed outlier: 3.681A pdb=" N PHE Y 154 " --> pdb=" O LYS Y 150 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA Y 155 " --> pdb=" O PRO Y 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP Y 156 " --> pdb=" O GLU Y 152 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY Y 165 " --> pdb=" O ALA Y 161 " (cutoff:3.500A) Processing helix chain 'Y' and resid 174 through 182 removed outlier: 3.699A pdb=" N ALA Y 178 " --> pdb=" O ASP Y 174 " (cutoff:3.500A) Processing helix chain 'Y' and resid 184 through 190 removed outlier: 3.665A pdb=" N GLU Y 188 " --> pdb=" O GLU Y 184 " (cutoff:3.500A) Processing helix chain 'Y' and resid 201 through 215 Processing helix chain 'Y' and resid 226 through 238 removed outlier: 3.538A pdb=" N GLU Y 238 " --> pdb=" O THR Y 234 " (cutoff:3.500A) Processing helix chain 'Y' and resid 240 through 258 Processing helix chain 'Y' and resid 264 through 274 removed outlier: 3.636A pdb=" N LEU Y 268 " --> pdb=" O ASP Y 264 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 30 Processing helix chain 'Z' and resid 36 through 52 removed outlier: 3.521A pdb=" N ALA Z 52 " --> pdb=" O GLY Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 65 through 77 removed outlier: 3.658A pdb=" N ALA Z 69 " --> pdb=" O GLY Z 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS Z 77 " --> pdb=" O TYR Z 73 " (cutoff:3.500A) Processing helix chain 'Z' and resid 101 through 113 Processing helix chain 'Z' and resid 121 through 136 Processing helix chain 'Z' and resid 150 through 165 removed outlier: 3.682A pdb=" N PHE Z 154 " --> pdb=" O LYS Z 150 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA Z 155 " --> pdb=" O PRO Z 151 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP Z 156 " --> pdb=" O GLU Z 152 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY Z 165 " --> pdb=" O ALA Z 161 " (cutoff:3.500A) Processing helix chain 'Z' and resid 174 through 183 removed outlier: 3.699A pdb=" N ALA Z 178 " --> pdb=" O ASP Z 174 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP Z 183 " --> pdb=" O VAL Z 179 " (cutoff:3.500A) Processing helix chain 'Z' and resid 185 through 190 Processing helix chain 'Z' and resid 201 through 215 Processing helix chain 'Z' and resid 226 through 238 removed outlier: 3.538A pdb=" N GLU Z 238 " --> pdb=" O THR Z 234 " (cutoff:3.500A) Processing helix chain 'Z' and resid 240 through 258 Processing helix chain 'Z' and resid 264 through 274 removed outlier: 3.638A pdb=" N LEU Z 268 " --> pdb=" O ASP Z 264 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 291 through 295 removed outlier: 4.941A pdb=" N LEU A 301 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE A 305 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 311 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU A 371 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 351 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP A 378 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 349 " --> pdb=" O ASP A 378 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 475 removed outlier: 6.835A pdb=" N VAL A 463 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N TYR A 474 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL A 461 " --> pdb=" O TYR A 474 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 464 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 448 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 449 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N VAL A 451 " --> pdb=" O PRO A 546 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 91 through 94 removed outlier: 6.424A pdb=" N LEU R 141 " --> pdb=" O VAL R 169 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL R 171 " --> pdb=" O LEU R 141 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE R 143 " --> pdb=" O VAL R 171 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N CYS R 56 " --> pdb=" O LEU R 170 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N GLY R 172 " --> pdb=" O CYS R 56 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL R 58 " --> pdb=" O GLY R 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 91 through 94 removed outlier: 6.566A pdb=" N VAL S 92 " --> pdb=" O ILE S 142 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU S 141 " --> pdb=" O VAL S 169 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL S 171 " --> pdb=" O LEU S 141 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE S 143 " --> pdb=" O VAL S 171 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N CYS S 56 " --> pdb=" O LEU S 170 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N GLY S 172 " --> pdb=" O CYS S 56 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL S 58 " --> pdb=" O GLY S 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 91 through 94 removed outlier: 6.565A pdb=" N VAL T 92 " --> pdb=" O ILE T 142 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU T 141 " --> pdb=" O VAL T 169 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL T 171 " --> pdb=" O LEU T 141 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE T 143 " --> pdb=" O VAL T 171 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N CYS T 56 " --> pdb=" O LEU T 170 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY T 172 " --> pdb=" O CYS T 56 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL T 58 " --> pdb=" O GLY T 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'U' and resid 91 through 94 removed outlier: 6.565A pdb=" N VAL U 92 " --> pdb=" O ILE U 142 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU U 141 " --> pdb=" O VAL U 169 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL U 171 " --> pdb=" O LEU U 141 