Starting phenix.real_space_refine on Sat Mar 7 04:04:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ur4_26704/03_2026/7ur4_26704_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ur4_26704/03_2026/7ur4_26704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ur4_26704/03_2026/7ur4_26704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ur4_26704/03_2026/7ur4_26704.map" model { file = "/net/cci-nas-00/data/ceres_data/7ur4_26704/03_2026/7ur4_26704_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ur4_26704/03_2026/7ur4_26704_trim.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9544 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 111 5.16 5 C 9534 2.51 5 N 2643 2.21 5 O 2994 1.98 5 H 14784 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30066 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 6543 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 416} Chain breaks: 1 Chain: "B" Number of atoms: 6543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 6543 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 416} Chain breaks: 1 Chain: "C" Number of atoms: 6538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 6538 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 416} Chain breaks: 1 Chain: "F" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1852 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "G" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1565 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1853 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "I" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1841 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1565 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "L" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1565 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.79, per 1000 atoms: 0.19 Number of scatterers: 30066 At special positions: 0 Unit cell: (145.935, 139.59, 107.865, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 111 16.00 O 2994 8.00 N 2643 7.00 C 9534 6.00 H 14784 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS C 249 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 322 " distance=2.03 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 153 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS B 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 463 " distance=2.02 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 322 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 153 " distance=2.04 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS C 84 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 463 " distance=2.03 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 182 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 322 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 153 " distance=2.04 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 365 " - pdb=" SG CYS C 463 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A 601 " - " ASN A 353 " " NAG A 602 " - " ASN A 57 " " NAG B 601 " - " ASN B 353 " " NAG B 602 " - " ASN B 57 " " NAG C 601 " - " ASN C 353 " " NAG C 602 " - " ASN C 57 " " NAG D 1 " - " ASN A 172 " " NAG E 1 " - " ASN B 172 " " NAG K 1 " - " ASN C 172 " Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 921.8 milliseconds 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3618 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 32 sheets defined 25.7% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 65 through 81 Processing helix chain 'A' and resid 104 through 129 removed outlier: 3.588A pdb=" N CYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 186 through 209 removed outlier: 4.480A pdb=" N ALA A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 237 through 247 removed outlier: 3.568A pdb=" N ILE A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 65 through 81 removed outlier: 3.522A pdb=" N ARG B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 104 through 129 removed outlier: 3.536A pdb=" N ILE B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 163 through 172 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 186 through 209 removed outlier: 4.237A pdb=" N ALA B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE B 200 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'B' and resid 237 through 246 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 441 through 445 Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 65 through 83 removed outlier: 4.021A pdb=" N ARG C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 129 removed outlier: 4.179A pdb=" N CYS C 110 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 111 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 178 through 181 Processing helix chain 'C' and resid 186 through 210 removed outlier: 4.490A pdb=" N ALA C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARG C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE C 200 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 237 through 246 Processing helix chain 'C' and resid 247 through 255 removed outlier: 3.634A pdb=" N VAL C 251 " --> pdb=" O ASN C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.550A pdb=" N LYS C 348 