Starting phenix.real_space_refine on Sun Jul 5 20:15:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bd6_15976/07_2026/8bd6_15976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bd6_15976/07_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_15976/07_2026/8bd6_15976.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bd6_15976/07_2026/8bd6_15976.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bd6_15976/07_2026/8bd6_15976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bd6_15976/07_2026/8bd6_15976.map" model { file = "/net/cci-nas-00/data/ceres_data/8bd6_15976/07_2026/8bd6_15976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bd6_15976/07_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-dev-6108/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: {'RNA': 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: 7.40, per 1000 atoms: 0.25 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: 3.17 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 4.37 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: 7.38 Time building geometry restraints manager: 4.13 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: 39585 2.19 - 4.37: 3123 4.37 - 6.56: 446 6.56 - 8.75: 183 8.75 - 10.94: 96 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 - 35.99: 16842 35.99 - 71.97: 1341 71.97 - 107.96: 56 107.96 - 143.94: 4 143.94 - 179.93: 8 Dihedral angle restraints: 18251 sinusoidal: 9829 harmonic: 8422 Sorted by residual: dihedral pdb=" O4' U B 23 " pdb=" C1' U B 23 " pdb=" N1 U B 23 " pdb=" C2 U B 23 " ideal model delta sinusoidal sigma weight residual -128.00 51.93 -179.93 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 129 " pdb=" C1' U B 129 " pdb=" N1 U B 129 " pdb=" C2 U B 129 " ideal model delta sinusoidal sigma weight residual -128.00 51.34 -179.34 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 138 " pdb=" C1' U B 138 " pdb=" N1 U B 138 " pdb=" C2 U B 138 " ideal model delta sinusoidal sigma weight residual 232.00 54.90 177.10 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 18248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 4011 0.103 - 0.205: 805 0.205 - 0.308: 209 0.308 - 0.411: 20 0.411 - 0.513: 20 Chirality restraints: 5065 Sorted by residual: 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 chirality pdb=" CA ARG S 76 " pdb=" N ARG S 76 " pdb=" C ARG S 76 " pdb=" CB ARG S 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 chirality pdb=" CA ARG Z 76 " pdb=" N ARG Z 76 " pdb=" C ARG Z 76 " pdb=" CB ARG Z 76 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.54e+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: 10.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.860 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 34.910 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.060 ------------------------------------------------------------------------------- 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= 0.586 Angle : 1.366 10.937 43433 Z= 0.968 Chirality : 0.095 0.513 5065 Planarity : 0.006 0.054 4372 Dihedral : 21.294 179.930 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 0.00919 / 0.59 (31089) covalent geometry : angle 1.36581 / 0.97 (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 : 1.101 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: 0.2542 time to fit residues: 196.5206 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 : 1.007 ------------------------------------------------------------------------------- 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 304 HIS A 420 GLN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 GLN S 38 GLN S 97 HIS T 38 GLN T 98 GLN ** T 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.087163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.068559 restraints weight = 318425.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.068939 restraints weight = 289079.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.068939 restraints weight = 294209.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.068939 restraints weight = 294209.