Starting phenix.real_space_refine on Mon Aug 25 19:09:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bd6_15976/08_2025/8bd6_15976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bd6_15976/08_2025/8bd6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bd6_15976/08_2025/8bd6_15976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bd6_15976/08_2025/8bd6_15976.map" model { file = "/net/cci-nas-00/data/ceres_data/8bd6_15976/08_2025/8bd6_15976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bd6_15976/08_2025/8bd6_15976.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 338 5.49 5 Mg 9 5.21 5 S 85 5.16 5 C 17646 2.51 5 N 5416 2.21 5 O 6457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 6.90, per 1000 atoms: 0.23 Number of scatterers: 29951 At special positions: 0 Unit cell: (149.5, 133.9, 198.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 85 16.00 P 338 15.00 Mg 9 11.99 O 6457 8.00 N 5416 7.00 C 17646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 4.46 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: 5.44 Time building geometry restraints manager: 3.25 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=" 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 bond pdb=" C ILE T 241 " pdb=" N GLY T 242 " ideal model delta sigma weight residual 1.334 1.274 0.060 1.21e-02 6.83e+03 2.42e+01 ... (remaining 31084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 39566 2.19 - 4.37: 3139 4.37 - 6.56: 448 6.56 - 8.75: 183 8.75 - 10.94: 97 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: 17404 35.99 - 71.97: 1814 71.97 - 107.96: 118 107.96 - 143.94: 4 143.94 - 179.93: 8 Dihedral angle restraints: 19348 sinusoidal: 10926 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 19345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 4010 0.103 - 0.205: 801 0.205 - 0.308: 215 0.308 - 0.411: 19 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: 14.780 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: 0.050 Extract box with map and model: 0.860 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 29.300 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 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 0.062 31089 Z= 0.574 Angle : 1.367 10.937 43433 Z= 0.960 Chirality : 0.095 0.513 5065 Planarity : 0.006 0.054 4372 Dihedral : 23.547 179.930 13894 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 aren 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 covalent geometry : bond 0.00917 (31089) covalent geometry : angle 1.36740 (43433) hydrogen bonds : bond 0.15810 ( 1470) hydrogen bonds : angle 7.47855 ( 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 : 0.691 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: 0.8368 (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: 0.4509 (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: 0.5996 (pt) REVERT: Y 95 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7123 (ptt90) REVERT: Y 199 LEU cc_start: -0.1685 (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: 0.0320 (pt) outliers start: 214 outliers final: 37 residues processed: 536 average time/residue: 0.2267 time to fit residues: 174.7859 Evaluate side-chains 244 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 185 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 38 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN A 370 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 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 38 GLN V 38 GLN V 43 HIS V 97 HIS 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.071081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.058204 restraints weight = 396694.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.058619 restraints weight = 364415.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.058911 restraints weight = 341617.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.059103 restraints weight = 325115.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.059291 restraints weight = 313772.957| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31089 Z= 0.159 Angle : 0.678 10.613 43433 Z= 0.359 Chirality : 0.042 0.349 5065 Planarity : 0.005 0.051 4372 Dihedral : 23.319 179.955 8056 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.15), residues: 2876 helix: 0.44 (0.12), residues: 1756 sheet: -1.31 (0.45), residues: 153 loop : -1.61 (0.18), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 100 TYR 0.036 0.002 TYR A 497 PHE 0.021 0.002 PHE Y 106 TRP 0.015 0.002 TRP U 211 HIS 0.009 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00328 (31089) covalent geometry : angle 0.67812 (43433) hydrogen bonds : bond 0.04859 ( 1470) hydrogen bonds : angle 4.34316 ( 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 230 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 