Starting phenix.real_space_refine on Thu Jun 26 02:15:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bd6_15976/06_2025/8bd6_15976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bd6_15976/06_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_15976/06_2025/8bd6_15976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bd6_15976/06_2025/8bd6_15976.map" model { file = "/net/cci-nas-00/data/ceres_data/8bd6_15976/06_2025/8bd6_15976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bd6_15976/06_2025/8bd6_15976.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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: 19.77, per 1000 atoms: 0.66 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: 8.94 Conformation dependent library (CDL) restraints added in 3.3 seconds 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5454 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 11 sheets defined 62.5% alpha, 6.7% beta 101 base pairs and 206 stacking pairs defined. Time for finding SS restraints: 12.64 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: 12.61 Time building geometry restraints manager: 9.22 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 276 or resid 301 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 276 or resid 301 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 276 or resid 301 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 276 or resid 301 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 276 or resid 301 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 276 or resid 301 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 276 or resid 301 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: 7.990 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: 0.020 Extract box with map and model: 1.510 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 79.160 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.040 ------------------------------------------------------------------------------- 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 : 17.28 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (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 TRP 0.020 0.003 TRP R 45 HIS 0.004 0.001 HIS S 43 PHE 0.017 0.002 PHE U 196 TYR 0.012 0.002 TYR X 275 ARG 0.026 0.001 ARG W 57 Details of bonding type rmsd hydrogen bonds : bond 0.15810 ( 1470) hydrogen bonds : angle 7.47855 ( 4109) covalent geometry : bond 0.00917 (31089) covalent geometry : angle 1.36740 (43433) *********************** 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 : 2.937 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: 0.5962 time to fit residues: 459.3664 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 : 3.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 0.0870 chunk 241 optimal weight: 10.0000 chunk 134 optimal weight: 0.1980 chunk 82 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 250 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 289 optimal weight: 5.9990 overall best weight: 3.4564 ------------------------------------------------------------------------------- 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 369 HIS 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 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 = 0.4306 r_free = 0.4306 target = 0.070505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.057668 restraints weight = 397204.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.058112 restraints weight = 366493.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.058366 restraints weight = 341926.256| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.3552 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= 0.170 Angle : 0.689 10.758 43433 Z= 0.365 Chirality : 0.042 0.395 5065 Planarity : 0.005 0.048 4372 Dihedral : 23.318 179.949 8056 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.12 % Allowed : 5.35 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 2876 helix: 0.44 (0.12), residues: 1756 sheet: -1.30 (0.45), residues: 153 loop : -1.59 (0.18), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Y 211 HIS 0.009 0.001 HIS A 522 PHE 0.021 0.002 PHE Y 106 TYR 0.037 0.002 TYR A 497 ARG 0.007 0.001 ARG U 63 Details of bonding type rmsd hydrogen bonds : bond 0.04793 ( 1470) hydrogen bonds : angle 4.33812 ( 4109) covalent geometry : bond 0.00357 (31089) covalent geometry : angle 0.68926 (43433) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5752 Ramachandran restraints generated. 