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE U 143 " --> pdb=" O VAL U 171 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N CYS U 56 " --> pdb=" O LEU U 170 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY U 172 " --> pdb=" O CYS U 56 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL U 58 " --> pdb=" O GLY U 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'V' and resid 91 through 94 removed outlier: 6.564A pdb=" N VAL V 92 " --> pdb=" O ILE V 142 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU V 141 " --> pdb=" O VAL V 169 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL V 171 " --> pdb=" O LEU V 141 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE V 143 " --> pdb=" O VAL V 171 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS V 56 " --> pdb=" O LEU V 170 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N GLY V 172 " --> pdb=" O CYS V 56 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL V 58 " --> pdb=" O GLY V 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'W' and resid 91 through 94 removed outlier: 6.566A pdb=" N VAL W 92 " --> pdb=" O ILE W 142 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU W 141 " --> pdb=" O VAL W 169 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL W 171 " --> pdb=" O LEU W 141 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE W 143 " --> pdb=" O VAL W 171 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS W 56 " --> pdb=" O LEU W 170 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY W 172 " --> pdb=" O CYS W 56 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL W 58 " --> pdb=" O GLY W 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'X' and resid 91 through 94 removed outlier: 6.564A pdb=" N VAL X 92 " --> pdb=" O ILE X 142 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU X 141 " --> pdb=" O VAL X 169 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL X 171 " --> pdb=" O LEU X 141 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE X 143 " --> pdb=" O VAL X 171 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N CYS X 56 " --> pdb=" O LEU X 170 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY X 172 " --> pdb=" O CYS X 56 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL X 58 " --> pdb=" O GLY X 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Y' and resid 91 through 94 removed outlier: 6.566A pdb=" N VAL Y 92 " --> pdb=" O ILE Y 142 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU Y 141 " --> pdb=" O VAL Y 169 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL Y 171 " --> pdb=" O LEU Y 141 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE Y 143 " --> pdb=" O VAL Y 171 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS Y 56 " --> pdb=" O LEU Y 170 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N GLY Y 172 " --> pdb=" O CYS Y 56 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL Y 58 " --> pdb=" O GLY Y 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Z' and resid 91 through 94 removed outlier: 6.424A pdb=" N LEU Z 141 " --> pdb=" O VAL Z 169 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL Z 171 " --> pdb=" O LEU Z 141 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE Z 143 " --> pdb=" O VAL Z 171 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N CYS Z 56 " --> pdb=" O LEU Z 170 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N GLY Z 172 " --> pdb=" O CYS Z 56 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL Z 58 " --> pdb=" O GLY Z 172 " (cutoff:3.500A) 1216 hydrogen bonds defined for protein. 3645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 254 hydrogen bonds 464 hydrogen bond angles 0 basepair planarities 101 basepair parallelities 206 stacking parallelities Total time for adding SS restraints: 6.34 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4224 1.30 - 1.43: 9119 1.43 - 1.55: 16921 1.55 - 1.68: 698 1.68 - 1.81: 127 Bond restraints: 31089 Sorted by residual: bond pdb=" CA LEU A 368 " pdb=" C LEU A 368 " ideal model delta sigma weight residual 1.521 1.464 0.057 9.90e-03 1.02e+04 3.28e+01 bond pdb=" C1' DC D 1 " pdb=" N1 DC D 1 " ideal model delta sigma weight residual 1.468 1.543 -0.075 1.40e-02 5.10e+03 2.90e+01 bond pdb=" C GLY T 242 " pdb=" O GLY T 242 " ideal model delta sigma weight residual 1.234 1.173 0.062 1.19e-02 7.06e+03 2.68e+01 bond pdb=" C GLY Z 242 " pdb=" O GLY Z 242 " ideal model delta sigma weight residual 1.234 1.172 0.062 1.21e-02 6.83e+03 2.59e+01 bond pdb=" C GLY S 242 " pdb=" O GLY S 242 " ideal model delta sigma weight residual 1.234 1.173 0.061 1.21e-02 6.83e+03 2.53e+01 ... (remaining 31084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 39282 2.19 - 4.37: 3389 4.37 - 6.56: 478 6.56 - 8.75: 183 8.75 - 10.94: 101 Bond angle restraints: 43433 Sorted by residual: angle pdb=" N LEU Y 244 " pdb=" CA LEU Y 244 " pdb=" C LEU Y 244 " ideal model delta sigma weight residual 111.14 100.42 10.72 1.08e+00 8.57e-01 9.86e+01 angle pdb=" N LEU R 244 " pdb=" CA LEU R 244 " pdb=" C LEU R 244 " ideal model delta sigma weight residual 111.14 100.44 10.70 1.08e+00 8.57e-01 9.82e+01 angle pdb=" N PHE T 204 " pdb=" CA PHE T 204 " pdb=" C PHE T 204 " ideal model delta sigma weight residual 111.36 101.94 9.42 1.09e+00 8.42e-01 7.47e+01 angle pdb=" N PHE Z 204 " pdb=" CA PHE Z 204 " pdb=" C PHE Z 204 " ideal model delta sigma weight residual 111.36 101.95 9.41 1.09e+00 8.42e-01 7.45e+01 angle pdb=" N PHE S 204 " pdb=" CA PHE S 204 " pdb=" C PHE S 204 " ideal model delta sigma weight residual 111.36 101.96 9.40 1.09e+00 8.42e-01 7.44e+01 ... (remaining 43428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 