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.068939 restraints weight = 294209.624| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 31089 Z= 0.182 Angle : 0.785 12.664 43433 Z= 0.409 Chirality : 0.047 0.423 5065 Planarity : 0.006 0.071 4372 Dihedral : 20.128 179.861 6959 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.25 % Allowed : 5.27 % Favored : 94.48 % 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: -1.05 (0.15), residues: 2876 helix: 0.02 (0.12), residues: 1738 sheet: -2.07 (0.32), residues: 245 loop : -1.50 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Z 191 TYR 0.037 0.003 TYR A 196 PHE 0.018 0.002 PHE Y 106 TRP 0.016 0.002 TRP S 211 HIS 0.012 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (31089) covalent geometry : angle 0.78494 / 0.41 (43433) hydrogen bonds : bond 0.05994 / 4.02 ( 1470) hydrogen bonds : angle 4.74731 / 3.47 ( 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 231 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 225 time to evaluate : 1.132 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: R 95 ARG cc_start: 0.8698 (ptm-80) cc_final: 0.8315 (tmm-80) REVERT: R 210 MET cc_start: 0.8625 (mmp) cc_final: 0.8257 (mmm) REVERT: R 214 MET cc_start: 0.9420 (tpp) cc_final: 0.8944 (tmm) REVERT: S 37 GLN cc_start: 0.8878 (tp40) cc_final: 0.8513 (pp30) REVERT: S 124 ASP cc_start: 0.9144 (m-30) cc_final: 0.8852 (t70) REVERT: S 159 ASP cc_start: 0.9462 (m-30) cc_final: 0.9167 (m-30) REVERT: S 210 MET cc_start: 0.9447 (mmp) cc_final: 0.9148 (mmm) REVERT: T 19 GLU cc_start: 0.9269 (tm-30) cc_final: 0.8832 (pm20) REVERT: T 142 ILE cc_start: 0.6504 (OUTLIER) cc_final: 0.6259 (tp) REVERT: T 156 ASP cc_start: 0.7956 (m-30) cc_final: 0.7704 (m-30) REVERT: T 206 ASN cc_start: 0.9658 (t0) cc_final: 0.9450 (t0) REVERT: U 95 ARG cc_start: 0.8995 (ptm-80) cc_final: 0.8763 (tmm-80) REVERT: U 104 ASP cc_start: 0.8926 (m-30) cc_final: 0.8725 (t0) REVERT: V 190 PHE cc_start: 0.8568 (m-10) cc_final: 0.8251 (m-80) REVERT: W 159 ASP cc_start: 0.8795 (m-30) cc_final: 0.8522 (m-30) REVERT: X 140 MET cc_start: 0.6648 (ptm) cc_final: 0.6403 (ptm) REVERT: X 210 MET cc_start: 0.9436 (mtm) cc_final: 0.9177 (ptp) REVERT: X 214 MET cc_start: 0.9365 (tpt) cc_final: 0.9088 (ttt) REVERT: Y 106 PHE cc_start: 0.8202 (m-80) cc_final: 0.7841 (m-80) REVERT: Z 21 LEU cc_start: 0.7360 (tt) cc_final: 0.6991 (mt) REVERT: Z 75 TYR cc_start: 0.8837 (m-10) cc_final: 0.8592 (m-10) REVERT: Z 108 LYS cc_start: 0.7612 (mptt) cc_final: 0.6853 (ptmm) REVERT: Z 112 TYR cc_start: 0.6731 (t80) cc_final: 0.6531 (t80) outliers start: 6 outliers final: 2 residues processed: 231 average time/residue: 0.2554 time to fit residues: 86.8733 Evaluate side-chains 156 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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: 8.9990 chunk 136 optimal weight: 0.0020 chunk 52 optimal weight: 40.0000 chunk 179 optimal weight: 8.9990 chunk 37 optimal weight: 0.0670 chunk 78 optimal weight: 30.0000 chunk 202 optimal weight: 0.6980 chunk 255 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 overall best weight: 2.3530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 351 ASN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 574 GLN A 598 GLN T 185 GLN ** V 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 97 HIS Y 43 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.071225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.058470 restraints weight = 400305.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.058974 restraints weight = 364700.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.059339 restraints weight = 336465.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.059560 restraints weight = 316977.