2876 Oldfield, 0 Emsley, 2876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 228 time to evaluate : 3.512 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: R 210 MET cc_start: 0.8829 (mmp) cc_final: 0.8558 (mmm) REVERT: S 37 GLN cc_start: 0.9254 (tp40) cc_final: 0.8806 (pp30) REVERT: S 124 ASP cc_start: 0.9045 (m-30) cc_final: 0.8810 (t70) REVERT: S 190 PHE cc_start: 0.8448 (m-10) cc_final: 0.8182 (m-80) REVERT: S 210 MET cc_start: 0.9506 (mmp) cc_final: 0.9267 (mmt) REVERT: T 19 GLU cc_start: 0.9637 (tm-30) cc_final: 0.9220 (pm20) REVERT: T 104 ASP cc_start: 0.9185 (m-30) cc_final: 0.8962 (t0) REVERT: T 105 LEU cc_start: 0.8731 (mt) cc_final: 0.8513 (mt) REVERT: T 229 MET cc_start: 0.2600 (mmt) cc_final: 0.2353 (mmp) REVERT: U 140 MET cc_start: 0.7529 (tpt) cc_final: 0.7126 (tpt) REVERT: V 190 PHE cc_start: 0.8539 (m-10) cc_final: 0.8309 (m-80) REVERT: W 159 ASP cc_start: 0.8927 (m-30) cc_final: 0.8568 (m-30) REVERT: W 247 ILE cc_start: 0.9803 (mt) cc_final: 0.9602 (pt) REVERT: W 271 VAL cc_start: 0.7773 (m) cc_final: 0.7428 (m) REVERT: X 210 MET cc_start: 0.9418 (mtm) cc_final: 0.9176 (ptt) REVERT: X 214 MET cc_start: 0.9281 (tpt) cc_final: 0.8933 (ttt) REVERT: Y 106 PHE cc_start: 0.8110 (m-80) cc_final: 0.7722 (m-80) REVERT: Z 21 LEU cc_start: 0.7257 (tt) cc_final: 0.6986 (mt) outliers start: 3 outliers final: 0 residues processed: 230 average time/residue: 0.6238 time to fit residues: 218.1704 Evaluate side-chains 147 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 4.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 303 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 301 optimal weight: 30.0000 chunk 36 optimal weight: 50.0000 chunk 108 optimal weight: 0.9980 chunk 232 optimal weight: 20.0000 chunk 82 optimal weight: 0.1980 chunk 100 optimal weight: 10.0000 chunk 311 optimal weight: 0.9990 chunk 153 optimal weight: 50.0000 chunk 121 optimal weight: 0.5980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 ASN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN R 81 GLN Y 43 HIS Z 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.069374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.056711 restraints weight = 408950.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.057210 restraints weight = 366924.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.057577 restraints weight = 336876.251| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.4323 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= 0.133 Angle : 0.595 10.233 43433 Z= 0.316 Chirality : 0.039 0.315 5065 Planarity : 0.004 0.050 4372 Dihedral : 22.921 178.910 8056 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 2876 helix: 0.91 (0.12), residues: 1760 sheet: -1.26 (0.43), residues: 155 loop : -1.34 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Y 211 HIS 0.005 0.001 HIS A 522 PHE 0.017 0.002 PHE A 347 TYR 0.037 0.002 TYR A 497 ARG 0.007 0.001 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 1470) hydrogen bonds : angle 4.06019 ( 4109) covalent geometry : bond 0.00277 (31089) covalent geometry : angle 0.59513 (43433) *********************** 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 193 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 3.105 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: A 114 MET cc_start: 0.2232 (tmm) cc_final: 0.1265 (tpt) REVERT: A 357 LEU cc_start: 0.9558 (mt) cc_final: 0.9316 (pp) REVERT: R 97 HIS cc_start: 0.9603 (m-70) cc_final: 0.9377 (p90) REVERT: R 210 MET cc_start: 0.8831 (mmp) cc_final: 0.8517 (mmm) REVERT: S 37 GLN cc_start: 0.9243 (tp40) cc_final: 0.8764 (pp30) REVERT: S 124 ASP cc_start: 0.9047 (m-30) cc_final: 0.8800 (t70) REVERT: T 19 GLU cc_start: 0.9662 (tm-30) cc_final: 0.9255 (pm20) REVERT: T 104 ASP cc_start: 0.9229 (m-30) cc_final: 0.8999 (t0) REVERT: U 140 MET cc_start: 0.7608 (tpt) cc_final: 0.7141 (tpt) REVERT: V 106 PHE cc_start: 0.8372 (m-80) cc_final: 0.8141 (m-80) REVERT: V 127 ASP cc_start: 0.9717 (m-30) cc_final: 0.9350 (m-30) REVERT: X 179 VAL cc_start: 0.7634 (t) cc_final: 0.7386 (p) REVERT: X 210 MET cc_start: 0.9418 (mtm) cc_final: 0.9179 (ptm) REVERT: X 214 MET cc_start: 0.9370 (tpt) cc_final: 0.9084 (ttt) REVERT: Y 106 PHE cc_start: 0.8134 (m-80) cc_final: 0.7826 (m-80) REVERT: Z 21 LEU cc_start: 0.7311 (tt) cc_final: 0.7032 (mt) REVERT: Z 75 TYR cc_start: 0.9060 (m-80) cc_final: 0.8841 (m-10) REVERT: Z 229 MET cc_start: 0.0019 (mmt) cc_final: -0.0797 (ttt) outliers start: 2 outliers final: 0 residues processed: 193 average time/residue: 0.5212 time to fit residues: 155.2011 Evaluate side-chains 127 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 189 optimal weight: 7.9990 chunk 121 optimal weight: 30.0000 chunk 138 optimal weight: 30.0000 chunk 257 optimal weight: 50.0000 chunk 169 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 62 optimal weight: 30.0000 chunk 170 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 chunk 263 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 598 GLN R 97 HIS ** S 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 185 GLN U 97 HIS ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 77 HIS ** Y 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.063467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.051555 restraints weight = 421900.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.052011 restraints weight = 381053.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.052329 restraints weight = 351269.179| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 31089 Z= 0.206 Angle : 0.719 15.394 43433 Z= 0.383 Chirality : 0.043 0.318 5065 Planarity : 0.006 0.142 4372 Dihedral : 23.223 179.721 8056 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 2876 helix: 0.53 (0.12), residues: 1762 sheet: -1.26 (0.43), residues: 155 loop : -1.43 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP U 45 HIS 0.011 0.002 HIS T 77 PHE 0.029 0.003 PHE Y 196 TYR 0.033 0.003 TYR V 112 ARG 0.013 0.001 ARG S 254 Details of bonding type rmsd hydrogen bonds : bond 0.05386 ( 1470) hydrogen bonds : angle 4.35432 ( 4109) covalent geometry : bond 0.00437 (31089) covalent geometry : angle 0.71932 (43433) *********************** 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 156 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 2.948 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: A 114 MET cc_start: 0.3061 (tmm) cc_final: 0.2312 (tpt) REVERT: A 357 LEU cc_start: 0.9550 (mt) cc_final: 0.9324 (pp) REVERT: R 97 HIS cc_start: 0.9668 (m170) cc_final: 0.9449 (p90) REVERT: R 206 ASN cc_start: 0.9564 (t0) cc_final: 0.9355 (m110) REVERT: R 214 MET cc_start: 0.9290 (tpp) cc_final: 0.8765 (tmm) REVERT: S 124 ASP cc_start: 0.8981 (m-30) cc_final: 0.8766 (t70) REVERT: S 214 MET cc_start: 0.9072 (mpp) cc_final: 0.8817 (mpp) REVERT: T 19 GLU cc_start: 0.9705 (tm-30) cc_final: 0.9369 (pm20) REVERT: T 56 CYS cc_start: 0.8709 (p) cc_final: 0.8508 (p) REVERT: T 104 ASP cc_start: 0.9239 (m-30) cc_final: 0.8971 (t0) REVERT: T 105 LEU cc_start: 0.8762 (mt) cc_final: 0.8541 (mt) REVERT: V 215 VAL cc_start: 0.8072 (t) cc_final: 0.7845 (p) REVERT: X 179 VAL cc_start: 0.7892 (t) cc_final: 0.7681 (p) REVERT: X 190 PHE cc_start: 0.8328 (m-80) cc_final: 0.7966 (m-80) REVERT: X 214 MET cc_start: 0.9386 (tpt) cc_final: 0.9122 (ttt) REVERT: Z 21 LEU cc_start: 0.7415 (tt) cc_final: 0.7172 (mt) REVERT: Z 75 TYR cc_start: 0.9058 (m-80) cc_final: 0.8847 (m-10) REVERT: Z 229 MET cc_start: 0.1331 (mmt) cc_final: 0.0466 (ttt) outliers start: 2 outliers final: 1 residues processed: 156 average time/residue: 0.4435 time to fit residues: 110.4600 