228 time to evaluate : 1.015 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 210 MET cc_start: 0.8809 (mmp) cc_final: 0.8502 (mmm) REVERT: R 214 MET cc_start: 0.9300 (tpp) cc_final: 0.8866 (tmm) REVERT: S 37 GLN cc_start: 0.9231 (tp40) cc_final: 0.8790 (pp30) REVERT: S 124 ASP cc_start: 0.9064 (m-30) cc_final: 0.8803 (t70) REVERT: S 159 ASP cc_start: 0.9354 (m-30) cc_final: 0.9129 (m-30) REVERT: S 210 MET cc_start: 0.9507 (mmp) cc_final: 0.9271 (mmt) REVERT: T 19 GLU cc_start: 0.9623 (tm-30) cc_final: 0.9192 (pm20) REVERT: T 104 ASP cc_start: 0.9194 (m-30) cc_final: 0.8970 (t0) REVERT: T 105 LEU cc_start: 0.8718 (mt) cc_final: 0.8500 (mt) REVERT: T 229 MET cc_start: 0.2673 (mmt) cc_final: 0.2437 (mmp) REVERT: U 140 MET cc_start: 0.7509 (tpt) cc_final: 0.7110 (tpt) REVERT: V 190 PHE cc_start: 0.8534 (m-10) cc_final: 0.8291 (m-80) REVERT: W 159 ASP cc_start: 0.8921 (m-30) cc_final: 0.8549 (m-30) REVERT: W 271 VAL cc_start: 0.7742 (m) cc_final: 0.7484 (m) REVERT: X 210 MET cc_start: 0.9419 (mtm) cc_final: 0.9178 (ptm) REVERT: X 214 MET cc_start: 0.9285 (tpt) cc_final: 0.8932 (ttt) REVERT: Y 106 PHE cc_start: 0.8120 (m-80) cc_final: 0.7730 (m-80) REVERT: Z 21 LEU cc_start: 0.7162 (tt) cc_final: 0.6895 (mt) REVERT: Z 75 TYR cc_start: 0.8958 (m-10) cc_final: 0.8752 (m-10) REVERT: Z 229 MET cc_start: -0.1058 (mmt) cc_final: -0.1290 (ttt) outliers start: 2 outliers final: 0 residues processed: 229 average time/residue: 0.2259 time to fit residues: 76.5438 Evaluate side-chains 150 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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: 30.0000 chunk 136 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 179 optimal weight: 20.0000 chunk 37 optimal weight: 30.0000 chunk 78 optimal weight: 30.0000 chunk 202 optimal weight: 6.9990 chunk 255 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 154 optimal weight: 30.0000 overall best weight: 12.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 HIS A 595 GLN A 598 GLN R 77 HIS R 81 GLN ** S 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 185 GLN U 97 HIS ** U 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 38 GLN W 43 HIS Y 77 HIS Z 185 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.059875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.047847 restraints weight = 441782.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.048239 restraints weight = 399980.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.048538 restraints weight = 370146.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.048680 restraints weight = 348570.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.048878 restraints weight = 336074.056| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.6941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 31089 Z= 0.341 Angle : 0.968 12.375 43433 Z= 0.514 Chirality : 0.052 0.444 5065 Planarity : 0.008 0.091 4372 Dihedral : 24.125 179.386 8056 Min Nonbonded Distance : 1.620 Molprobity Statistics. All-atom Clashscore : 32.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.59 % Favored : 95.31 % Rotamer: Outliers : 0.58 % Allowed : 7.25 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.14), residues: 2876 helix: -0.59 (0.11), residues: 1755 sheet: -2.07 (0.32), residues: 274 loop : -1.68 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG S 249 TYR 0.047 0.004 TYR A 497 PHE 0.046 0.004 PHE Y 196 TRP 0.040 0.003 TRP U 45 HIS 0.014 0.003 HIS W 77 Details of bonding type rmsd covalent geometry : bond 0.00698 (31089) covalent geometry : angle 0.96820 (43433) hydrogen bonds : bond 0.07803 ( 1470) hydrogen bonds : angle 5.14473 ( 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 175 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.3479 (tmm) cc_final: 0.3137 (tpt) REVERT: A 357 LEU cc_start: 0.9549 (mt) cc_final: 0.9349 (pp) REVERT: R 140 MET cc_start: 0.9035 (ppp) cc_final: 0.8743 (ppp) REVERT: R 214 MET cc_start: 0.9271 (tpp) cc_final: 0.8677 (tmm) REVERT: S 124 ASP cc_start: 0.8970 (m-30) cc_final: 0.8764 (t70) REVERT: U 125 PHE cc_start: 0.6408 (m-10) cc_final: 0.6087 (m-80) REVERT: V 127 ASP cc_start: 0.9656 (m-30) cc_final: 0.9350 (p0) REVERT: X 179 VAL cc_start: 0.8025 (t) cc_final: 0.7813 (p) REVERT: X 190 PHE cc_start: 0.8079 (m-80) cc_final: 0.7759 (m-80) REVERT: X 214 MET cc_start: 0.9320 (tpt) cc_final: 0.9085 (ttt) REVERT: Z 21 LEU cc_start: 0.7423 (tt) cc_final: 0.7203 (mt) outliers start: 14 outliers final: 9 residues processed: 175 average time/residue: 0.1792 time to fit residues: 48.0879 Evaluate side-chains 116 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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: 10.0000 chunk 310 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 291 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 53 optimal weight: 50.0000 chunk 114 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 85 HIS ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN A 431 ASN A 469 ASN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 GLN ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 HIS ** X 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 HIS ** Z 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.061210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.048708 restraints weight = 421621.