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.059773 restraints weight = 303434.914| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 31089 Z= 0.150 Angle : 0.665 9.674 43433 Z= 0.352 Chirality : 0.043 0.345 5065 Planarity : 0.005 0.074 4372 Dihedral : 19.802 179.908 6959 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.29 % Allowed : 3.50 % Favored : 96.21 % 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: -0.50 (0.15), residues: 2876 helix: 0.42 (0.12), residues: 1753 sheet: -1.38 (0.44), residues: 153 loop : -1.45 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG W 95 TYR 0.030 0.002 TYR A 497 PHE 0.030 0.002 PHE A 347 TRP 0.016 0.002 TRP Y 211 HIS 0.008 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (31089) covalent geometry : angle 0.66527 / 0.35 (43433) hydrogen bonds : bond 0.05025 / 3.39 ( 1470) hydrogen bonds : angle 4.34086 / 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 204 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 197 time to evaluate : 1.153 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: R 140 MET cc_start: 0.8532 (tmm) cc_final: 0.8216 (tmm) REVERT: R 206 ASN cc_start: 0.9495 (t0) cc_final: 0.9275 (t0) REVERT: R 214 MET cc_start: 0.9326 (tpp) cc_final: 0.8677 (tmm) REVERT: S 37 GLN cc_start: 0.9204 (tp40) cc_final: 0.8761 (pp30) REVERT: S 124 ASP cc_start: 0.9064 (m-30) cc_final: 0.8808 (t70) REVERT: S 159 ASP cc_start: 0.9387 (m-30) cc_final: 0.9174 (m-30) REVERT: S 264 ASP cc_start: 0.8215 (m-30) cc_final: 0.7884 (m-30) REVERT: T 19 GLU cc_start: 0.9583 (tm-30) cc_final: 0.9127 (pm20) REVERT: T 229 MET cc_start: 0.2540 (mmm) cc_final: 0.2333 (mmp) REVERT: U 104 ASP cc_start: 0.9025 (m-30) cc_final: 0.8683 (t0) REVERT: U 140 MET cc_start: 0.7523 (tpt) cc_final: 0.7203 (tpt) REVERT: V 78 LYS cc_start: 0.9372 (mmpt) cc_final: 0.9159 (mmmt) REVERT: V 95 ARG cc_start: 0.7801 (ptp-170) cc_final: 0.7488 (mtt180) REVERT: X 140 MET cc_start: 0.6761 (ptm) cc_final: 0.6498 (ptm) REVERT: X 210 MET cc_start: 0.9429 (mtm) cc_final: 0.9211 (ptp) REVERT: X 214 MET cc_start: 0.9336 (tpt) cc_final: 0.9021 (ttt) REVERT: Y 106 PHE cc_start: 0.8094 (m-80) cc_final: 0.7783 (m-80) REVERT: Z 21 LEU cc_start: 0.7185 (tt) cc_final: 0.6898 (mt) REVERT: Z 75 TYR cc_start: 0.8949 (m-10) cc_final: 0.8732 (m-10) REVERT: Z 113 LEU cc_start: 0.6091 (mt) cc_final: 0.5876 (mt) outliers start: 7 outliers final: 2 residues processed: 204 average time/residue: 0.2167 time to fit residues: 68.0249 Evaluate side-chains 139 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 137 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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: 6.9990 chunk 97 optimal weight: 8.9990 chunk 291 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 281 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 114 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN A 370 HIS A 469 ASN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 HIS T 98 GLN ** T 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 43 HIS ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 77 HIS Y 43 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.068761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.056121 restraints weight = 406011.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.056619 restraints weight = 366398.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.056978 restraints weight = 338026.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.057207 restraints weight = 317258.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.057432 restraints weight = 303346.166| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31089 Z= 0.181 Angle : 0.683 8.956 43433 Z= 0.361 Chirality : 0.043 0.400 5065 Planarity : 0.005 0.052 4372 Dihedral : 19.588 178.559 6959 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.08 % Allowed : 3.71 % Favored : 96.21 % 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: 0.58 (0.12), residues: 1752 sheet: -1.42 (0.42), residues: 153 loop : -1.37 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 116 TYR 0.020 0.002 TYR T 112 PHE 0.017 0.002 PHE S 154 TRP 0.014 0.002 TRP A 21 HIS 0.008 0.001 HIS A 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 (31089) covalent geometry : angle 0.68283 / 0.36 (43433) hydrogen bonds : bond 0.05047 / 3.39 ( 1470) hydrogen bonds : angle 4.28709 / 3.11 ( 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 180 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 178 time to evaluate : 1.051 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: R 210 MET cc_start: 0.9245 (tpt) cc_final: 0.8947 (mmp) REVERT: S 37 GLN cc_start: 0.9261 (tp40) cc_final: 0.8774 (pp30) REVERT: S 124 ASP cc_start: 0.9021 (m-30) cc_final: 0.8789 (t70) REVERT: S 159 ASP cc_start: 0.9360 (m-30) cc_final: 0.9096 (m-30) REVERT: T 19 GLU cc_start: 0.9628 (tm-30) cc_final: 0.9186 (pm20) REVERT: T 136 CYS cc_start: 0.3802 (m) cc_final: 0.0807 (m) REVERT: T 139 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8558 (tt0) REVERT: U 54 LYS cc_start: 0.8897 (mmpt) cc_final: 0.8634 (mtmt) REVERT: U 104 ASP cc_start: 0.9061 (m-30) cc_final: 0.8584 (t0) REVERT: U 140 MET cc_start: 0.7606 (tpt) cc_final: 0.7240 (tpt) REVERT: V 95 ARG cc_start: 0.8009 (ptp-170) cc_final: 0.7802 (mtm-85) REVERT: V 215 VAL cc_start: 0.8133 (t) cc_final: 0.7652 (t) REVERT: X 140 MET cc_start: 0.6767 (ptm) cc_final: 0.6521 (ptm) REVERT: X 210 MET cc_start: 0.9422 (mtm) cc_final: 0.9210 (ptp) REVERT: X 214 MET cc_start: 0.9349 (tpt) cc_final: 0.9078 (ttt) REVERT: Y 106 PHE cc_start: 0.8135 (m-80) cc_final: 0.7867 (m-80) REVERT: Z 21 LEU cc_start: 0.7305 (tt) cc_final: 0.7040 (mt) REVERT: Z 75 TYR cc_start: 0.8987 (m-10) cc_final: 0.8782 (m-10) REVERT: Z 113 LEU cc_start: 0.6366 (mt) cc_final: 0.6035 (mt) REVERT: Z 207 THR cc_start: -0.0792 (m) cc_final: -0.1192 (m) outliers start: 2 outliers final: 0 residues processed: 180 average time/residue: 0.2198 time to fit residues: 61.7525 Evaluate side-chains 133 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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: 8.9990 chunk 258 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 227 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 295 optimal weight: 2.9990 chunk 3 optimal weight: 30.0000 chunk 117 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 S 77 HIS ** T 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.080930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.062834 restraints weight = 325748.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.062917 restraints weight = 304752.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.062917 restraints weight = 277778.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.062917 restraints weight = 277778.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.062917 restraints weight = 277778.913| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6164 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 31089 Z= 0.184 Angle : 0.689 10.108 43433 Z= 0.364 Chirality : 0.044 0.318 5065 Planarity : 0.005 0.073 4372 Dihedral : 19.516 179.128 6959 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.04 % Allowed : 3.87 % 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: -0.33 (0.15), residues: 2876 helix: 0.56 (0.12), residues: 1765 sheet: -1.44 (0.41), residues: 155 loop : -1.38 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG T 53 TYR 0.027 0.002 TYR V 112 PHE 0.022 0.002 PHE V 190 TRP 0.017 0.002 TRP Y 211 HIS 0.008 0.002 HIS A 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (31089) covalent geometry : angle 0.68876 / 0.36 (43433) hydrogen bonds : bond 0.04886 / 3.31 ( 1470) hydrogen bonds : angle 4.25978 / 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 170 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 LEU cc_start: 0.9104 (mt) cc_final: 0.8902 (pp) REVERT: R 214 MET cc_start: 0.9472 (mmp) cc_final: 0.9072 (tpt) REVERT: S 37 GLN cc_start: 0.8688 (tp40) cc_final: 0.8185 (pp30) REVERT: S 124 ASP cc_start: 0.9204 (m-30) cc_final: 0.8931 (t70) REVERT: S 190 PHE cc_start: 0.7351 (m-80) cc_final: 0.6760 (m-80) REVERT: T 19 GLU cc_start: 0.9445 (tm-30) cc_final: 0.8922 (pm20) REVERT: T 139 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8652 (tt0) REVERT: U 104 ASP cc_start: 0.8933 (m-30) cc_final: 0.8611 (t0) REVERT: U 125 PHE cc_start: 0.5905 (m-10) cc_final: 0.5317 (m-80) REVERT: U 140 MET cc_start: 0.7693 (tpt) cc_final: 0.7394 (tpt) REVERT: V 215 VAL cc_start: 0.8495 (t) cc_final: 0.8202 (t) REVERT: X 140 MET cc_start: 0.6735 (ptm) cc_final: 0.6450 (ptm) REVERT: X 210 MET cc_start: 0.9475 (mtm) cc_final: 0.9225 (mmp) REVERT: Y 106 PHE cc_start: 0.8120 (m-80) cc_final: 0.7680 (m-80) REVERT: Z 21 LEU cc_start: 0.7484 (tt) cc_final: 0.7112 (mt) REVERT: Z 75 TYR cc_start: 0.8885 (m-10) cc_final: 0.8661 (m-10) REVERT: Z 276 LYS cc_start: 0.5788 (mptt) cc_final: 0.5279 (mmtt) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.2137 time to fit residues: 56.7313 Evaluate side-chains 117 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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: 6.9990 chunk 131 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 292 optimal weight: 3.9990 chunk 49 optimal weight: 40.0000 chunk 32 optimal weight: 40.0000 chunk 291 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 T 213 GLN ** T 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4627 r_free = 0.4627 target = 0.080113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.061636 restraints weight = 326960.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.062324 restraints weight = 282026.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.062664 restraints weight = 247449.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.062807 restraints weight = 233718.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.062926 restraints weight = 226500.710| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31089 Z= 0.164 Angle : 0.655 10.668 43433 Z= 0.345 Chirality : 0.042 0.284 5065 Planarity : 0.005 0.048 4372 Dihedral : 19.483 178.903 6959 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % 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: -0.28 (0.15), residues: 2876 helix: 0.61 (0.12), residues: 1765 sheet: -1.49 (0.40), residues: 155 loop : -1.36 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 78 TYR 0.023 0.002 TYR A 497 PHE 0.016 0.002 PHE Y 196 TRP 0.026 0.002 TRP U 45 HIS 0.008 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (31089) covalent geometry : angle 0.65504 / 0.35 (43433) hydrogen bonds : bond 0.04717 / 3.18 ( 1470) hydrogen bonds : angle 4.27123 / 3.09 ( 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 165 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7346 (tpt170) cc_final: 0.6231 (mtt180) REVERT: A 357 LEU cc_start: 0.9189 (mt) cc_final: 0.8949 (pp) REVERT: R 140 MET cc_start: 0.8862 (ppp) cc_final: 0.8482 (ppp) REVERT: R 210 MET cc_start: 0.9094 (tpt) cc_final: 0.8694 (mmp) REVERT: S 37 GLN cc_start: 0.8756 (tp40) cc_final: 0.8217 (pp30) REVERT: S 124 ASP cc_start: 0.9216 (m-30) cc_final: 0.8963 (t70) REVERT: T 19 GLU cc_start: 0.9384 (tm-30) cc_final: 0.8835 (pm20) REVERT: T 136 CYS cc_start: 0.4511 (m) cc_final: 0.4196 (m) REVERT: U 104 ASP cc_start: 0.8582 (m-30) cc_final: 0.8353 (t0) REVERT: U 125 PHE cc_start: 0.5853 (m-10) cc_final: 0.5325 (m-80) REVERT: U 140 MET cc_start: 0.7631 (tpt) cc_final: 0.7404 (tpt) REVERT: V 106 PHE cc_start: 0.8723 (m-80) cc_final: 0.8340 (m-80) REVERT: V 127 ASP cc_start: 0.9655 (m-30) cc_final: 0.9429 (m-30) REVERT: X 105 LEU cc_start: 0.9222 (tp) cc_final: 0.8915 (pp) REVERT: X 179 VAL cc_start: 0.8322 (t) cc_final: 0.8017 (p) REVERT: X 210 MET cc_start: 0.9471 (mtm) cc_final: 0.9246 (mmp) REVERT: Y 106 PHE cc_start: 0.8183 (m-80) cc_final: 0.7982 (m-80) REVERT: Z 21 LEU cc_start: 0.7461 (tt) cc_final: 0.7096 (mt) REVERT: Z 75 TYR cc_start: 0.8917 (m-10) cc_final: 0.8674 (m-10) REVERT: Z 140 MET cc_start: 0.3979 (mtm) cc_final: 0.2841 (mtm) REVERT: Z 276 LYS cc_start: 0.6206 (mptt) cc_final: 0.5860 (mmtt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1913 time to fit residues: 49.7713 Evaluate side-chains 118 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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: 5.9990 chunk 162 optimal weight: 9.9990 chunk 140 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 126 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 7 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 182 optimal weight: 5.9990 chunk 75 optimal weight: 30.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 598 GLN T 22 GLN V 37 GLN W 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.063289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.051580 restraints weight = 420863.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.051992 restraints weight = 384558.