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.553A pdb=" N THR F 87 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 30 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.638A pdb=" N GLU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.623A pdb=" N THR I 87 " --> pdb=" O VAL I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 30 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.664A pdb=" N GLU J 83 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 removed outlier: 3.506A pdb=" N ARG L 29 " --> pdb=" O ASP L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 326 through 329 removed outlier: 3.506A pdb=" N HIS A 332 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL A 333 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU A 36 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N CYS A 335 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL A 38 " --> pdb=" O CYS A 335 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER A 29 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA A 288 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 31 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 286 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLU A 33 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TRP A 284 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TYR A 35 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N SER A 37 " --> pdb=" O ASP A 280 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 278 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP A 309 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR A 317 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329 removed outlier: 3.506A pdb=" N HIS A 332 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL A 333 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU A 36 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N CYS A 335 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL A 38 " --> pdb=" O CYS A 335 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU A 21 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE A 437 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR A 23 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 6.633A pdb=" N THR A 45 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N THR A 160 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL A 47 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL A 162 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR A 49 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET A 270 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU A 259 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN A 272 " --> pdb=" O GLY A 257 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLY A 257 " --> pdb=" O GLN A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 295 removed outlier: 3.756A pdb=" N ASN A 298 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N CYS A 365 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N PHE A 456 " --> pdb=" O CYS A 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 376 Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.599A pdb=" N LYS A 401 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 316 through 320 removed outlier: 3.946A pdb=" N TRP B 309 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE B 279 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU B 39 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR B 281 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 35 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE B 285 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLU B 33 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LYS B 287 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE B 31 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL B 333 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 36 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N CYS B 335 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL B 38 " --> pdb=" O CYS B 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 316 through 320 removed outlier: 3.946A pdb=" N TRP B 309 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE B 279 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU B 39 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR B 281 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 35 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE B 285 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLU B 33 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LYS B 287 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE B 31 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU B 21 " --> pdb=" O HIS B 435 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 437 " --> pdb=" O GLU B 21 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR B 23 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 150 removed outlier: 5.678A pdb=" N THR B 45 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL B 262 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE B 268 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 293 through 295 removed outlier: 3.747A pdb=" N GLY B 366 " --> pdb=" O CYS B 301 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N