Starting phenix.real_space_refine on Sat Aug 8 06:35:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21rp_67947/08_2026/21rp_67947.cif Found real_map, /net/cci-nas-00/data/ceres_data/21rp_67947/08_2026/21rp_67947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21rp_67947/08_2026/21rp_67947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21rp_67947/08_2026/21rp_67947.map" model { file = "/net/cci-nas-00/data/ceres_data/21rp_67947/08_2026/21rp_67947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21rp_67947/08_2026/21rp_67947.cif" } resolution = 2.84 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= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 12 5.21 5 S 132 5.16 5 C 16344 2.51 5 N 4338 2.21 5 O 4986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25860 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4173 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 491} Chain: "B" Number of atoms: 4173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4173 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 491} Chain: "C" Number of atoms: 4173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4173 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 491} Chain: "D" Number of atoms: 4173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4173 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 491} Chain: "E" Number of atoms: 4173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4173 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 491} Chain: "F" Number of atoms: 4173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4173 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 491} Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "I" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "J" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "K" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.56, per 1000 atoms: 0.22 Number of scatterers: 25860 At special positions: 0 Unit cell: (149.144, 135.96, 106.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 132 16.00 P 48 15.00 Mg 12 11.99 O 4986 8.00 N 4338 7.00 C 16344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.1 seconds 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 12 sheets defined 60.0% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 Processing helix chain 'A' and resid 40 through 49 Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.618A pdb=" N LYS A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 160 through 168 removed outlier: 4.213A pdb=" N TRP A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 179 removed outlier: 3.952A pdb=" N ASN A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.970A pdb=" N LYS A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 231 removed outlier: 3.830A pdb=" N SER A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 265 removed outlier: 3.736A pdb=" N LYS A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.695A pdb=" N SER A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 350 through 365 Processing helix chain 'A' and resid 366 through 374 Proline residue: A 370 - end of helix Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.863A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 402 Processing helix chain 'A' and resid 403 through 417 Processing helix chain 'A' and resid 422 through 433 Processing helix chain 'A' and resid 434 through 445 removed outlier: 3.520A pdb=" N ASP A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 461 Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'B' and resid 6 through 17 Processing helix chain 'B' and resid 40 through 49 Processing helix chain 'B' and resid 81 through 95 removed outlier: 3.618A pdb=" N LYS B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 128 through 139 Processing helix chain 'B' and resid 160 through 168 removed outlier: 4.213A pdb=" N TRP B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 179 removed outlier: 3.952A pdb=" N ASN B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.970A pdb=" N LYS B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 231 removed outlier: 3.830A pdb=" N SER B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.736A pdb=" N LYS B 265 " --> pdb=" O MET B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.695A pdb=" N SER B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 350 through 365 Processing helix chain 'B' and resid 366 through 374 Proline residue: B 370 - end of helix Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.862A pdb=" N VAL B 379 " --> pdb=" O ILE B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 402 Processing helix chain 'B' and resid 403 through 417 Processing helix chain 