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.052272 restraints weight = 356991.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.052446 restraints weight = 337292.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.052606 restraints weight = 324519.996| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 31089 Z= 0.217 Angle : 0.752 11.769 43433 Z= 0.398 Chirality : 0.046 0.450 5065 Planarity : 0.006 0.091 4372 Dihedral : 19.564 179.201 6959 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.04 % Allowed : 2.35 % Favored : 97.61 % 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: -0.74 (0.15), residues: 2876 helix: 0.28 (0.12), residues: 1757 sheet: -2.06 (0.31), residues: 254 loop : -1.39 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG W 254 TYR 0.028 0.003 TYR X 73 PHE 0.026 0.003 PHE Y 196 TRP 0.028 0.002 TRP X 45 HIS 0.011 0.002 HIS T 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 (31089) covalent geometry : angle 0.75155 / 0.40 (43433) hydrogen bonds : bond 0.05554 / 3.73 ( 1470) hydrogen bonds : angle 4.53349 / 3.28 ( 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 151 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.120 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: A 110 ARG cc_start: 0.7229 (tpt170) cc_final: 0.6250 (mtt90) REVERT: A 357 LEU cc_start: 0.9549 (mt) cc_final: 0.9310 (pp) REVERT: R 140 MET cc_start: 0.9115 (ppp) cc_final: 0.8692 (ppp) REVERT: R 214 MET cc_start: 0.9379 (tpp) cc_final: 0.8754 (tmm) REVERT: S 124 ASP cc_start: 0.9031 (m-30) cc_final: 0.8784 (t70) REVERT: S 162 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7326 (mt-10) REVERT: T 19 GLU cc_start: 0.9674 (tm-30) cc_final: 0.9284 (pm20) REVERT: T 56 CYS cc_start: 0.8581 (p) cc_final: 0.8344 (p) REVERT: U 104 ASP cc_start: 0.8948 (m-30) cc_final: 0.8446 (t0) REVERT: U 125 PHE cc_start: 0.5606 (m-10) cc_final: 0.5313 (m-80) REVERT: U 140 MET cc_start: 0.7938 (tpt) cc_final: 0.7727 (tpt) REVERT: X 97 HIS cc_start: 0.8551 (p90) cc_final: 0.8274 (p90) REVERT: Z 21 LEU cc_start: 0.7448 (tt) cc_final: 0.7184 (mt) REVERT: Z 140 MET cc_start: 0.3404 (mtm) cc_final: 0.2493 (mtm) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.2179 time to fit residues: 51.9160 Evaluate side-chains 111 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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: 8.9990 chunk 105 optimal weight: 0.9980 chunk 198 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 chunk 199 optimal weight: 7.9990 chunk 248 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN A 297 GLN A 494 GLN A 598 GLN T 213 GLN W 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.062993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.050648 restraints weight = 427001.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.051121 restraints weight = 383018.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 14)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.051321 restraints weight = 352139.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.051662 restraints weight = 333766.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.051852 restraints weight = 317606.953| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.6375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31089 Z= 0.171 Angle : 0.680 13.692 43433 Z= 0.358 Chirality : 0.043 0.391 5065 Planarity : 0.005 0.051 4372 Dihedral : 19.567 177.882 6959 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.04 % Allowed : 1.61 % Favored : 98.35 % 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: -0.63 (0.15), residues: 2876 helix: 0.40 (0.12), residues: 1754 sheet: -2.02 (0.32), residues: 254 loop : -1.40 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG U 195 TYR 0.025 0.002 TYR Z 73 PHE 0.023 0.002 PHE A 401 TRP 0.022 0.002 TRP X 45 HIS 0.027 0.002 HIS Z 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (31089) covalent geometry : angle 0.68001 / 0.36 (43433) hydrogen bonds : bond 0.04774 / 3.24 ( 1470) hydrogen bonds : angle 4.46101 / 3.22 ( 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 147 