CYS B 365 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE B 456 " --> pdb=" O CYS B 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 372 through 376 Processing sheet with id=AB3, first strand: chain 'B' and resid 399 through 402 removed outlier: 6.919A pdb=" N ILE B 392 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLN B 402 " --> pdb=" O CYS B 390 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N CYS B 390 " --> pdb=" O GLN B 402 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 326 through 329 removed outlier: 3.549A pdb=" N HIS C 332 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL C 333 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU C 36 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N CYS C 335 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL C 38 " --> pdb=" O CYS C 335 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE C 31 " --> pdb=" O LYS C 287 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LYS C 287 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLU C 33 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE C 285 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C 35 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR C 281 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU C 39 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE C 279 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP C 309 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR C 317 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 326 through 329 removed outlier: 3.549A pdb=" N HIS C 332 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL C 333 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU C 36 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N CYS C 335 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL C 38 " --> pdb=" O CYS C 335 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU C 21 " --> pdb=" O HIS C 435 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ILE C 437 " --> pdb=" O GLU C 21 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR C 23 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 146 through 150 removed outlier: 6.701A pdb=" N THR C 45 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N THR C 160 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL C 47 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N VAL C 162 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR C 49 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER C 266 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL C 262 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE C 268 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 293 through 295 removed outlier: 3.550A pdb=" N GLY C 366 " --> pdb=" O CYS C 301 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 372 through 376 Processing sheet with id=AB9, first strand: chain 'C' and resid 401 through 402 removed outlier: 3.518A pdb=" N LYS C 401 " --> pdb=" O ILE C 392 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.844A pdb=" N VAL F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AC4, first strand: chain 'G' and resid 9 through 13 removed outlier: 6.004A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 9 through 13 Processing sheet with id=AC6, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AC7, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.012A pdb=" N GLY H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.915A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY I 33 " --> pdb=" O ASP I 95 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 5 through 6 Processing sheet with id=AD2, first strand: chain 'J' and resid 9 through 14 removed outlier: 6.750A pdb=" N VAL J 11 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LEU J 106A" --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL J 13 " --> pdb=" O LEU J 106A" (cutoff:3.500A) removed outlier: 6.055A pdb=" N CYS J 88 " --> pdb=" O GLY J 99 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLY J 101 " --> pdb=" O TYR J 86 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N TYR J 86 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AD4, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.696A pdb=" N VAL L 11 " --> pdb=" O ARG L 103 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.696A pdb=" N VAL L 11 " --> pdb=" O ARG L 103 " (cutoff:3.500A) 709 hydrogen bonds defined for protein. 