'B' and resid 422 through 433 Processing helix chain 'B' and resid 434 through 445 removed outlier: 3.520A pdb=" N ASP B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'C' and resid 6 through 17 Processing helix chain 'C' and resid 40 through 49 Processing helix chain 'C' and resid 81 through 95 removed outlier: 3.618A pdb=" N LYS C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 128 through 139 Processing helix chain 'C' and resid 160 through 168 removed outlier: 4.214A pdb=" N TRP C 164 " --> pdb=" O HIS C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 179 removed outlier: 3.952A pdb=" N ASN C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 199 removed outlier: 3.970A pdb=" N LYS C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 231 removed outlier: 3.831A pdb=" N SER C 214 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA C 223 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 265 removed outlier: 3.736A pdb=" N LYS C 265 " --> pdb=" O MET C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.696A pdb=" N SER C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 329 Processing helix chain 'C' and resid 333 through 343 Processing helix chain 'C' and resid 350 through 365 Processing helix chain 'C' and resid 366 through 374 Proline residue: C 370 - end of helix Processing helix chain 'C' and resid 375 through 379 removed outlier: 3.863A pdb=" N VAL C 379 " --> pdb=" O ILE C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 402 Processing helix chain 'C' and resid 403 through 417 Processing helix chain 'C' and resid 422 through 433 Processing helix chain 'C' and resid 434 through 445 removed outlier: 3.520A pdb=" N ASP C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 461 Processing helix chain 'C' and resid 463 through 469 Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 490 through 498 Processing helix chain 'D' and resid 6 through 17 Processing helix chain 'D' and resid 40 through 49 Processing helix chain 'D' and resid 81 through 95 removed outlier: 3.617A pdb=" N LYS D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 128 through 139 Processing helix chain 'D' and resid 160 through 168 removed outlier: 4.213A pdb=" N TRP D 164 " --> pdb=" O HIS D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 179 removed outlier: 3.952A pdb=" N ASN D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 199 removed outlier: 3.970A pdb=" N LYS D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.830A pdb=" N SER D 214 " --> pdb=" O PRO D 210 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL D 224 " --> pdb=" O ILE D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 265 removed outlier: 3.736A pdb=" N LYS D 265 " --> pdb=" O MET D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.695A pdb=" N SER D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 329 Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 350 through 365 Processing helix chain 'D' and resid 366 through 374 Proline residue: D 370 - end of helix Processing helix chain 'D' and resid 375 through 379 removed outlier: 3.864A pdb=" N VAL D 379 " --> pdb=" O ILE D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 402 Processing helix chain 'D' and resid 403 through 417 Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 434 through 445 removed outlier: 3.519A pdb=" N ASP D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 461 Processing helix chain 'D' and resid 463 through 469 Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 490 through 498 Processing helix chain 'E' and resid 6 through 17 Processing helix chain 'E' and resid 40 through 49 Processing helix chain 'E' and resid 81 through 95 removed outlier: 3.618A pdb=" N LYS E 87 " --> pdb=" O LYS E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 101 through 105 Processing helix chain 'E' and resid 128 through 139 Processing helix chain 'E' and resid 160 through 168 removed outlier: 4.213A pdb=" N TRP E 164 " --> pdb=" O HIS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 179 removed outlier: 3.952A pdb=" N ASN E 177 " --> pdb=" O LYS E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 199 removed outlier: 3.971A pdb=" N LYS E 199 " --> pdb=" O GLN E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 231 removed outlier: 3.830A pdb=" N SER E 214 " --> pdb=" O PRO E 210 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA E 223 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 265 removed outlier: 3.737A pdb=" N LYS E 265 " --> pdb=" O MET E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.696A pdb=" N SER E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 329 Processing helix chain 'E' and resid 