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.049143 restraints weight = 381630.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.049324 restraints weight = 352323.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.049648 restraints weight = 335991.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.049759 restraints weight = 320037.667| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.7232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31089 Z= 0.170 Angle : 0.680 9.250 43433 Z= 0.361 Chirality : 0.042 0.366 5065 Planarity : 0.005 0.058 4372 Dihedral : 23.707 179.360 8056 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.16 % Allowed : 3.50 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.15), residues: 2876 helix: 0.17 (0.12), residues: 1754 sheet: -1.95 (0.32), residues: 272 loop : -1.49 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 148 TYR 0.031 0.002 TYR A 497 PHE 0.022 0.002 PHE Y 196 TRP 0.020 0.002 TRP W 211 HIS 0.020 0.002 HIS Z 43 Details of bonding type rmsd covalent geometry : bond 0.00359 (31089) covalent geometry : angle 0.67991 (43433) hydrogen bonds : bond 0.04793 ( 1470) hydrogen bonds : angle 4.51933 ( 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 160 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 156 time to evaluate : 0.965 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 114 MET cc_start: 0.3335 (tmm) cc_final: 0.3119 (tpt) REVERT: S 124 ASP cc_start: 0.8966 (m-30) cc_final: 0.8748 (t70) REVERT: T 19 GLU cc_start: 0.9719 (tm-30) cc_final: 0.9449 (pm20) REVERT: V 106 PHE cc_start: 0.8586 (m-80) cc_final: 0.8257 (m-80) REVERT: W 140 MET cc_start: 0.8617 (tpp) cc_final: 0.8343 (tpp) REVERT: X 190 PHE cc_start: 0.8208 (m-80) cc_final: 0.7858 (m-80) REVERT: X 214 MET cc_start: 0.9301 (tpt) cc_final: 0.9059 (ttt) REVERT: Z 21 LEU cc_start: 0.7556 (tt) cc_final: 0.7314 (mt) outliers start: 4 outliers final: 1 residues processed: 160 average time/residue: 0.2044 time to fit residues: 50.5458 Evaluate side-chains 108 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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: 20.0000 chunk 258 optimal weight: 30.0000 chunk 182 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 238 optimal weight: 30.0000 chunk 227 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 295 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 117 optimal weight: 30.0000 chunk 223 optimal weight: 6.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.059098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.047286 restraints weight = 432862.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.047737 restraints weight = 389024.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.047930 restraints weight = 356780.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.048226 restraints weight = 338714.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.048337 restraints weight = 323165.566| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.8285 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= 0.209 Angle : 0.725 11.852 43433 Z= 0.384 Chirality : 0.043 0.304 5065 Planarity : 0.006 0.060 4372 Dihedral : 23.626 179.800 8056 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 0.12 % Allowed : 3.71 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.15), residues: 2876 helix: 0.03 (0.12), residues: 1754 sheet: -2.14 (0.32), residues: 256 loop : -1.64 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 249 TYR 0.021 0.003 TYR A 497 PHE 0.034 0.003 PHE U 190 TRP 0.018 0.002 TRP W 211 HIS 0.015 0.002 HIS Z 43 Details of bonding type rmsd covalent geometry : bond 0.00447 (31089) covalent geometry : angle 0.72494 (43433) hydrogen bonds : bond 0.05591 ( 1470) hydrogen bonds : angle 4.71963 ( 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 137 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 0.983 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: R 140 MET cc_start: 0.9005 (ppp) cc_final: 0.8744 (ppp) REVERT: S 124 ASP cc_start: 0.9058 (m-30) cc_final: 0.8694 (t70) REVERT: V 47 ASP cc_start: 0.9199 (t0) cc_final: 0.8949 (m-30) REVERT: Z 21 LEU cc_start: 0.7704 (tt) cc_final: 0.7450 (mt) outliers start: 3 outliers final: 2 residues processed: 137 average time/residue: 0.1989 time to fit residues: 42.8589 Evaluate side-chains 99 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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: 8.9990 chunk 131 optimal weight: 8.9990 chunk 139 optimal weight: 20.0000 chunk 158 optimal weight: 0.0000 chunk 196 optimal weight: 2.9990 chunk 292 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 291 optimal weight: 20.0000 chunk 207 optimal weight: 30.0000 chunk 84 optimal weight: 20.0000 overall best weight: 4.