16516 35.91 - 71.82: 1667 71.82 - 107.73: 63 107.73 - 143.64: 2 143.64 - 179.55: 3 Dihedral angle restraints: 18251 sinusoidal: 9829 harmonic: 8422 Sorted by residual: dihedral pdb=" C4' A B 50 " pdb=" C3' A B 50 " pdb=" C2' A B 50 " pdb=" C1' A B 50 " ideal model delta sinusoidal sigma weight residual 36.34 -43.13 79.47 1 3.10e+00 1.04e-01 8.16e+02 dihedral pdb=" C4' G B 231 " pdb=" C3' G B 231 " pdb=" C2' G B 231 " pdb=" C1' G B 231 " ideal model delta sinusoidal sigma weight residual 36.34 -42.04 78.38 1 3.10e+00 1.04e-01 7.98e+02 dihedral pdb=" C4' G B 31 " pdb=" C3' G B 31 " pdb=" C2' G B 31 " pdb=" C1' G B 31 " ideal model delta sinusoidal sigma weight residual 36.34 -41.31 77.65 1 3.10e+00 1.04e-01 7.85e+02 ... (remaining 18248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 4237 0.148 - 0.296: 722 0.296 - 0.443: 63 0.443 - 0.591: 42 0.591 - 0.739: 1 Chirality restraints: 5065 Sorted by residual: chirality pdb=" P G B 231 " pdb=" OP1 G B 231 " pdb=" OP2 G B 231 " pdb=" O5' G B 231 " both_signs ideal model delta sigma weight residual True 2.17 -2.91 -0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" P G B 131 " pdb=" OP1 G B 131 " pdb=" OP2 G B 131 " pdb=" O5' G B 131 " both_signs ideal model delta sigma weight residual True 2.17 -2.71 -0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" CA ARG R 76 " pdb=" N ARG R 76 " pdb=" C ARG R 76 " pdb=" CB ARG R 76 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.58e+00 ... (remaining 5062 not shown) Planarity restraints: 4372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE U 241 " 0.027 2.00e-02 2.50e+03 5.37e-02 2.88e+01 pdb=" C ILE U 241 " -0.093 2.00e-02 2.50e+03 pdb=" O ILE U 241 " 0.035 2.00e-02 2.50e+03 pdb=" N GLY U 242 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY W 242 " -0.025 2.00e-02 2.50e+03 5.12e-02 2.62e+01 pdb=" C GLY W 242 " 0.088 2.00e-02 2.50e+03 pdb=" O GLY W 242 " -0.034 2.00e-02 2.50e+03 pdb=" N ARG W 243 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP V 301 " 0.063 2.00e-02 2.50e+03 2.75e-02 2.07e+01 pdb=" C2 ATP V 301 " -0.033 2.00e-02 2.50e+03 pdb=" C4 ATP V 301 " -0.007 2.00e-02 2.50e+03 pdb=" C5 ATP V 301 " -0.008 2.00e-02 2.50e+03 pdb=" C6 ATP V 301 " 0.028 2.00e-02 2.50e+03 pdb=" C8 ATP V 301 " -0.021 2.00e-02 2.50e+03 pdb=" N1 ATP V 301 " 0.006 2.00e-02 2.50e+03 pdb=" N3 ATP V 301 " -0.004 2.00e-02 2.50e+03 pdb=" N6 ATP V 301 " 0.024 2.00e-02 2.50e+03 pdb=" N7 ATP V 301 " -0.015 2.00e-02 2.50e+03 pdb=" N9 ATP V 301 " -0.033 2.00e-02 2.50e+03 ... (remaining 4369 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.83: 17 1.83 - 2.60: 426 2.60 - 3.36: 39272 3.36 - 4.13: 80659 4.13 - 4.90: 132513 Nonbonded interactions: 252887 Sorted by model distance: nonbonded pdb=" CE1 HIS A 500 " pdb=" O2 U B 117 " model vdw 1.062 3.260 nonbonded pdb=" ND1 HIS A 500 " pdb=" O2 U B 117 " model vdw 1.086 3.120 nonbonded pdb=" CG2 ILE A 97 " pdb=" O2' G B 236 " model vdw 1.119 3.460 nonbonded pdb=" NE2 GLN A 513 " pdb=" C5' DT C -9 " model vdw 1.142 3.520 nonbonded pdb=" O1B ATP R 301 " pdb="MG MG R 302 " model vdw 1.185 2.170 ... (remaining 252882 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 'R' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 302)) selection = chain 'S' selection = (chain 'T' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 302)) selection = (chain 'U' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 302)) selection = (chain 'V' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 302)) selection = (chain 'W' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 302)) selection = (chain 'X' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 302)) selection = (chain 'Y' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 302)) selection = chain 'Z' } ncs_group { reference = chain 'c' selection = chain 'd' } 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: 8.130 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: 0.660 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 29.300 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 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 : 0.009 0.075 31089 Z= 0.581 Angle : 1.399 10.937 43433 Z= 0.940 Chirality : 0.112 0.739 5065 Planarity : 0.006 0.054 4372 Dihedral : 22.447 179.547 12797 Min Nonbonded Distance : 1.062 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 8.81 % Allowed : 12.27 % Favored : 78.91 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.14), residues: 2876 helix: -0.84 (0.11), residues: 1716 sheet: -1.86 (0.36), residues: 218 loop : -2.04 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG W 57 TYR 0.012 0.002 TYR X 275 PHE 0.017 0.002 PHE U 196 TRP 0.020 0.003 TRP R 45 HIS 0.004 0.001 HIS S 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00917 / 0.58 (31089) covalent geometry : angle 1.39938 / 0.94 (43433) hydrogen bonds : bond 0.15810 / 10.63 ( 1470) hydrogen bonds : angle 7.47855 / 5.47 ( 4109) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 341 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 63 ARG cc_start: 0.4484 (OUTLIER) cc_final: 0.3920 (ttm170) REVERT: R 91 VAL cc_start: 0.7848 (OUTLIER) cc_final: 0.6775 (p) REVERT: R 95 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8014 (tmm-80) REVERT: R 153 THR cc_start: 0.6204 (OUTLIER) cc_final: 0.5972 (p) REVERT: R 208 VAL cc_start: 0.8913 (t) cc_final: 0.8648 (t) REVERT: S 37 GLN cc_start: 0.9245 (tp40) cc_final: 0.8747 (pp30) REVERT: S 124 ASP cc_start: 0.9083 (m-30) cc_final: 0.8834 (t70) REVERT: S 130 ILE cc_start: 0.9049 (mt) cc_final: 0.8286 (mt) REVERT: S 159 ASP cc_start: 0.9182 (m-30) cc_final: 0.8914 (m-30) REVERT: S 255 SER cc_start: 0.3167 (OUTLIER) cc_final: 0.2158 (p) REVERT: S 264 ASP cc_start: 0.8684 (t70) cc_final: 0.8448 (m-30) REVERT: S 276 LYS cc_start: 0.6230 (OUTLIER) cc_final: 0.5789 (mmtt) REVERT: T 156 ASP cc_start: 0.8562 (m-30) cc_final: 0.8003 (p0) REVERT: T 232 ILE cc_start: 0.6016 (OUTLIER) cc_final: 0.5728 (mt) REVERT: T 255 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.8051 (p) REVERT: U 91 VAL cc_start: 0.5209 (OUTLIER) cc_final: 0.4940 (p) REVERT: U 104 ASP cc_start: 0.9027 (m-30) cc_final: 0.8582 (t0) REVERT: U 117 VAL cc_start: 0.8658 (m) cc_final: 0.8120 (m) REVERT: V 95 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7174 (tmm-80) REVERT: V 213 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8956 (mp10) REVERT: W 159 ASP cc_start: 0.9052 (m-30) cc_final: 0.8668 (m-30) REVERT: W 271 VAL cc_start: 0.8419 (m) cc_final: 0.7996 (t) REVERT: X 36 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8064 (pp) REVERT: X 91 VAL cc_start: 0.4813 (OUTLIER) cc_final: 0.4508 (p) REVERT: X 108 LYS cc_start: 0.9471 (mtpt) cc_final: 0.9135 (ptpp) REVERT: X 153 THR cc_start: 0.6489 (OUTLIER) cc_final: 0.6194 (p) REVERT: X 180 ILE cc_start: 0.6382 (pt) cc_final: 0.5997 (pt) REVERT: Y 95 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7123 (ptt90) REVERT: Y 199 LEU cc_start: -0.1684 (OUTLIER) cc_final: -0.2005 (mt) REVERT: Y 232 ILE cc_start: -0.0744 (OUTLIER) cc_final: -0.1020 (mm) REVERT: Y 255 SER cc_start: 0.5871 (OUTLIER) cc_final: 0.5356 (p) REVERT: Z 21 LEU cc_start: 0.7019 (tt) cc_final: 0.6751 (mt) REVERT: Z 36 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7987 (pt) REVERT: Z 63 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8195 (ttp-170) REVERT: Z 81 GLN cc_start: 0.1313 (OUTLIER) cc_final: 0.0658 (pt0) REVERT: Z 113 LEU cc_start: 0.4936 (mt) cc_final: 0.4093 (mt) REVERT: Z 229 MET cc_start: -0.0517 (mmt) cc_final: -0.0753 (ttt) REVERT: Z 263 ILE cc_start: 0.0630 (OUTLIER) cc_final: 0.0321 (pt) outliers start: 214 outliers final: 37 residues processed: 536 average time/residue: 0.2618 time to fit residues: 202.8415 Evaluate side-chains 244 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 185 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 420 GLN A 494 GLN R 38 GLN S 38 GLN S 97 HIS T 38 GLN T 98 GLN T 185 GLN U 38 GLN U 97 HIS V 38 GLN ** V 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 38 GLN X 38 GLN X 213 GLN Y 38 GLN Y 43 HIS Z 38 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.087147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.068932 restraints weight = 317703.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.068932 restraints weight = 305400.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.068930 restraints weight = 305250.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.068930 restraints weight = 304600.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.068930 restraints weight = 304513.590| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 31089 Z= 0.230 Angle : 1.219 21.009 43433 Z= 0.533 Chirality : 0.114 1.961 5065 Planarity : 0.006 0.079 4372 Dihedral : 20.343 178.118 6959 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.25 % Allowed : 5.97 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.15), residues: 2876 helix: 0.00 (0.12), residues: 1742 sheet: -2.06 (0.32), residues: 243 loop : -1.52 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG Z 191 TYR 0.031 0.003 TYR A 196 PHE 0.020 0.002 PHE Y 106 TRP 0.023 0.002 TRP A 94 HIS 0.011 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.23 (31089) covalent geometry : angle 1.21864 / 0.53 (43433) hydrogen bonds : bond 0.06035 / 4.06 ( 1470) hydrogen bonds : angle 4.72946 / 3.45 ( 4109) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 226 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 95 ARG cc_start: 0.8709 (ptm-80) cc_final: 0.8309 (tmm-80) REVERT: R 206 ASN cc_start: 0.9463 (t0) cc_final: 0.9199 (t0) REVERT: R 214 MET cc_start: 0.9434 (tpp) cc_final: 0.8743 (tmm) REVERT: S 37 GLN cc_start: 0.8904 (tp40) cc_final: 0.8537 (pp30) REVERT: S 124 ASP cc_start: 0.9172 (m-30) cc_final: 0.8881 (t70) REVERT: S 159 ASP cc_start: 0.9510 (m-30) cc_final: 0.9270 (m-30) REVERT: S 210 MET cc_start: 0.9416 (mmp) cc_final: 0.9074 (mmm) REVERT: T 19 GLU cc_start: 0.9325 (tm-30) cc_final: 0.8865 (pm20) REVERT: T 142 ILE cc_start: 0.6422 (OUTLIER) cc_final: 0.6185 (tp) REVERT: T 156 ASP cc_start: 0.8071 (m-30) cc_final: 0.7837 (m-30) REVERT: T 206 ASN cc_start: 0.9691 (t0) cc_final: 0.9470 (t0) REVERT: U 104 ASP cc_start: 0.8961 (m-30) cc_final: 0.8761 (t0) REVERT: U 140 MET cc_start: 0.7652 (tpt) cc_final: 0.7386 (tpt) REVERT: V 190 PHE cc_start: 0.8486 (m-10) cc_final: 0.8190 (m-80) REVERT: W 159 ASP cc_start: 0.8779 (m-30) cc_final: 0.8523 (m-30) REVERT: W 247 ILE cc_start: 0.9661 (mt) cc_final: 0.9402 (mt) REVERT: X 210 MET cc_start: 0.9446 (mtm) cc_final: 0.9217 (ptp) REVERT: X 214 MET cc_start: 0.9360 (tpt) cc_final: 0.9096 (ttt) REVERT: Y 106 PHE cc_start: 0.8281 (m-80) cc_final: 0.7925 (m-80) REVERT: Z 21 LEU cc_start: 0.7316 (tt) cc_final: 0.6950 (mt) REVERT: Z 75 TYR cc_start: 0.8833 (m-10) cc_final: 0.8593 (m-10) REVERT: Z 108 LYS cc_start: 0.7707 (mptt) cc_final: 0.6953 (ptmm) outliers start: 6 outliers final: 2 residues processed: 232 average time/residue: 0.2531 time to fit residues: 86.7561 Evaluate side-chains 151 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 215 optimal weight: 20.0000 chunk 136 optimal weight: 0.0170 chunk 52 optimal weight: 7.9990 chunk 179 optimal weight: 20.0000 chunk 37 optimal weight: 50.0000 chunk 78 optimal weight: 20.0000 chunk 202 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN A 494 GLN A 506 GLN A 574 GLN A 598 GLN T 98 GLN V 43 HIS V 97 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.085230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.066433 restraints weight = 322213.