333 through 343 Processing helix chain 'E' and resid 350 through 365 Processing helix chain 'E' and resid 366 through 374 Proline residue: E 370 - end of helix Processing helix chain 'E' and resid 375 through 379 removed outlier: 3.863A pdb=" N VAL E 379 " --> pdb=" O ILE E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 402 Processing helix chain 'E' and resid 403 through 417 Processing helix chain 'E' and resid 422 through 433 Processing helix chain 'E' and resid 434 through 445 removed outlier: 3.520A pdb=" N ASP E 445 " --> pdb=" O LEU E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 461 Processing helix chain 'E' and resid 463 through 469 Processing helix chain 'E' and resid 470 through 480 Processing helix chain 'E' and resid 490 through 498 Processing helix chain 'F' and resid 6 through 17 Processing helix chain 'F' and resid 40 through 49 Processing helix chain 'F' and resid 81 through 95 removed outlier: 3.618A pdb=" N LYS F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 100 Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'F' and resid 128 through 139 Processing helix chain 'F' and resid 160 through 168 removed outlier: 4.214A pdb=" N TRP F 164 " --> pdb=" O HIS F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 179 removed outlier: 3.952A pdb=" N ASN F 177 " --> pdb=" O LYS F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 199 removed outlier: 3.970A pdb=" N LYS F 199 " --> pdb=" O GLN F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 231 removed outlier: 3.830A pdb=" N SER F 214 " --> pdb=" O PRO F 210 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA F 223 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL F 224 " --> pdb=" O ILE F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 265 removed outlier: 3.736A pdb=" N LYS F 265 " --> pdb=" O MET F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.696A pdb=" N SER F 290 " --> pdb=" O ASP F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 329 Processing helix chain 'F' and resid 333 through 343 Processing helix chain 'F' and resid 350 through 365 Processing helix chain 'F' and resid 366 through 374 Proline residue: F 370 - end of helix Processing helix chain 'F' and resid 375 through 379 removed outlier: 3.863A pdb=" N VAL F 379 " --> pdb=" O ILE F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 402 Processing helix chain 'F' and resid 403 through 417 Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 434 through 445 removed outlier: 3.520A pdb=" N ASP F 445 " --> pdb=" O LEU F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 461 Processing helix chain 'F' and resid 463 through 469 Processing helix chain 'F' and resid 470 through 480 Processing helix chain 'F' and resid 490 through 498 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 235 through 237 removed outlier: 11.100A pdb=" N LYS A 145 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N THR A 275 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N ASN A 147 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N HIS A 273 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASP A 149 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 66 Processing sheet with id=AA4, first strand: chain 'B' and resid 235 through 237 removed outlier: 11.101A pdb=" N LYS B 145 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N THR B 275 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N ASN B 147 " --> pdb=" O HIS B 273 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N HIS B 273 " --> pdb=" O ASN B 147 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASP B 149 " --> pdb=" O ASN B 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 62 through 66 Processing sheet with id=AA6, first strand: chain 'C' and resid 235 through 237 removed outlier: 11.100A pdb=" N LYS C 145 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N THR C 275 " --> pdb=" O LYS C 145 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N ASN C 147 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N HIS C 273 " --> pdb=" O ASN C 147 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASP C 149 " --> pdb=" O ASN C 271 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 62 through 66 Processing sheet with id=AA8, first strand: chain 'D' and resid 235 through 237 removed outlier: 11.101A pdb=" N LYS D 145 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N THR D 275 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N ASN D 147 " --> pdb=" O HIS D 273 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N HIS D 273 " --> pdb=" O ASN D 147 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASP D 149 " --> pdb=" O ASN D 