Evaluate side-chains 102 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 80 optimal weight: 20.0000 chunk 160 optimal weight: 0.0470 chunk 249 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 190 optimal weight: 8.9990 chunk 62 optimal weight: 30.0000 chunk 264 optimal weight: 20.0000 chunk 127 optimal weight: 30.0000 chunk 168 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 302 optimal weight: 10.0000 overall best weight: 5.4084 ------------------------------------------------------------------------------- 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 494 GLN ** S 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 43 HIS Y 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.063168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.050531 restraints weight = 417298.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.051030 restraints weight = 375941.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.051373 restraints weight = 343593.412| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.6672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31089 Z= 0.162 Angle : 0.632 8.400 43433 Z= 0.336 Chirality : 0.041 0.293 5065 Planarity : 0.005 0.045 4372 Dihedral : 23.154 179.712 8056 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.04 % Allowed : 2.72 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 2876 helix: 0.68 (0.12), residues: 1758 sheet: -1.73 (0.32), residues: 272 loop : -1.12 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Z 211 HIS 0.006 0.001 HIS W 77 PHE 0.043 0.002 PHE A 401 TYR 0.014 0.002 TYR A 196 ARG 0.011 0.001 ARG U 182 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 1470) hydrogen bonds : angle 4.25115 ( 4109) covalent geometry : bond 0.00334 (31089) covalent geometry : angle 0.63172 (43433) *********************** 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 145 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.3091 (tmm) cc_final: 0.2539 (tpt) REVERT: A 291 MET cc_start: 0.7947 (mpp) cc_final: 0.7735 (pmm) REVERT: A 357 LEU cc_start: 0.9567 (mt) cc_final: 0.9355 (pp) REVERT: S 124 ASP cc_start: 0.8990 (m-30) cc_final: 0.8586 (t70) REVERT: T 19 GLU cc_start: 0.9726 (tm-30) cc_final: 0.9413 (pm20) REVERT: T 56 CYS cc_start: 0.8507 (p) cc_final: 0.8288 (p) REVERT: V 106 PHE cc_start: 0.8474 (m-80) cc_final: 0.8157 (m-80) REVERT: X 179 VAL cc_start: 0.7832 (t) cc_final: 0.7624 (p) REVERT: X 190 PHE cc_start: 0.8252 (m-80) cc_final: 0.7826 (m-80) REVERT: X 214 MET cc_start: 0.9446 (tpt) cc_final: 0.9185 (ttt) REVERT: Z 21 LEU cc_start: 0.7519 (tt) cc_final: 0.7255 (mt) REVERT: Z 75 TYR cc_start: 0.9027 (m-80) cc_final: 0.8811 (m-10) REVERT: Z 229 MET cc_start: 0.0737 (mmt) cc_final: -0.0056 (ttt) outliers start: 1 outliers final: 1 residues processed: 145 average time/residue: 0.4678 time to fit residues: 110.7755 Evaluate side-chains 106 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 35 optimal weight: 20.0000 chunk 203 optimal weight: 7.9990 chunk 216 optimal weight: 30.0000 chunk 33 optimal weight: 30.0000 chunk 13 optimal weight: 40.0000 chunk 118 optimal weight: 10.0000 chunk 258 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 233 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN A 431 ASN A 494 GLN ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN R 81 GLN S 77 HIS S 98 GLN ** U 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.059343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.047250 restraints weight = 430223.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.047684 restraints weight = 385754.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.047971 restraints weight = 354797.121| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.8236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 31089 Z= 0.227 Angle : 0.751 9.303 43433 Z= 0.398 Chirality : 0.044 0.302 5065 Planarity : 0.006 0.060 4372 Dihedral : 23.469 179.986 8056 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 25.