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.066944 restraints weight = 287674.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.067637 restraints weight = 240231.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.067682 restraints weight = 223724.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.068040 restraints weight = 207621.546| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 31089 Z= 0.182 Angle : 0.956 16.984 43433 Z= 0.431 Chirality : 0.083 1.317 5065 Planarity : 0.005 0.103 4372 Dihedral : 19.844 179.632 6959 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.15), residues: 2876 helix: 0.42 (0.12), residues: 1752 sheet: -1.52 (0.43), residues: 153 loop : -1.46 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG W 95 TYR 0.042 0.002 TYR A 497 PHE 0.032 0.002 PHE A 347 TRP 0.016 0.002 TRP A 21 HIS 0.008 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (31089) covalent geometry : angle 0.95632 / 0.43 (43433) hydrogen bonds : bond 0.05495 / 3.66 ( 1470) hydrogen bonds : angle 4.35368 / 3.16 ( 4109) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 195 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 140 MET cc_start: 0.8439 (tmm) cc_final: 0.8230 (tmm) REVERT: R 210 MET cc_start: 0.9207 (tpt) cc_final: 0.8806 (mmp) REVERT: S 37 GLN cc_start: 0.8725 (tp40) cc_final: 0.8383 (pp30) REVERT: S 124 ASP cc_start: 0.9202 (m-30) cc_final: 0.8920 (t70) REVERT: S 159 ASP cc_start: 0.9412 (m-30) cc_final: 0.9179 (m-30) REVERT: T 19 GLU cc_start: 0.9344 (tm-30) cc_final: 0.8827 (pm20) REVERT: V 78 LYS cc_start: 0.9148 (mmpt) cc_final: 0.8936 (mmmt) REVERT: V 95 ARG cc_start: 0.7717 (ptp-170) cc_final: 0.7289 (mtt180) REVERT: V 215 VAL cc_start: 0.8244 (t) cc_final: 0.7979 (t) REVERT: X 210 MET cc_start: 0.9450 (mtm) cc_final: 0.9216 (ptp) REVERT: Y 106 PHE cc_start: 0.8024 (m-80) cc_final: 0.7695 (m-80) REVERT: Y 112 TYR cc_start: 0.6300 (t80) cc_final: 0.5848 (m-80) REVERT: Z 21 LEU cc_start: 0.7310 (tt) cc_final: 0.6948 (mt) REVERT: Z 75 TYR cc_start: 0.8852 (m-10) cc_final: 0.8602 (m-10) REVERT: Z 276 LYS cc_start: 0.6143 (mptt) cc_final: 0.5762 (mmtt) outliers start: 3 outliers final: 1 residues processed: 198 average time/residue: 0.2103 time to fit residues: 63.6083 Evaluate side-chains 135 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 242 optimal weight: 20.0000 chunk 310 optimal weight: 50.0000 chunk 120 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 291 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 281 optimal weight: 30.0000 chunk 53 optimal weight: 0.0870 chunk 114 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 HIS A 469 ASN A 494 GLN A 598 GLN S 43 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.083128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.064587 restraints weight = 327014.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.064906 restraints weight = 289018.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.065202 restraints weight = 266241.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.065413 restraints weight = 248159.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.065936 restraints weight = 225790.587| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6032 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 31089 Z= 0.188 Angle : 0.927 15.388 43433 Z= 0.422 Chirality : 0.076 1.340 5065 Planarity : 0.005 0.079 4372 Dihedral : 19.589 179.310 6959 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.15), residues: 2876 helix: 0.51 (0.12), residues: 1763 sheet: -1.58 (0.41), residues: 153 loop : -1.46 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 78 TYR 0.020 0.002 TYR T 112 PHE 0.017 0.002 PHE S 154 TRP 0.016 0.002 TRP Y 211 HIS 0.007 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (31089) covalent geometry : angle 0.92707 / 0.42 (43433) hydrogen bonds : bond 0.05203 / 3.41 ( 1470) hydrogen bonds : angle 4.28274 / 3.10 ( 4109) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 LEU cc_start: 0.9171 (mt) cc_final: 0.8918 (pp) REVERT: R 210 MET cc_start: 0.9081 (tpt) cc_final: 0.8722 (mmp) REVERT: S 37 GLN cc_start: 0.8750 (tp40) cc_final: 0.8355 (pp30) REVERT: S 124 ASP cc_start: 0.9214 (m-30) cc_final: 0.8935 (t70) REVERT: S 159 ASP cc_start: 0.9386 (m-30) cc_final: 0.9094 (m-30) REVERT: S 190 PHE cc_start: 0.7351 (m-80) cc_final: 0.7018 (m-80) REVERT: T 19 GLU cc_start: 0.9383 (tm-30) cc_final: 0.8843 (pm20) REVERT: T 139 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8554 (tt0) REVERT: T 156 ASP cc_start: 0.7466 (m-30) cc_final: 0.7233 (m-30) REVERT: U 140 MET cc_start: 0.7465 (tpt) cc_final: 0.7258 (tpt) REVERT: V 215 VAL cc_start: 0.8451 (t) cc_final: 0.8051 (t) REVERT: W 271 VAL cc_start: 0.8240 (t) cc_final: 0.8013 (m) REVERT: X 210 MET cc_start: 0.9453 (mtm) cc_final: 0.9220 (ptp) REVERT: Y 106 PHE cc_start: 0.8062 (m-80) cc_final: 0.7731 (m-80) REVERT: Z 21 LEU cc_start: 0.7379 (tt) cc_final: 0.7012 (mt) REVERT: Z 75 TYR cc_start: 0.8877 (m-10) cc_final: 0.8653 (m-10) REVERT: Z 276 LYS cc_start: 0.6242 (mptt) cc_final: 0.5831 (mmtt) outliers start: 2 outliers final: 0 residues processed: 175 average time/residue: 0.1996 time to fit residues: 55.6841 Evaluate side-chains 126 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 18 optimal weight: 0.9980 chunk 258 optimal weight: 30.0000 chunk 182 optimal weight: 20.0000 chunk 180 optimal weight: 20.0000 chunk 238 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 295 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 117 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN R 77 HIS R 97 HIS V 97 HIS ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.081383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.062912 restraints weight = 323670.