1746 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.06 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14782 1.03 - 1.23: 120 1.23 - 1.43: 6391 1.43 - 1.62: 8902 1.62 - 1.82: 138 Bond restraints: 30333 Sorted by residual: bond pdb=" N HIS C 368 " pdb=" H HIS C 368 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.72e+01 bond pdb=" CA HIS C 368 " pdb=" HA HIS C 368 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.30e+00 bond pdb=" N HIS C 368 " pdb=" CA HIS C 368 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.47e-02 4.63e+03 4.86e+00 bond pdb=" C1 NAG B 602 " pdb=" O5 NAG B 602 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.16e+00 ... (remaining 30328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 51902 1.27 - 2.53: 2494 2.53 - 3.80: 149 3.80 - 5.06: 18 5.06 - 6.33: 8 Bond angle restraints: 54571 Sorted by residual: angle pdb=" CA CYS F 92 " pdb=" CB CYS F 92 " pdb=" SG CYS F 92 " ideal model delta sigma weight residual 114.40 120.61 -6.21 2.30e+00 1.89e-01 7.30e+00 angle pdb=" CA CYS H 92 " pdb=" CB CYS H 92 " pdb=" SG CYS H 92 " ideal model delta sigma weight residual 114.40 120.52 -6.12 2.30e+00 1.89e-01 7.08e+00 angle pdb=" N ASP H 31 " pdb=" CA ASP H 31 " pdb=" C ASP H 31 " ideal model delta sigma weight residual 110.80 116.24 -5.44 2.13e+00 2.20e-01 6.52e+00 angle pdb=" CA CYS I 92 " pdb=" CB CYS I 92 " pdb=" SG CYS I 92 " ideal model delta sigma weight residual 114.40 120.11 -5.71 2.30e+00 1.89e-01 6.17e+00 angle pdb=" N LEU F 108 " pdb=" CA LEU F 108 " pdb=" C LEU F 108 " ideal model delta sigma weight residual 107.73 111.66 -3.93 1.80e+00 3.09e-01 4.78e+00 ... (remaining 54566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.38: 13410 20.38 - 40.77: 661 40.77 - 61.15: 412 61.15 - 81.53: 116 81.53 - 101.92: 20 Dihedral angle restraints: 14619 sinusoidal: 8126 harmonic: 6493 Sorted by residual: dihedral pdb=" CB CYS A 384 " pdb=" SG CYS A 384 " pdb=" SG CYS A 390 " pdb=" CB CYS A 390 " ideal model delta sinusoidal sigma weight residual -86.00 -145.12 59.12 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CA ASN B 178 " pdb=" C ASN B 178 " pdb=" N LYS B 179 " pdb=" CA LYS B 179 " ideal model delta harmonic sigma weight residual -180.00 -153.32 -26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA VAL A 162 " pdb=" C VAL A 162 " pdb=" N ARG A 163 " pdb=" CA ARG A 163 " ideal model delta harmonic sigma weight residual -180.00 -153.52 -26.48 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 14616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2177 0.078 - 0.155: 252 0.155 - 0.233: 4 0.233 - 0.310: 5 0.310 - 0.388: 1 Chirality restraints: 2439 Sorted by residual: chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 353 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 172 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 2436 not shown) Planarity restraints: 4611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 47 " 0.009 2.00e-02 2.50e+03 1.97e-02 1.56e+01 pdb=" CG TRP F 47 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP F 47 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP F 47 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 47 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP F 47 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 47 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 47 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 47 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 47 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP F 47 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP F 47 " 0.049 2.00e-02 2.50e+03 pdb=" HE3 TRP F 47 " -0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP F 47 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP F 47 " 0.004 2.00e-02 2.50e+03 pdb=" HH2 TRP F 47 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 367 " 0.147 9.50e-02 1.11e+02 5.45e-02 1.53e+01 pdb=" NE ARG A 367 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 367 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 367 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG A 367 " -0.042 2.00e-02 2.50e+03 pdb="HH11 ARG A 367 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 367 " 0.015 2.00e-02 2.50e+03 pdb="HH21 ARG A 367 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 367 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 61 " -0.215 9.50e-02 1.11e+02 7.45e-02 1.48e+01 pdb=" NE ARG G 61 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG G 61 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG G 61 " 0.047 2.00e-02 2.50e+03 pdb=" NH2 ARG G 61 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG G 61 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG G 61 " -0.039 2.00e-02 2.50e+03 pdb="HH21 ARG G 61 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG G 61 " -0.001 2.00e-02 2.50e+03 ... (remaining 4608 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 732 2.11 - 2.73: 53231 2.73 - 3.36: 82211 3.36 - 3.98: 107251 3.98 - 4.60: 170006 Nonbonded interactions: 413431 Sorted by model distance: nonbonded pdb=" OE2 GLU C 25 " pdb=" H GLY C 439 " model vdw 1.489 2.450 nonbonded pdb=" OE2 GLU A 25 " pdb=" H GLY A 439 " model vdw 1.510 2.450 nonbonded pdb=" HG SER A 37 " pdb=" OG1 THR A 281 " model vdw 1.523 2.450 nonbonded pdb="HH22 ARG C 156 " pdb=" O ASP H 31 " model vdw 1.542 2.450 nonbonded pdb=" OD1 ASP L 92 " pdb=" HG SER L 94 " model vdw 1.544 2.450 ... (remaining 413426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 367 or (resid 368 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA )) or resid 369 through 602)) selection = (chain 'B' and (resid 19 through 367 or (resid 368 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA )) or resid 369 through 602)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'K' } ncs_group { reference = (chain 'F' and (resid 4 through 63 or (resid 64 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA )) or resid 65 through 113)) selection = (chain 'H' and (resid 