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.25 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 2876 helix: 0.17 (0.12), residues: 1756 sheet: -1.91 (0.33), residues: 256 loop : -1.42 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 45 HIS 0.011 0.002 HIS W 77 PHE 0.029 0.003 PHE Y 196 TYR 0.021 0.003 TYR V 112 ARG 0.009 0.001 ARG X 63 Details of bonding type rmsd hydrogen bonds : bond 0.05814 ( 1470) hydrogen bonds : angle 4.61571 ( 4109) covalent geometry : bond 0.00478 (31089) covalent geometry : angle 0.75134 (43433) *********************** 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 139 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.7863 (mpp) cc_final: 0.7569 (pmm) REVERT: S 124 ASP cc_start: 0.8883 (m-30) cc_final: 0.8601 (t70) REVERT: T 56 CYS cc_start: 0.8289 (p) cc_final: 0.8022 (p) REVERT: T 276 LYS cc_start: 0.7515 (mmmt) cc_final: 0.7287 (mmmm) REVERT: U 125 PHE cc_start: 0.6102 (m-10) cc_final: 0.5833 (m-80) REVERT: Z 21 LEU cc_start: 0.7756 (tt) cc_final: 0.7499 (mt) REVERT: Z 75 TYR cc_start: 0.8972 (m-80) cc_final: 0.8762 (m-10) REVERT: Z 229 MET cc_start: 0.1957 (mmt) cc_final: 0.1207 (ttt) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.4689 time to fit residues: 103.4414 Evaluate side-chains 96 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 153 optimal weight: 30.0000 chunk 317 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 157 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 115 optimal weight: 30.0000 chunk 149 optimal weight: 5.9990 chunk 308 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 586 HIS T 213 GLN ** T 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 37 GLN ** V 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.059358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.047273 restraints weight = 416009.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.047703 restraints weight = 375023.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.047916 restraints weight = 345073.369| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.8680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31089 Z= 0.177 Angle : 0.677 8.925 43433 Z= 0.358 Chirality : 0.042 0.369 5065 Planarity : 0.005 0.062 4372 Dihedral : 23.376 179.284 8056 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 2876 helix: 0.33 (0.12), residues: 1757 sheet: -2.02 (0.32), residues: 261 loop : -1.47 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP Z 211 HIS 0.012 0.001 HIS S 43 PHE 0.022 0.002 PHE Y 196 TYR 0.020 0.002 TYR S 275 ARG 0.016 0.001 ARG U 182 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 1470) hydrogen bonds : angle 4.54947 ( 4109) covalent geometry : bond 0.00373 (31089) covalent geometry : angle 0.67701 (43433) *********************** 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 144 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.7865 (mpp) cc_final: 0.7539 (pmm) REVERT: A 501 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7714 (mm-30) REVERT: S 124 ASP cc_start: 0.8839 (m-30) cc_final: 0.8571 (t70) REVERT: T 56 CYS cc_start: 0.8004 (p) cc_final: 0.7761 (p) REVERT: U 125 PHE cc_start: 0.6065 (m-10) cc_final: 0.5749 (m-80) REVERT: Z 21 LEU cc_start: 0.7766 (tt) cc_final: 0.7509 (mt) REVERT: Z 75 TYR cc_start: 0.8916 (m-80) cc_final: 0.8714 (m-80) REVERT: Z 229 MET cc_start: 0.2322 (mmt) cc_final: 0.1623 (ttt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.4381 time to fit residues: 100.6873 Evaluate side-chains 106 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 297 optimal weight: 1.9990 chunk 285 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 274 optimal weight: 8.9990 chunk 238 optimal weight: 30.0000 chunk 310 optimal weight: 50.0000 chunk 32 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 317 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN T 213 GLN ** T 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.058746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.046763 restraints weight = 432046.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.047226 restraints weight = 388215.