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.063164 restraints weight = 300974.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.063203 restraints weight = 282865.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.064339 restraints weight = 254038.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.063702 restraints weight = 227949.576| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 31089 Z= 0.187 Angle : 0.887 13.070 43433 Z= 0.411 Chirality : 0.071 1.439 5065 Planarity : 0.005 0.091 4372 Dihedral : 19.493 177.921 6959 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.15), residues: 2876 helix: 0.57 (0.12), residues: 1767 sheet: -1.55 (0.40), residues: 155 loop : -1.36 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 525 TYR 0.038 0.002 TYR A 497 PHE 0.025 0.002 PHE X 196 TRP 0.014 0.002 TRP W 211 HIS 0.007 0.001 HIS T 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 (31089) covalent geometry : angle 0.88705 / 0.41 (43433) hydrogen bonds : bond 0.05049 / 3.38 ( 1470) hydrogen bonds : angle 4.26235 / 3.08 ( 4109) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 LEU cc_start: 0.9115 (mt) cc_final: 0.8879 (pp) REVERT: S 37 GLN cc_start: 0.8825 (tp40) cc_final: 0.8270 (pp30) REVERT: S 124 ASP cc_start: 0.9206 (m-30) cc_final: 0.8946 (t70) REVERT: S 190 PHE cc_start: 0.7457 (m-80) cc_final: 0.7112 (m-80) REVERT: T 19 GLU cc_start: 0.9419 (tm-30) cc_final: 0.8900 (pm20) REVERT: T 136 CYS cc_start: 0.4670 (m) cc_final: 0.3112 (m) REVERT: T 139 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8581 (tt0) REVERT: U 125 PHE cc_start: 0.5810 (m-10) cc_final: 0.5279 (m-10) REVERT: W 213 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7726 (pm20) REVERT: X 210 MET cc_start: 0.9477 (mtm) cc_final: 0.9233 (mmp) REVERT: Y 106 PHE cc_start: 0.8138 (m-80) cc_final: 0.7708 (m-80) REVERT: Z 21 LEU cc_start: 0.7436 (tt) cc_final: 0.7058 (mt) REVERT: Z 75 TYR cc_start: 0.8897 (m-10) cc_final: 0.8670 (m-10) REVERT: Z 207 THR cc_start: 0.3558 (m) cc_final: 0.3080 (m) REVERT: Z 276 LYS cc_start: 0.6137 (mptt) cc_final: 0.5740 (mmtt) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.2107 time to fit residues: 54.5628 Evaluate side-chains 116 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 159 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 292 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 30.0000 chunk 291 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN R 77 HIS R 97 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.080983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.062713 restraints weight = 326140.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.062890 restraints weight = 295980.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.062958 restraints weight = 272840.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.063007 restraints weight = 271089.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.063025 restraints weight = 262351.974| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31089 Z= 0.157 Angle : 0.845 12.197 43433 Z= 0.389 Chirality : 0.069 1.429 5065 Planarity : 0.005 0.077 4372 Dihedral : 19.455 178.613 6959 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 2876 helix: 0.74 (0.12), residues: 1756 sheet: -1.49 (0.41), residues: 155 loop : -1.35 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 63 TYR 0.025 0.002 TYR A 497 PHE 0.020 0.002 PHE V 190 TRP 0.024 0.002 TRP U 45 HIS 0.009 0.001 HIS T 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (31089) covalent geometry : angle 0.84496 / 0.39 (43433) hydrogen bonds : bond 0.04633 / 3.09 ( 1470) hydrogen bonds : angle 4.21887 / 3.05 ( 4109) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 LEU cc_start: 0.9144 (mt) cc_final: 0.8906 (pp) REVERT: R 210 MET cc_start: 0.9087 (tpt) cc_final: 0.8850 (mmp) REVERT: S 37 GLN cc_start: 0.8803 (tp40) cc_final: 0.8260 (pp30) REVERT: S 124 ASP cc_start: 0.9173 (m-30) cc_final: 0.8903 (t70) REVERT: S 190 PHE cc_start: 0.7436 (m-80) cc_final: 0.6993 (m-80) REVERT: T 19 GLU cc_start: 0.9399 (tm-30) cc_final: 0.8858 (pm20) REVERT: T 112 TYR cc_start: 0.8389 (t80) cc_final: 0.7962 (t80) REVERT: T 136 CYS cc_start: 0.3662 (m) cc_final: 0.3096 (m) REVERT: T 139 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8642 (mp0) REVERT: T 229 MET cc_start: 0.3089 (mmp) cc_final: 0.2767 (mmp) REVERT: U 125 PHE cc_start: 0.5525 (m-10) cc_final: 0.4925 (m-80) REVERT: V 106 PHE cc_start: 0.8484 (m-80) cc_final: 0.8051 (m-80) REVERT: V 127 ASP cc_start: 0.9539 (m-30) cc_final: 0.9278 (m-30) REVERT: X 179 VAL cc_start: 0.8321 (t) cc_final: 0.8001 (p) REVERT: X 210 MET cc_start: 0.9489 (mtm) cc_final: 0.9228 (mmp) REVERT: Y 106 PHE cc_start: 0.8209 (m-80) cc_final: 0.7764 (m-80) REVERT: Z 21 LEU cc_start: 0.7485 (tt) cc_final: 0.7116 (mt) REVERT: Z 75 TYR cc_start: 0.8974 (m-10) cc_final: 0.8745 (m-10) REVERT: Z 276 LYS cc_start: 0.6474 (mptt) cc_final: 0.6114 (mmtt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2042 time to fit residues: 51.4815 Evaluate side-chains 114 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 307 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 126 optimal weight: 30.0000 chunk 135 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 182 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN S 77 HIS ** V 269 GLN ** 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 = 0.4607 r_free = 0.4607 target = 0.078863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.060540 restraints weight = 328390.