4 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE \ 1)) or resid 36 through 63 or (resid 64 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name CE or name NZ or name H or name HA ) \ ) or resid 65 through 113)) selection = chain 'I' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'L' } 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 individual isotropic 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.170 Extract box with map and model: 0.400 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 30.340 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 : 0.006 0.050 15606 Z= 0.249 Angle : 0.651 9.394 21201 Z= 0.350 Chirality : 0.048 0.388 2439 Planarity : 0.008 0.106 2706 Dihedral : 14.498 101.917 5874 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.42 % Allowed : 2.89 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.18), residues: 1950 helix: -1.30 (0.20), residues: 396 sheet: -0.09 (0.20), residues: 624 loop : -0.47 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG I 71 TYR 0.019 0.003 TYR I 52A PHE 0.018 0.002 PHE B 451 TRP 0.038 0.003 TRP F 47 HIS 0.007 0.002 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00565 (15549) covalent geometry : angle 0.63234 (21072) SS BOND : bond 0.00454 ( 42) SS BOND : angle 1.23800 ( 84) hydrogen bonds : bond 0.21338 ( 680) hydrogen bonds : angle 7.99501 ( 1746) link_BETA1-4 : bond 0.00595 ( 6) link_BETA1-4 : angle 2.74197 ( 18) link_NAG-ASN : bond 0.00446 ( 9) link_NAG-ASN : angle 3.34177 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 0.813 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 72 ASP cc_start: 0.8600 (t0) cc_final: 0.8206 (t0) REVERT: C 72 ASP cc_start: 0.8517 (t0) cc_final: 0.8295 (t0) REVERT: G 79 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7979 (mm110) REVERT: J 79 GLN cc_start: 0.8467 (mm-40) cc_final: 0.7756 (mm110) REVERT: L 79 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8264 (mp10) outliers start: 7 outliers final: 1 residues processed: 171 average time/residue: 0.4182 time to fit residues: 96.6983 Evaluate side-chains 84 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN I 56 ASN L 42 GLN L 95AASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.054292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.042803 restraints weight = 138665.211| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 3.68 r_work: 0.2509 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15606 Z= 0.154 Angle : 0.606 7.456 21201 Z= 0.329 Chirality : 0.045 0.344 2439 Planarity : 0.004 0.071 2706 Dihedral : 9.002 61.540 2450 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.72 % Allowed : 5.17 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.18), residues: 1950 helix: -0.07 (0.24), residues: 429 sheet: -0.06 (0.19), residues: 620 loop : -0.41 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 61 TYR 0.011 0.001 TYR J 49 PHE 0.015 0.001 PHE I 29 TRP 0.007 0.001 TRP A 284 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00323 (15549) covalent geometry : angle 0.59264 (21072) SS BOND : bond 0.00379 ( 42) SS BOND : angle 1.36286 ( 84) hydrogen bonds : bond 0.06000 ( 680) hydrogen bonds : angle 5.84181 ( 1746) link_BETA1-4 : bond 0.00221 ( 6) link_BETA1-4 : angle 2.39308 ( 18) link_NAG-ASN : bond 0.00378 ( 9) link_NAG-ASN : angle 2.12959 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.807 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 72 ASP cc_start: 0.9383 (t0) cc_final: 0.9108 (t0) REVERT: G 6 GLN cc_start: 0.7121 (tt0) cc_final: 0.6786 (tt0) outliers start: 12 outliers final: 5 residues processed: 111 average time/residue: 0.3214 time to fit residues: 52.4052 Evaluate side-chains 93 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 149 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 56 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.052311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.041223 restraints weight = 141486.446| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 3.57 r_work: 0.2491 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15606 Z= 0.288 Angle : 0.606 6.917 21201 Z= 0.328 Chirality : 0.044 0.268 2439 Planarity : 0.004 0.055 2706 Dihedral : 7.054 58.700 2450 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.84 % Allowed : 6.38 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.19), residues: 1950 helix: 0.38 (0.25), residues: 435 sheet: -0.32 (0.20), residues: 620 loop : -0.64 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 91 TYR 0.014 0.002 TYR J 49 PHE 0.012 0.001 PHE A 456 TRP 0.009 0.001 TRP I 47 HIS 0.005 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00632 (15549) covalent geometry : angle 0.59737 (21072) SS BOND : bond 0.00417 ( 42) SS BOND : angle 1.16672 ( 84) hydrogen bonds : bond 0.04856 ( 680) hydrogen bonds : angle 5.44454 ( 1746) link_BETA1-4 : bond 0.00478 ( 6) link_BETA1-4 : angle 2.05760 ( 18) link_NAG-ASN : bond 0.00298 ( 9) link_NAG-ASN : angle 1.80376 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.9382 (t0) cc_final: 0.9123 (t0) REVERT: G 60 ASP cc_start: 0.8899 (p0) cc_final: 0.8642 (t0) REVERT: G 81 GLU cc_start: 0.8874 (tp30) cc_final: 0.8556 (tp30) REVERT: I 75 GLN cc_start: 0.8863 (mp10) cc_final: 0.8482 (mp10) REVERT: L 60 ASP cc_start: 0.8769 (p0) cc_final: 0.8372 (t0) REVERT: L 79 GLN cc_start: 0.7399 (mp10) cc_final: 0.7100 (mp10) REVERT: L 82 ASP cc_start: 0.7948 (m-30) cc_final: 0.7730 (m-30) outliers start: 14 outliers final: 12 residues processed: 100 average time/residue: 0.3065 time to fit residues: 45.4702 Evaluate side-chains 90 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 160 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 189 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.053769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.042265 restraints weight = 139743.907| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 3.62 r_work: 0.2513 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15606 Z= 0.127 Angle : 0.509 5.713 21201 Z= 0.275 Chirality : 0.043 0.279 2439 Planarity : 0.003 0.057 2706 Dihedral : 6.290 59.084 2450 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.78 % Allowed : 6.26 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.19), residues: 1950 helix: 0.92 (0.26), residues: 435 sheet: -0.28 (0.20), residues: 614 loop : -0.49 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 29 TYR 0.008 0.001 TYR C 269 PHE 0.009 0.001 PHE G 98 TRP 0.006 0.001 TRP I 47 HIS 0.002 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00274 (15549) covalent geometry : angle 0.49874 (21072) SS BOND : bond 0.00295 ( 42) SS BOND : angle 1.22310 ( 84) hydrogen bonds : bond 0.04046 ( 680) hydrogen bonds : angle 5.12448 ( 1746) link_BETA1-4 : bond 0.00500 ( 6) link_BETA1-4 : angle 1.80677 ( 18) link_NAG-ASN : bond 0.00274 ( 9) link_NAG-ASN : angle 1.59491 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.938 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: A 72 ASP cc_start: 0.9377 (t0) cc_final: 0.9131 (t0) REVERT: G 60 ASP cc_start: 0.8879 (p0) cc_final: 0.8633 (t0) REVERT: G 81 GLU cc_start: 0.8829 (tp30) cc_final: 0.8497 (tp30) REVERT: L 79 GLN cc_start: 0.7486 (mp10) cc_final: 0.7277 (mp10) REVERT: L 82 ASP cc_start: 0.7831 (m-30) cc_final: 0.7576 (m-30) outliers start: 13 outliers final: 10 residues processed: 94 average time/residue: 0.3106 time to fit residues: 43.1460 Evaluate side-chains 87 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 131 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 190 optimal weight: 0.0270 chunk 168 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.053111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.041462 restraints weight = 136461.339| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 3.66 r_work: 0.2456 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15606 Z= 0.191 Angle : 0.520 6.389 21201 Z= 0.280 Chirality : 0.042 0.257 2439 Planarity : 0.003 0.038 2706 Dihedral : 5.975 59.572 2450 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.20 % Allowed : 5.78 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.19), residues: 1950 helix: 1.08 (0.26), residues: 438 sheet: -0.32 (0.20), residues: 613 loop : -0.60 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 29 TYR 0.008 0.001 TYR L 49 PHE 0.010 0.001 PHE A 456 TRP 0.009 0.001 TRP I 47 HIS 0.003 0.001 HIS J 95B Details of bonding type rmsd covalent geometry : bond 0.00418 (15549) covalent geometry : angle 0.51061 (21072) SS BOND : bond 0.00329 ( 42) SS BOND : angle 1.22412 ( 84) hydrogen bonds : bond 0.03875 ( 680) hydrogen bonds : angle 5.01752 ( 1746) link_BETA1-4 : bond 0.00429 ( 6) link_BETA1-4 : angle 1.59955 ( 18) link_NAG-ASN : bond 0.00241 ( 9) link_NAG-ASN : angle 1.52970 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.906 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: A 72 ASP cc_start: 0.9320 (t0) cc_final: 0.9119 (t0) REVERT: C 140 CYS cc_start: 0.6897 (OUTLIER) cc_final: 0.6683 (t) REVERT: F 75 GLN cc_start: 0.8322 (mp10) cc_final: 0.7969 (mp10) REVERT: G 60 ASP cc_start: 0.9019 (p0) cc_final: 0.8747 (t0) REVERT: G 81 GLU cc_start: 0.8840 (tp30) cc_final: 0.8448 (tp30) REVERT: I 34 MET cc_start: 0.8782 (mmm) cc_final: 0.8360 (mmt) REVERT: L 60 ASP cc_start: 0.8890 (p0) cc_final: 0.8493 (t0) outliers start: 20 outliers final: 15 residues processed: 101 average time/residue: 0.2905 time to fit residues: 44.5682 Evaluate side-chains 93 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 96 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.053200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.041543 restraints weight = 135714.912| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 3.67 r_work: 0.2461 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15606 Z= 0.165 Angle : 0.500 7.897 21201 Z= 0.270 Chirality : 0.042 0.258 2439 Planarity : 0.003 0.037 2706 Dihedral : 5.789 59.159 2450 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.78 % Allowed : 6.38 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.19), residues: 1950 helix: 1.24 (0.26), residues: 438 sheet: -0.31 (0.20), residues: 613 loop : -0.60 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 29 TYR 0.007 0.001 TYR C 269 PHE 0.010 0.001 PHE I 29 TRP 0.008 0.001 TRP I 47 HIS 0.002 0.001 HIS J 95B Details of bonding type rmsd covalent geometry : bond 0.00361 (15549) covalent geometry : angle 0.49007 (21072) SS BOND : bond 