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.111 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: A 110 ARG cc_start: 0.7236 (tpt170) cc_final: 0.6281 (mtm-85) REVERT: A 357 LEU cc_start: 0.9574 (mt) cc_final: 0.9324 (pp) REVERT: R 140 MET cc_start: 0.9199 (ppp) cc_final: 0.8800 (ppp) REVERT: R 214 MET cc_start: 0.9352 (tpp) cc_final: 0.8744 (tmm) REVERT: S 124 ASP cc_start: 0.8991 (m-30) cc_final: 0.8746 (t70) REVERT: T 19 GLU cc_start: 0.9697 (tm-30) cc_final: 0.9327 (pm20) REVERT: T 56 CYS cc_start: 0.8534 (p) cc_final: 0.8288 (p) REVERT: U 140 MET cc_start: 0.7973 (tpt) cc_final: 0.7696 (tpt) REVERT: V 106 PHE cc_start: 0.8650 (m-80) cc_final: 0.8343 (m-80) REVERT: X 179 VAL cc_start: 0.7992 (t) cc_final: 0.7784 (p) REVERT: Z 21 LEU cc_start: 0.7481 (tt) cc_final: 0.7218 (mt) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.2177 time to fit residues: 50.9557 Evaluate side-chains 109 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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: 3.9990 chunk 144 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 247 optimal weight: 7.9990 chunk 219 optimal weight: 7.9990 chunk 262 optimal weight: 20.0000 chunk 267 optimal weight: 40.0000 chunk 141 optimal weight: 2.9990 chunk 46 optimal weight: 50.0000 chunk 92 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 494 GLN A 598 GLN R 97 HIS S 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.062669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.050234 restraints weight = 416762.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.050673 restraints weight = 379338.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.050995 restraints weight = 351198.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.051182 restraints weight = 330330.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.051182 restraints weight = 313831.930| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.6653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 31089 Z= 0.161 Angle : 0.679 10.900 43433 Z= 0.358 Chirality : 0.043 0.369 5065 Planarity : 0.005 0.064 4372 Dihedral : 19.495 177.751 6959 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: -0.61 (0.15), residues: 2876 helix: 0.41 (0.12), residues: 1754 sheet: -2.01 (0.32), residues: 254 loop : -1.40 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 254 TYR 0.035 0.002 TYR Z 75 PHE 0.019 0.002 PHE V 154 TRP 0.023 0.002 TRP X 45 HIS 0.018 0.002 HIS Z 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (31089) covalent geometry : angle 0.67904 / 0.36 (43433) hydrogen bonds : bond 0.04695 / 3.19 ( 1470) hydrogen bonds : angle 4.46510 / 3.22 ( 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 144 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.104 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: A 291 MET cc_start: 0.8001 (mpp) cc_final: 0.7772 (pmm) REVERT: A 405 MET cc_start: -0.2287 (mtt) cc_final: -0.2507 (mtt) REVERT: R 140 MET cc_start: 0.9189 (ppp) cc_final: 0.8803 (ppp) REVERT: R 214 MET cc_start: 0.9379 (tpp) cc_final: 0.8785 (tmm) REVERT: S 124 ASP cc_start: 0.9006 (m-30) cc_final: 0.8762 (t70) REVERT: T 19 GLU cc_start: 0.9695 (tm-30) cc_final: 0.9325 (pm20) REVERT: T 56 CYS cc_start: 0.8567 (p) cc_final: 0.8321 (p) REVERT: U 125 PHE cc_start: 0.5949 (m-10) cc_final: 0.5622 (m-80) REVERT: U 140 MET cc_start: 0.7984 (tpt) cc_final: 0.7682 (tpt) REVERT: V 106 PHE cc_start: 0.8623 (m-80) cc_final: 0.8256 (m-80) REVERT: Z 21 LEU cc_start: 0.7546 (tt) cc_final: 0.7259 (mt) REVERT: Z 75 TYR cc_start: 0.9038 (m-80) cc_final: 0.8836 (m-80) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2054 time to fit residues: 47.7648 Evaluate side-chains 110 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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: 7.9990 chunk 8 optimal weight: 5.9990 chunk 307 optimal weight: 20.0000 chunk 253 optimal weight: 6.9990 chunk 239 optimal weight: 0.7980 chunk 259 optimal weight: 3.9990 chunk 12 optimal weight: 40.0000 chunk 156 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 598 GLN R 97 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 = 0.4198 r_free = 0.4198 target = 0.063048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.050435 restraints weight = 417259.