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.047553 restraints weight = 354339.322| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.9246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31089 Z= 0.178 Angle : 0.687 10.529 43433 Z= 0.361 Chirality : 0.042 0.333 5065 Planarity : 0.005 0.099 4372 Dihedral : 23.304 179.866 8056 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 2876 helix: 0.26 (0.12), residues: 1757 sheet: -2.13 (0.32), residues: 261 loop : -1.53 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP Z 211 HIS 0.013 0.002 HIS S 43 PHE 0.024 0.002 PHE U 196 TYR 0.020 0.002 TYR S 275 ARG 0.017 0.001 ARG U 148 Details of bonding type rmsd hydrogen bonds : bond 0.05056 ( 1470) hydrogen bonds : angle 4.57189 ( 4109) covalent geometry : bond 0.00378 (31089) covalent geometry : angle 0.68738 (43433) *********************** 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 127 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 4.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.8152 (mpp) cc_final: 0.7751 (pmm) REVERT: S 124 ASP cc_start: 0.8938 (m-30) cc_final: 0.8664 (t70) REVERT: T 56 CYS cc_start: 0.8274 (p) cc_final: 0.7986 (p) REVERT: U 125 PHE cc_start: 0.6712 (m-10) cc_final: 0.6441 (m-80) REVERT: V 126 ARG cc_start: 0.9221 (ptm-80) cc_final: 0.8944 (tmm-80) REVERT: V 127 ASP cc_start: 0.9696 (m-30) cc_final: 0.9478 (m-30) REVERT: Z 21 LEU cc_start: 0.7777 (tt) cc_final: 0.7492 (mt) REVERT: Z 75 TYR cc_start: 0.8952 (m-80) cc_final: 0.8726 (m-80) REVERT: Z 164 LEU cc_start: 0.6411 (tt) cc_final: 0.6159 (tt) REVERT: Z 229 MET cc_start: 0.1099 (mmt) cc_final: 0.0498 (ttm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4638 time to fit residues: 96.4262 Evaluate side-chains 96 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 12 optimal weight: 20.0000 chunk 160 optimal weight: 9.9990 chunk 46 optimal weight: 50.0000 chunk 233 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 202 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 266 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 278 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 496 GLN A 584 ASN R 77 HIS T 213 GLN V 37 GLN X 80 GLN X 193 HIS Y 77 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.057058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.045626 restraints weight = 453728.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.046098 restraints weight = 402880.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.046432 restraints weight = 366896.123| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 1.0395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31089 Z= 0.202 Angle : 0.740 11.929 43433 Z= 0.390 Chirality : 0.044 0.440 5065 Planarity : 0.006 0.087 4372 Dihedral : 23.423 179.531 8056 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 25.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.15), residues: 2876 helix: -0.07 (0.12), residues: 1770 sheet: -2.29 (0.31), residues: 259 loop : -1.64 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP Z 211 HIS 0.014 0.002 HIS S 43 PHE 0.049 0.003 PHE X 106 TYR 0.022 0.002 TYR Z 275 ARG 0.011 0.001 ARG U 95 Details of bonding type rmsd hydrogen bonds : bond 0.05698 ( 1470) hydrogen bonds : angle 4.81289 ( 4109) covalent geometry : bond 0.00433 (31089) covalent geometry : angle 0.74000 (43433) *********************** 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 127 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 4.097 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: A 114 MET cc_start: 0.2078 (tpt) cc_final: 0.1836 (tpt) REVERT: A 291 MET cc_start: 0.8002 (mpp) cc_final: 0.7420 (pmm) REVERT: S 124 ASP cc_start: 0.8921 (m-30) cc_final: 0.8667 (t70) REVERT: U 125 PHE cc_start: 0.6572 (m-10) cc_final: 0.6275 (m-80) REVERT: W 271 VAL cc_start: 0.6307 (m) cc_final: 0.6065 (m) REVERT: Z 229 MET cc_start: 0.1434 (mmt) cc_final: 0.0962 (ttm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.7381 time to fit residues: 160.2342 Evaluate side-chains 88 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 3.