0.00341 ( 42) SS BOND : angle 1.28419 ( 84) hydrogen bonds : bond 0.03683 ( 680) hydrogen bonds : angle 4.91460 ( 1746) link_BETA1-4 : bond 0.00357 ( 6) link_BETA1-4 : angle 1.55000 ( 18) link_NAG-ASN : bond 0.00224 ( 9) link_NAG-ASN : angle 1.44970 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 CYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6775 (t) REVERT: F 34 MET cc_start: 0.8692 (mmm) cc_final: 0.8369 (mmm) REVERT: G 60 ASP cc_start: 0.9025 (p0) cc_final: 0.8748 (t0) REVERT: G 81 GLU cc_start: 0.8796 (tp30) cc_final: 0.8435 (tp30) REVERT: I 34 MET cc_start: 0.8784 (mmm) cc_final: 0.8428 (mmt) REVERT: J 79 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8446 (mm110) REVERT: L 60 ASP cc_start: 0.8875 (p0) cc_final: 0.8515 (t0) outliers start: 13 outliers final: 12 residues processed: 92 average time/residue: 0.3093 time to fit residues: 42.6471 Evaluate side-chains 91 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 31 optimal weight: 0.6980 chunk 151 optimal weight: 0.0970 chunk 103 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.053958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.042372 restraints weight = 134185.545| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 3.65 r_work: 0.2481 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15606 Z= 0.105 Angle : 0.473 6.219 21201 Z= 0.254 Chirality : 0.042 0.260 2439 Planarity : 0.003 0.043 2706 Dihedral : 5.518 58.661 2450 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.08 % Allowed : 6.62 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.19), residues: 1950 helix: 1.48 (0.26), residues: 438 sheet: -0.18 (0.21), residues: 613 loop : -0.49 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 30 TYR 0.008 0.001 TYR C 269 PHE 0.009 0.001 PHE I 29 TRP 0.006 0.001 TRP I 47 HIS 0.002 0.001 HIS I 100F Details of bonding type rmsd covalent geometry : bond 0.00232 (15549) covalent geometry : angle 0.46484 (21072) SS BOND : bond 0.00277 ( 42) SS BOND : angle 1.10542 ( 84) hydrogen bonds : bond 0.03348 ( 680) hydrogen bonds : angle 4.75290 ( 1746) link_BETA1-4 : bond 0.00358 ( 6) link_BETA1-4 : angle 1.47777 ( 18) link_NAG-ASN : bond 0.00277 ( 9) link_NAG-ASN : angle 1.34323 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.813 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: A 325 ASP cc_start: 0.7771 (t70) cc_final: 0.7548 (t0) REVERT: F 34 MET cc_start: 0.8768 (mmm) cc_final: 0.8453 (mmm) REVERT: F 75 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8679 (mp10) REVERT: G 60 ASP cc_start: 0.8983 (p0) cc_final: 0.8687 (t0) REVERT: J 79 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8435 (mm110) REVERT: L 60 ASP cc_start: 0.8912 (p0) cc_final: 0.8464 (t0) REVERT: L 81 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8245 (pp20) outliers start: 18 outliers final: 16 residues processed: 96 average time/residue: 0.3087 time to fit residues: 44.5361 Evaluate side-chains 96 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 174 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 187 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 172 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.054074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.042390 restraints weight = 135158.129| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 3.68 r_work: 0.2480 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15606 Z= 0.119 Angle : 0.469 5.992 21201 Z= 0.252 Chirality : 0.042 0.250 2439 Planarity : 0.003 0.036 2706 Dihedral : 5.379 58.195 2450 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.90 % Allowed : 7.10 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.19), residues: 1950 helix: 1.56 (0.26), residues: 438 sheet: -0.12 (0.21), residues: 613 loop : -0.48 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 30 TYR 0.013 0.001 TYR F 79 PHE 0.009 0.001 PHE I 29 TRP 0.007 0.001 TRP A 284 HIS 0.001 0.001 HIS J 95B Details of bonding type rmsd covalent geometry : bond 0.00262 (15549) covalent geometry : angle 0.46158 (21072) SS BOND : bond 0.00247 ( 42) SS BOND : angle 1.01276 ( 84) hydrogen bonds : bond 0.03263 ( 680) hydrogen bonds : angle 4.68035 ( 1746) link_BETA1-4 : bond 0.00376 ( 6) link_BETA1-4 : angle 1.47141 ( 18) link_NAG-ASN : bond 0.00249 ( 9) link_NAG-ASN : angle 1.31526 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 ASP cc_start: 0.7836 (t70) cc_final: 0.7615 (t0) REVERT: C 140 CYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6604 (t) REVERT: F 34 MET cc_start: 0.8780 (mmm) cc_final: 0.8469 (mmm) REVERT: F 75 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8682 (mp10) REVERT: G 60 ASP cc_start: 0.8965 (p0) cc_final: 0.8673 (t0) REVERT: G 81 GLU cc_start: 0.8777 (tp30) cc_final: 0.8483 (tp30) REVERT: J 79 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8546 (mm110) REVERT: L 60 ASP cc_start: 0.8931 (p0) cc_final: 0.8492 (t0) outliers start: 15 outliers final: 11 residues processed: 95 average time/residue: 0.2977 time to fit residues: 41.6822 Evaluate side-chains 92 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 85 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 67 optimal weight: 0.0970 chunk 149 