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 213 GLN U 206 ASN X 81 GLN ** Y 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.059614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.047736 restraints weight = 430364.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.048198 restraints weight = 385555.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.048542 restraints weight = 352420.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.048763 restraints weight = 328288.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.048971 restraints weight = 313012.787| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.8633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31089 Z= 0.154 Angle : 0.641 8.737 43433 Z= 0.339 Chirality : 0.041 0.389 5065 Planarity : 0.005 0.057 4372 Dihedral : 23.421 179.816 8056 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.15), residues: 2876 helix: 0.37 (0.12), residues: 1758 sheet: -2.22 (0.32), residues: 261 loop : -1.60 (0.19), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 148 TYR 0.021 0.002 TYR A 497 PHE 0.027 0.002 PHE U 190 TRP 0.022 0.002 TRP W 211 HIS 0.013 0.001 HIS Z 43 Details of bonding type rmsd covalent geometry : bond 0.00319 (31089) covalent geometry : angle 0.64066 (43433) hydrogen bonds : bond 0.04490 ( 1470) hydrogen bonds : angle 4.48424 ( 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 140 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.846 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: A 405 MET cc_start: 0.1056 (mtm) cc_final: 0.0837 (mtm) REVERT: R 140 MET cc_start: 0.9008 (ppp) cc_final: 0.8774 (ppp) REVERT: S 124 ASP cc_start: 0.9005 (m-30) cc_final: 0.8743 (t70) REVERT: V 47 ASP cc_start: 0.9210 (t0) cc_final: 0.8968 (m-30) REVERT: V 106 PHE cc_start: 0.8495 (m-80) cc_final: 0.8259 (m-80) REVERT: X 190 PHE cc_start: 0.8366 (m-80) cc_final: 0.7987 (m-80) REVERT: Z 21 LEU cc_start: 0.7703 (tt) cc_final: 0.7432 (mt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1816 time to fit residues: 39.4082 Evaluate side-chains 105 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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: 20.0000 chunk 162 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 182 optimal weight: 5.9990 chunk 75 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 213 GLN ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.058681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.046720 restraints weight = 440413.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.047203 restraints weight = 391831.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.047543 restraints weight = 356403.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.047770 restraints weight = 333109.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.047981 restraints weight = 317088.491| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.9121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31089 Z= 0.169 Angle : 0.660 9.337 43433 Z= 0.350 Chirality : 0.041 0.320 5065 Planarity : 0.005 0.054 4372 Dihedral : 23.336 179.216 8056 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.15), residues: 2876 helix: 0.34 (0.12), residues: 1758 sheet: -2.24 (0.31), residues: 261 loop : -1.59 (0.19), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Z 50 TYR 0.021 0.002 TYR Z 75 PHE 0.023 0.002 PHE A 401 TRP 0.024 0.002 TRP X 45 HIS 0.013 0.001 HIS Z 43 Details of bonding type rmsd covalent geometry : bond 0.00354 (31089) covalent geometry : angle 0.65980 (43433) hydrogen bonds : bond 0.04863 ( 1470) hydrogen bonds : angle 4.57174 ( 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 135 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.674 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: R 214 MET cc_start: 0.9258 (mmp) cc_final: 0.8769 (tmm) REVERT: S 124 ASP cc_start: 0.8946 (m-30) cc_final: 0.8694 (t70) REVERT: U 125 PHE cc_start: 0.6378 (m-10) cc_final: 0.6079 (m-80) REVERT: V 47 ASP cc_start: 0.9171 (t0) cc_final: 0.8965 (m-30) REVERT: Z 21 LEU cc_start: 0.7690 (tt) cc_final: 0.7443 (mt) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1693 time to fit residues: 35.8230 Evaluate side-chains 102 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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: 6.9990 chunk 105 optimal weight: 8.9990 chunk 198 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 283 optimal weight: 50.0000 chunk 199 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 64 GLN A 415 GLN A 494 GLN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 38 GLN T 213 GLN U 206 ASN ** X 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.058358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.046318 restraints weight = 428814.