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 289 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 69 optimal weight: 50.0000 chunk 200 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 259 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN T 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.056951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.045227 restraints weight = 448491.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.045712 restraints weight = 394280.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.046049 restraints weight = 357152.287| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 1.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 31089 Z= 0.174 Angle : 0.698 10.008 43433 Z= 0.365 Chirality : 0.043 0.365 5065 Planarity : 0.005 0.066 4372 Dihedral : 23.240 179.750 8056 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.15), residues: 2876 helix: 0.10 (0.12), residues: 1765 sheet: -2.24 (0.31), residues: 261 loop : -1.69 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP Z 211 HIS 0.014 0.002 HIS S 43 PHE 0.021 0.002 PHE Y 196 TYR 0.021 0.002 TYR S 275 ARG 0.015 0.001 ARG R 231 Details of bonding type rmsd hydrogen bonds : bond 0.05207 ( 1470) hydrogen bonds : angle 4.66286 ( 4109) covalent geometry : bond 0.00371 (31089) covalent geometry : angle 0.69826 (43433) ********************** 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 125 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 4.781 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: A 114 MET cc_start: 0.1862 (tpt) cc_final: 0.1656 (tpt) REVERT: A 291 MET cc_start: 0.8243 (mpp) cc_final: 0.7638 (pmm) REVERT: S 124 ASP cc_start: 0.8906 (m-30) cc_final: 0.8643 (t70) REVERT: S 229 MET cc_start: -0.5285 (mtm) cc_final: -0.5535 (mmt) REVERT: U 125 PHE cc_start: 0.6908 (m-10) cc_final: 0.6643 (m-80) REVERT: X 193 HIS cc_start: 0.8461 (p-80) cc_final: 0.8242 (p-80) REVERT: Z 229 MET cc_start: 0.1222 (mmt) cc_final: 0.0553 (ttm) REVERT: Z 276 LYS cc_start: 0.6598 (mptt) cc_final: 0.6371 (mmtt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.7904 time to fit residues: 163.2575 Evaluate side-chains 92 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 4.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 129 optimal weight: 1.9990 chunk 234 optimal weight: 7.9990 chunk 157 optimal weight: 30.0000 chunk 63 optimal weight: 20.0000 chunk 236 optimal weight: 8.9990 chunk 298 optimal weight: 30.0000 chunk 147 optimal weight: 20.0000 chunk 199 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 37 optimal weight: 30.0000 chunk 207 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN R 81 GLN R 97 HIS T 213 GLN U 269 GLN W 269 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.068919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.052695 restraints weight = 361586.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.053298 restraints weight = 297660.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.053793 restraints weight = 252332.684| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 1.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 31089 Z= 0.191 Angle : 0.733 10.841 43433 Z= 0.383 Chirality : 0.044 0.367 5065 Planarity : 0.006 0.089 4372 Dihedral : 23.274 179.961 8056 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.15), residues: 2876 helix: -0.04 (0.12), residues: 1765 sheet: -2.27 (0.36), residues: 202 loop : -1.83 (0.18), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP Z 211 HIS 0.015 0.002 HIS S 43 PHE 0.027 0.002 PHE X 190 TYR 0.021 0.002 TYR A 474 ARG 0.010 0.001 ARG R 231 Details of bonding type rmsd hydrogen bonds : bond 0.05579 ( 1470) hydrogen bonds : angle 4.75206 ( 4109) covalent geometry : bond 0.00408 (31089) covalent geometry : angle 0.73309 (43433) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14956.90 seconds wall clock time: 271 minutes 34.97 seconds (16294.97 seconds total)