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.053837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.042408 restraints weight = 136882.052| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 3.67 r_work: 0.2495 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15606 Z= 0.110 Angle : 0.466 6.543 21201 Z= 0.249 Chirality : 0.042 0.250 2439 Planarity : 0.003 0.036 2706 Dihedral : 5.271 58.326 2450 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.66 % Allowed : 7.40 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.19), residues: 1950 helix: 1.66 (0.26), residues: 438 sheet: -0.08 (0.21), residues: 613 loop : -0.40 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 396 TYR 0.019 0.001 TYR F 79 PHE 0.009 0.001 PHE I 29 TRP 0.006 0.001 TRP I 47 HIS 0.001 0.000 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00244 (15549) covalent geometry : angle 0.45882 (21072) SS BOND : bond 0.00243 ( 42) SS BOND : angle 0.98655 ( 84) hydrogen bonds : bond 0.03176 ( 680) hydrogen bonds : angle 4.62182 ( 1746) link_BETA1-4 : bond 0.00365 ( 6) link_BETA1-4 : angle 1.44894 ( 18) link_NAG-ASN : bond 0.00265 ( 9) link_NAG-ASN : angle 1.28565 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 ASP cc_start: 0.7883 (t70) cc_final: 0.7668 (t0) REVERT: F 34 MET cc_start: 0.8806 (mmm) cc_final: 0.8501 (mmm) REVERT: F 75 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8723 (mp10) REVERT: G 60 ASP cc_start: 0.8953 (p0) cc_final: 0.8656 (t0) REVERT: G 81 GLU cc_start: 0.8733 (tp30) cc_final: 0.8392 (tp30) REVERT: J 75 ILE cc_start: 0.8274 (mt) cc_final: 0.7946 (mt) REVERT: J 79 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8586 (mm110) REVERT: L 60 ASP cc_start: 0.8974 (p0) cc_final: 0.8510 (t0) outliers start: 11 outliers final: 11 residues processed: 97 average time/residue: 0.3551 time to fit residues: 49.7315 Evaluate side-chains 91 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 85 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.052778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.041351 restraints weight = 138635.415| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 3.67 r_work: 0.2465 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15606 Z= 0.198 Angle : 0.505 5.989 21201 Z= 0.270 Chirality : 0.042 0.239 2439 Planarity : 0.003 0.037 2706 Dihedral : 5.365 58.791 2450 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.84 % Allowed : 7.34 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.19), residues: 1950 helix: 1.54 (0.26), residues: 438 sheet: -0.11 (0.21), residues: 606 loop : -0.53 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 396 TYR 0.009 0.001 TYR L 49 PHE 0.011 0.001 PHE I 29 TRP 0.008 0.001 TRP I 47 HIS 0.002 0.001 HIS J 95B Details of bonding type rmsd covalent geometry : bond 0.00434 (15549) covalent geometry : angle 0.49768 (21072) SS BOND : bond 0.00309 ( 42) SS BOND : angle 1.04111 ( 84) hydrogen bonds : bond 0.03449 ( 680) hydrogen bonds : angle 4.67672 ( 1746) link_BETA1-4 : bond 0.00338 ( 6) link_BETA1-4 : angle 1.46145 ( 18) link_NAG-ASN : bond 0.00234 ( 9) link_NAG-ASN : angle 1.36127 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 CYS cc_start: 0.7017 (OUTLIER) cc_final: 0.6709 (t) REVERT: F 34 MET cc_start: 0.8807 (mmm) cc_final: 0.8490 (mmm) REVERT: F 75 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8765 (mp10) REVERT: G 60 ASP cc_start: 0.8918 (p0) cc_final: 0.8584 (t0) REVERT: G 81 GLU cc_start: 0.8804 (tp30) cc_final: 0.8442 (tp30) REVERT: I 34 MET cc_start: 0.8862 (mmm) cc_final: 0.8509 (mmt) REVERT: J 79 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8655 (mm110) REVERT: L 60 ASP cc_start: 0.8915 (p0) cc_final: 0.8469 (t0) outliers start: 14 outliers final: 13 residues processed: 92 average time/residue: 0.3478 time to fit residues: 46.5776 Evaluate side-chains 92 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 143 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.052437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.041014 restraints weight = 139274.577| |-----------------------------------------------------------------------------| r_work (start): 0.2587 rms_B_bonded: 3.67 r_work: 0.2459 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15606 Z= 0.195 Angle : 0.502 5.941 21201 Z= 0.270 Chirality : 0.043 0.245 2439 Planarity : 0.003 0.038 2706 Dihedral : 5.395 59.908 2450 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.84 % Allowed : 7.40 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 1950 helix: 1.51 (0.26), residues: 438 sheet: -0.18 (0.20), residues: 619 loop : -0.57 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 396 TYR 0.010 0.001 TYR F 79 PHE 0.010 0.001 PHE I 29 TRP 0.007 0.001 TRP A 284 HIS 0.002 0.001 HIS J 95B Details of bonding type rmsd covalent geometry : bond 0.00429 (15549) covalent geometry : angle 0.49493 (21072) SS BOND : bond 0.00309 ( 42) SS BOND : angle 1.06125 ( 84) hydrogen bonds : bond 0.03487 ( 680) hydrogen bonds : angle 4.70026 ( 1746) link_BETA1-4 : bond 0.00355 ( 6) link_BETA1-4 : angle 1.46186 ( 18) link_NAG-ASN : bond 0.00206 ( 9) link_NAG-ASN : angle 1.37086 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5122.46 seconds wall clock time: 88 minutes 3.17 seconds (5283.17 seconds total)