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.060709 restraints weight = 306044.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.061572 restraints weight = 270471.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.061862 restraints weight = 238950.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.062044 restraints weight = 222590.728| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 31089 Z= 0.189 Angle : 0.863 12.322 43433 Z= 0.403 Chirality : 0.067 1.408 5065 Planarity : 0.005 0.080 4372 Dihedral : 19.440 177.033 6959 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.15), residues: 2876 helix: 0.63 (0.12), residues: 1755 sheet: -2.00 (0.32), residues: 254 loop : -1.20 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG W 258 TYR 0.032 0.002 TYR X 73 PHE 0.020 0.002 PHE Y 196 TRP 0.025 0.002 TRP X 45 HIS 0.008 0.002 HIS W 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (31089) covalent geometry : angle 0.86350 / 0.40 (43433) hydrogen bonds : bond 0.05091 / 3.41 ( 1470) hydrogen bonds : angle 4.31607 / 3.11 ( 4109) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 LEU cc_start: 0.9087 (mt) cc_final: 0.8827 (pp) REVERT: S 124 ASP cc_start: 0.9255 (m-30) cc_final: 0.8987 (t70) REVERT: T 19 GLU cc_start: 0.9395 (tm-30) cc_final: 0.8837 (pm20) REVERT: T 136 CYS cc_start: 0.4565 (m) cc_final: 0.3834 (m) REVERT: U 21 LEU cc_start: 0.8818 (tt) cc_final: 0.8589 (mt) REVERT: U 125 PHE cc_start: 0.6085 (m-10) cc_final: 0.5423 (m-80) REVERT: V 106 PHE cc_start: 0.8677 (m-80) cc_final: 0.8434 (m-80) REVERT: X 105 LEU cc_start: 0.9226 (tp) cc_final: 0.9005 (tp) REVERT: X 179 VAL cc_start: 0.8412 (t) cc_final: 0.8125 (p) REVERT: X 210 MET cc_start: 0.9466 (mtm) cc_final: 0.9211 (mmp) REVERT: Y 106 PHE cc_start: 0.8202 (m-80) cc_final: 0.8000 (m-80) REVERT: Z 21 LEU cc_start: 0.7461 (tt) cc_final: 0.7094 (mt) REVERT: Z 75 TYR cc_start: 0.8961 (m-10) cc_final: 0.8722 (m-10) REVERT: Z 276 LYS cc_start: 0.6465 (mptt) cc_final: 0.6136 (mmtt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2026 time to fit residues: 48.9474 Evaluate side-chains 108 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 196 optimal weight: 7.9990 chunk 105 optimal weight: 0.0870 chunk 198 optimal weight: 0.9980 chunk 298 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 283 optimal weight: 50.0000 chunk 199 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 128 optimal weight: 40.0000 chunk 142 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 64 GLN A 297 GLN A 494 GLN A 598 GLN S 77 HIS ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.065483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.052476 restraints weight = 417749.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.052945 restraints weight = 375324.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.053287 restraints weight = 345744.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.053467 restraints weight = 324589.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.053695 restraints weight = 310923.149| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.6001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 31089 Z= 0.142 Angle : 0.816 11.981 43433 Z= 0.376 Chirality : 0.065 1.399 5065 Planarity : 0.004 0.044 4372 Dihedral : 19.409 179.506 6959 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.04 % Allowed : 1.11 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.15), residues: 2876 helix: 0.82 (0.12), residues: 1757 sheet: -2.00 (0.32), residues: 254 loop : -1.16 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 100 TYR 0.034 0.002 TYR A 497 PHE 0.014 0.001 PHE U 196 TRP 0.025 0.002 TRP X 45 HIS 0.005 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (31089) covalent geometry : angle 0.81623 / 0.38 (43433) hydrogen bonds : bond 0.04338 / 2.95 ( 1470) hydrogen bonds : angle 4.22542 / 3.05 ( 4109) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 LEU cc_start: 0.9558 (mt) cc_final: 0.9293 (pp) REVERT: S 37 GLN cc_start: 0.9298 (tp40) cc_final: 0.8724 (pp30) REVERT: S 124 ASP cc_start: 0.9009 (m-30) cc_final: 0.8762 (t70) REVERT: T 19 GLU cc_start: 0.9682 (tm-30) cc_final: 0.9298 (pm20) REVERT: T 56 CYS cc_start: 0.8347 (p) cc_final: 0.8124 (p) REVERT: V 106 PHE cc_start: 0.8625 (m-80) cc_final: 0.8314 (m-80) REVERT: Z 21 LEU cc_start: 0.7355 (tt) cc_final: 0.7062 (mt) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.1987 time to fit residues: 48.1413 Evaluate side-chains 105 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 43 optimal weight: 0.0470 chunk 144 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 247 optimal weight: 6.9990 chunk 219 optimal weight: 7.9990 chunk 262 optimal weight: 30.0000 chunk 267 optimal weight: 9.9990 chunk 141 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 494 GLN A 598 GLN ** V 269 GLN ** 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 = 0.4221 r_free = 0.4221 target = 0.064685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.051770 restraints weight = 412205.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.052218 restraints weight = 375686.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.052537 restraints weight = 348684.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.052740 restraints weight = 328751.