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.050895 restraints weight = 375036.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.051192 restraints weight = 344259.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.051383 restraints weight = 324341.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.051675 restraints weight = 307846.133| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31089 Z= 0.137 Angle : 0.654 11.371 43433 Z= 0.343 Chirality : 0.043 0.360 5065 Planarity : 0.004 0.046 4372 Dihedral : 19.416 178.047 6959 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -0.44 (0.15), residues: 2876 helix: 0.57 (0.12), residues: 1754 sheet: -1.95 (0.33), residues: 254 loop : -1.37 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 254 TYR 0.024 0.002 TYR A 497 PHE 0.031 0.002 PHE A 401 TRP 0.025 0.002 TRP X 45 HIS 0.019 0.001 HIS Z 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (31089) covalent geometry : angle 0.65352 / 0.34 (43433) hydrogen bonds : bond 0.04326 / 2.94 ( 1470) hydrogen bonds : angle 4.41587 / 3.17 ( 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 : 0.984 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 291 MET cc_start: 0.8071 (mpp) cc_final: 0.7866 (pmm) REVERT: A 598 GLN cc_start: 0.8558 (tp40) cc_final: 0.8312 (mt0) REVERT: R 140 MET cc_start: 0.9214 (ppp) cc_final: 0.8748 (ppp) REVERT: S 124 ASP cc_start: 0.9028 (m-30) cc_final: 0.8610 (t70) REVERT: T 19 GLU cc_start: 0.9695 (tm-30) cc_final: 0.9323 (pm20) REVERT: T 56 CYS cc_start: 0.8527 (p) cc_final: 0.8262 (p) REVERT: T 214 MET cc_start: 0.8229 (ppp) cc_final: 0.8027 (ppp) REVERT: U 105 LEU cc_start: 0.8735 (tp) cc_final: 0.8417 (pp) REVERT: U 125 PHE cc_start: 0.6145 (m-10) cc_final: 0.5810 (m-80) REVERT: V 106 PHE cc_start: 0.8599 (m-80) cc_final: 0.8253 (m-80) REVERT: X 190 PHE cc_start: 0.8507 (m-80) cc_final: 0.8015 (m-80) REVERT: Z 21 LEU cc_start: 0.7500 (tt) cc_final: 0.7208 (mt) REVERT: Z 75 TYR cc_start: 0.9044 (m-80) cc_final: 0.8810 (m-80) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2040 time to fit residues: 46.5617 Evaluate side-chains 111 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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: 10.0000 chunk 93 optimal weight: 30.0000 chunk 142 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 258 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 47 optimal weight: 0.0870 chunk 126 optimal weight: 20.0000 chunk 156 optimal weight: 8.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 494 GLN ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.063257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.050449 restraints weight = 409458.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.050896 restraints weight = 368727.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.051195 restraints weight = 340383.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.051440 restraints weight = 321627.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.051597 restraints weight = 307577.663| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.6891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31089 Z= 0.136 Angle : 0.634 10.785 43433 Z= 0.334 Chirality : 0.041 0.346 5065 Planarity : 0.004 0.045 4372 Dihedral : 19.316 178.490 6959 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % 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: -0.34 (0.15), residues: 2876 helix: 0.65 (0.12), residues: 1756 sheet: -1.91 (0.33), residues: 254 loop : -1.35 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG T 148 TYR 0.022 0.002 TYR Z 75 PHE 0.014 0.002 PHE S 154 TRP 0.061 0.002 TRP Z 211 HIS 0.018 0.001 HIS Z 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (31089) covalent geometry : angle 0.63419 / 0.33 (43433) hydrogen bonds : bond 0.04244 / 2.89 ( 1470) hydrogen bonds : angle 4.32496 / 3.12 ( 4109) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8290.74 seconds wall clock time: 143 minutes 1.23 seconds (8581.23 seconds total)