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.046737 restraints weight = 387445.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.046931 restraints weight = 356644.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.047231 restraints weight = 338516.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.047320 restraints weight = 323005.963| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.9608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31089 Z= 0.166 Angle : 0.658 9.063 43433 Z= 0.349 Chirality : 0.041 0.310 5065 Planarity : 0.005 0.057 4372 Dihedral : 23.301 179.935 8056 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.15), residues: 2876 helix: 0.30 (0.12), residues: 1756 sheet: -2.27 (0.31), residues: 261 loop : -1.62 (0.19), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG W 63 TYR 0.024 0.002 TYR A 497 PHE 0.022 0.002 PHE A 401 TRP 0.026 0.002 TRP W 211 HIS 0.011 0.001 HIS Z 43 Details of bonding type rmsd covalent geometry : bond 0.00353 (31089) covalent geometry : angle 0.65847 (43433) hydrogen bonds : bond 0.04842 ( 1470) hydrogen bonds : angle 4.57828 ( 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 137 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.2414 (tpt) cc_final: 0.2199 (tpt) REVERT: R 140 MET cc_start: 0.9013 (ppp) cc_final: 0.8743 (ppp) REVERT: S 124 ASP cc_start: 0.8996 (m-30) cc_final: 0.8736 (t70) REVERT: U 125 PHE cc_start: 0.6666 (m-10) cc_final: 0.6234 (m-80) REVERT: V 47 ASP cc_start: 0.9154 (t0) cc_final: 0.8927 (m-30) REVERT: V 106 PHE cc_start: 0.8419 (m-80) cc_final: 0.8165 (m-80) REVERT: X 193 HIS cc_start: 0.8393 (p-80) cc_final: 0.8160 (p-80) REVERT: Z 21 LEU cc_start: 0.7759 (tt) cc_final: 0.7471 (mt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1592 time to fit residues: 35.0296 Evaluate side-chains 105 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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: 7.9990 chunk 144 optimal weight: 30.0000 chunk 200 optimal weight: 0.7980 chunk 247 optimal weight: 20.0000 chunk 219 optimal weight: 0.7980 chunk 262 optimal weight: 30.0000 chunk 267 optimal weight: 30.0000 chunk 141 optimal weight: 0.6980 chunk 46 optimal weight: 50.0000 chunk 92 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 overall best weight: 3.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 213 GLN W 43 HIS ** X 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 98 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 = 0.4129 r_free = 0.4129 target = 0.058914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.046811 restraints weight = 433829.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.047290 restraints weight = 382923.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.047640 restraints weight = 349204.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 14)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.047809 restraints weight = 326044.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.048074 restraints weight = 312113.130| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.9750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31089 Z= 0.138 Angle : 0.635 9.954 43433 Z= 0.333 Chirality : 0.040 0.295 5065 Planarity : 0.005 0.056 4372 Dihedral : 23.104 179.590 8056 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % 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 aren not related in a simple way. whole: -0.60 (0.15), residues: 2876 helix: 0.53 (0.12), residues: 1754 sheet: -2.25 (0.31), residues: 261 loop : -1.58 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 525 TYR 0.021 0.002 TYR A 497 PHE 0.030 0.002 PHE A 401 TRP 0.025 0.002 TRP W 211 HIS 0.012 0.001 HIS Z 43 Details of bonding type rmsd covalent geometry : bond 0.00290 (31089) covalent geometry : angle 0.63470 (43433) hydrogen bonds : bond 0.04393 ( 1470) hydrogen bonds : angle 4.48879 ( 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 138 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.025 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 114 MET cc_start: 0.2133 (tpt) cc_final: 0.1899 (tpt) REVERT: R 214 MET cc_start: 0.9219 (mmp) cc_final: 0.8696 (tmm) REVERT: S 124 ASP cc_start: 0.8923 (m-30) cc_final: 0.8670 (t70) REVERT: U 125 PHE cc_start: 0.6379 (m-10) cc_final: 0.5917 (m-80) REVERT: Z 21 LEU cc_start: 0.7725 (tt) cc_final: 0.7462 (mt) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1777 time to fit residues: 39.2823 Evaluate side-chains 107 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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: 50.0000 chunk 307 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 259 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 chunk 182 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN A 494 GLN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 213 GLN ** T 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 206 ASN W 43 HIS ** X 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 98 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 = 0.4486 r_free = 0.4486 target = 0.070890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.054102 restraints weight = 356766.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.054671 restraints weight = 310937.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.054957 restraints weight = 278115.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.055057 restraints weight = 239035.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.055179 restraints weight = 245846.863| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 1.0282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31089 Z= 0.167 Angle : 0.671 10.450 43433 Z= 0.353 Chirality : 0.041 0.310 5065 Planarity : 0.005 0.057 4372 Dihedral : 23.131 179.168 8056 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.15), residues: 2876 helix: 0.35 (0.12), residues: 1762 sheet: -2.32 (0.30), residues: 261 loop : -1.59 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 191 TYR 0.022 0.002 TYR A 497 PHE 0.028 0.002 PHE A 401 TRP 0.026 0.002 TRP W 211 HIS 0.011 0.001 HIS Z 43 Details of bonding type rmsd covalent geometry : bond 0.00356 (31089) covalent geometry : angle 0.67149 (43433) hydrogen bonds : bond 0.04997 ( 1470) hydrogen bonds : angle 4.58669 ( 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 132 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.936 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 114 MET cc_start: 0.2497 (tpt) cc_final: 0.2023 (tpt) REVERT: S 124 ASP cc_start: 0.9273 (m-30) cc_final: 0.8978 (t70) REVERT: U 125 PHE cc_start: 0.6889 (m-10) cc_final: 0.6574 (m-80) REVERT: V 229 MET cc_start: -0.3186 (mmp) cc_final: -0.3393 (mmp) REVERT: X 193 HIS cc_start: 0.8217 (p90) cc_final: 0.7903 (p90) REVERT: Y 112 TYR cc_start: 0.5866 (t80) cc_final: 0.4799 (m-10) REVERT: Y 140 MET cc_start: 0.3386 (tpp) cc_final: 0.3174 (tpp) REVERT: Z 75 TYR cc_start: 0.9006 (m-80) cc_final: 0.8606 (m-80) REVERT: Z 214 MET cc_start: 0.7831 (tmm) cc_final: 0.7628 (tmm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1622 time to fit residues: 34.6272 Evaluate side-chains 103 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 155 optimal weight: 30.0000 chunk 93 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 258 optimal weight: 9.9990 chunk 159 optimal weight: 0.0050 chunk 165 optimal weight: 7.9990 chunk 47 optimal weight: 0.4980 chunk 126 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 overall best weight: 2.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 213 GLN ** T 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 HIS ** X 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 77 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.059093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.046897 restraints weight = 436685.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.047389 restraints weight = 386243.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.047756 restraints weight = 351145.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 14)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.047920 restraints weight = 327517.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.048085 restraints weight = 314155.714| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 1.0328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31089 Z= 0.127 Angle : 0.616 9.824 43433 Z= 0.323 Chirality : 0.039 0.287 5065 Planarity : 0.004 0.058 4372 Dihedral : 22.906 179.938 8056 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.15), residues: 2876 helix: 0.71 (0.12), residues: 1746 sheet: -2.23 (0.31), residues: 261 loop : -1.54 (0.19), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 525 TYR 0.020 0.001 TYR A 497 PHE 0.032 0.002 PHE A 401 TRP 0.034 0.002 TRP W 211 HIS 0.011 0.001 HIS Z 43 Details of bonding type rmsd covalent geometry : bond 0.00263 (31089) covalent geometry : angle 0.61584 (43433) hydrogen bonds : bond 0.04249 ( 1470) hydrogen bonds : angle 4.37773 ( 4109) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7288.13 seconds wall clock time: 125 minutes 45.64 seconds (7545.64 seconds total)