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.052933 restraints weight = 316076.990| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31089 Z= 0.153 Angle : 0.817 12.752 43433 Z= 0.378 Chirality : 0.064 1.343 5065 Planarity : 0.004 0.056 4372 Dihedral : 19.363 178.663 6959 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 2876 helix: 0.80 (0.12), residues: 1757 sheet: -2.03 (0.32), residues: 254 loop : -1.13 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 100 TYR 0.023 0.002 TYR T 112 PHE 0.018 0.002 PHE X 106 TRP 0.021 0.002 TRP X 45 HIS 0.006 0.001 HIS T 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (31089) covalent geometry : angle 0.81745 / 0.38 (43433) hydrogen bonds : bond 0.04496 / 3.04 ( 1470) hydrogen bonds : angle 4.30253 / 3.10 ( 4109) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.7936 (mpp) cc_final: 0.7353 (pmm) REVERT: A 357 LEU cc_start: 0.9560 (mt) cc_final: 0.9280 (pp) REVERT: R 210 MET cc_start: 0.9153 (tpt) cc_final: 0.8929 (mmp) REVERT: S 37 GLN cc_start: 0.9306 (tp40) cc_final: 0.8727 (pp30) REVERT: S 124 ASP cc_start: 0.9066 (m-30) cc_final: 0.8825 (t70) REVERT: T 19 GLU cc_start: 0.9680 (tm-30) cc_final: 0.9287 (pm20) REVERT: T 56 CYS cc_start: 0.8393 (p) cc_final: 0.8160 (p) REVERT: T 229 MET cc_start: 0.1827 (mmp) cc_final: 0.1621 (mmp) REVERT: U 125 PHE cc_start: 0.5836 (m-10) cc_final: 0.5488 (m-80) REVERT: V 106 PHE cc_start: 0.8656 (m-80) cc_final: 0.8334 (m-80) REVERT: Z 21 LEU cc_start: 0.7433 (tt) cc_final: 0.7136 (mt) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1957 time to fit residues: 45.6377 Evaluate side-chains 107 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 252 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 307 optimal weight: 9.9990 chunk 253 optimal weight: 0.5980 chunk 239 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 156 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 35 optimal weight: 0.0030 overall best weight: 2.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 494 GLN A 598 GLN S 98 GLN V 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.064916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.051802 restraints weight = 413389.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.052302 restraints weight = 377021.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.052636 restraints weight = 347797.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.052794 restraints weight = 327112.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.053028 restraints weight = 315824.848| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.6368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31089 Z= 0.139 Angle : 0.804 12.112 43433 Z= 0.372 Chirality : 0.063 1.329 5065 Planarity : 0.004 0.043 4372 Dihedral : 19.328 179.842 6959 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 2876 helix: 0.86 (0.12), residues: 1758 sheet: -1.99 (0.32), residues: 254 loop : -1.11 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG T 148 TYR 0.030 0.002 TYR A 497 PHE 0.018 0.001 PHE V 190 TRP 0.025 0.002 TRP W 211 HIS 0.005 0.001 HIS T 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (31089) covalent geometry : angle 0.80415 / 0.37 (43433) hydrogen bonds : bond 0.04251 / 2.90 ( 1470) hydrogen bonds : angle 4.24304 / 3.07 ( 4109) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.7880 (mpp) cc_final: 0.7281 (pmm) REVERT: A 357 LEU cc_start: 0.9565 (mt) cc_final: 0.9302 (pp) REVERT: R 210 MET cc_start: 0.9140 (tpt) cc_final: 0.8874 (mmp) REVERT: S 37 GLN cc_start: 0.9254 (tp40) cc_final: 0.8707 (pp30) REVERT: S 124 ASP cc_start: 0.9020 (m-30) cc_final: 0.8611 (t70) REVERT: T 19 GLU cc_start: 0.9695 (tm-30) cc_final: 0.9335 (pm20) REVERT: T 56 CYS cc_start: 0.8280 (p) cc_final: 0.8050 (p) REVERT: U 105 LEU cc_start: 0.8796 (tp) cc_final: 0.8504 (pp) REVERT: U 125 PHE cc_start: 0.5734 (m-10) cc_final: 0.5390 (m-80) REVERT: V 106 PHE cc_start: 0.8583 (m-80) cc_final: 0.8281 (m-80) REVERT: Z 21 LEU cc_start: 0.7430 (tt) cc_final: 0.7129 (mt) REVERT: Z 75 TYR cc_start: 0.9019 (m-80) cc_final: 0.8805 (m-80) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1934 time to fit residues: 45.1791 Evaluate side-chains 108 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 155 optimal weight: 30.0000 chunk 93 optimal weight: 30.0000 chunk 142 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 258 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 165 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 494 GLN A 584 ASN S 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.064140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.051342 restraints weight = 418211.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.051803 restraints weight = 379381.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.052123 restraints weight = 350453.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.052290 restraints weight = 329437.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.052495 restraints weight = 316348.372| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 31089 Z= 0.159 Angle : 0.812 12.476 43433 Z= 0.378 Chirality : 0.063 1.292 5065 Planarity : 0.004 0.041 4372 Dihedral : 19.302 178.963 6959 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 2876 helix: 0.77 (0.12), residues: 1758 sheet: -1.98 (0.32), residues: 254 loop : -1.15 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 63 TYR 0.023 0.002 TYR Z 75 PHE 0.020 0.002 PHE X 190 TRP 0.030 0.002 TRP W 211 HIS 0.007 0.001 HIS T 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (31089) covalent geometry : angle 0.81184 / 0.38 (43433) hydrogen bonds : bond 0.04569 / 3.09 ( 1470) hydrogen bonds : angle 4.32185 / 3.12 ( 4109) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8525.82 seconds wall clock time: 146 minutes 47.10 seconds (8807.10 seconds total)