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 62 through 66 Processing sheet with id=AB1, first strand: chain 'E' and resid 235 through 237 removed outlier: 11.100A pdb=" N LYS E 145 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N THR E 275 " --> pdb=" O LYS E 145 " (cutoff:3.500A) removed outlier: 9.863A pdb=" N ASN E 147 " --> pdb=" O HIS E 273 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N HIS E 273 " --> pdb=" O ASN E 147 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASP E 149 " --> pdb=" O ASN E 271 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 62 through 66 Processing sheet with id=AB3, first strand: chain 'F' and resid 235 through 237 removed outlier: 11.101A pdb=" N LYS F 145 " --> pdb=" O THR F 275 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N THR F 275 " --> pdb=" O LYS F 145 " (cutoff:3.500A) removed outlier: 9.864A pdb=" N ASN F 147 " --> pdb=" O HIS F 273 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N HIS F 273 " --> pdb=" O ASN F 147 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASP F 149 " --> pdb=" O ASN F 271 " (cutoff:3.500A) 1243 hydrogen bonds defined for protein. 3603 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: 4.78 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8294 1.34 - 1.47: 6627 1.47 - 1.59: 11347 1.59 - 1.71: 84 1.71 - 1.83: 186 Bond restraints: 26538 Sorted by residual: bond pdb=" C3' DA I 7 " pdb=" C2' DA I 7 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 4.98e+00 bond pdb=" C3' DA H 7 " pdb=" C2' DA H 7 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.74e+00 bond pdb=" C3' DA K 7 " pdb=" C2' DA K 7 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.72e+00 bond pdb=" O5' DTP C 601 " pdb=" PA DTP C 601 " ideal model delta sigma weight residual 1.579 1.603 -0.024 1.10e-02 8.26e+03 4.69e+00 bond pdb=" C3' DA L 7 " pdb=" C2' DA L 7 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.66e+00 ... (remaining 26533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 35531 1.99 - 3.98: 463 3.98 - 5.96: 72 5.96 - 7.95: 6 7.95 - 9.94: 6 Bond angle restraints: 36078 Sorted by residual: angle pdb=" PB DTP F 601 " pdb=" O3B DTP F 601 " pdb=" PG DTP F 601 " ideal model delta sigma weight residual 139.87 129.93 9.94 1.00e+00 1.00e+00 9.88e+01 angle pdb=" PB DTP C 601 " pdb=" O3B DTP C 601 " pdb=" PG DTP C 601 " ideal model delta sigma weight residual 139.87 129.93 9.94 1.00e+00 1.00e+00 9.87e+01 angle pdb=" PB DTP D 601 " pdb=" O3B DTP D 601 " pdb=" PG DTP D 601 " ideal model delta sigma weight residual 139.87 129.94 9.93 1.00e+00 1.00e+00 9.86e+01 angle pdb=" PB DTP A 601 " pdb=" O3B DTP A 601 " pdb=" PG DTP A 601 " ideal model delta sigma weight residual 139.87 129.97 9.90 1.00e+00 1.00e+00 9.81e+01 angle pdb=" PB DTP B 601 " pdb=" O3B DTP B 601 " pdb=" PG DTP B 601 " ideal model delta sigma weight residual 139.87 129.98 9.89 1.00e+00 1.00e+00 9.79e+01 ... (remaining 36073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 13226 17.88 - 35.75: 1993 35.75 - 53.63: 514 53.63 - 71.50: 167 71.50 - 89.38: 48 Dihedral angle restraints: 15948 sinusoidal: 6864 harmonic: 9084 Sorted by residual: dihedral pdb=" CB GLU C 506 " pdb=" CG GLU C 506 " pdb=" CD GLU C 506 " pdb=" OE1 GLU C 506 " ideal model delta sinusoidal sigma weight residual 0.00 89.38 -89.38 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU D 506 " pdb=" CG GLU D 506 " pdb=" CD GLU D 506 " pdb=" OE1 GLU D 506 " ideal model delta sinusoidal sigma weight residual 0.00 89.37 -89.37 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 506 " pdb=" CG GLU A 506 " pdb=" CD GLU A 506 " pdb=" OE1 GLU A 506 " ideal model delta sinusoidal sigma weight residual 0.00 89.37 -89.37 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 15945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3263 0.056 - 0.111: 512 0.111 - 0.167: 83 0.167 - 0.223: 6 0.223 - 0.278: 6 Chirality restraints: 3870 Sorted by residual: chirality pdb=" CG LEU B 258 " pdb=" CB LEU B 258 " pdb=" CD1 LEU B 258 " pdb=" CD2 LEU B 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU C 258 " pdb=" CB LEU C 258 " pdb=" CD1 LEU C 258 " pdb=" CD2 LEU C 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CG LEU A 258 " pdb=" CB LEU A 258 " pdb=" CD1 LEU A 258 " pdb=" CD2 LEU A 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 3867 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA J 7 " -0.008 2.00e-02 2.50e+03 2.40e-02 1.59e+01 pdb=" N9 DA J 7 " 0.012 2.00e-02 2.50e+03 pdb=" C8 DA J 7 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA J 7 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DA J 7 " -0.019 2.00e-02 2.50e+03 pdb=" C6 DA J 7 " 0.067 2.00e-02 2.50e+03 pdb=" N6 DA J 7 " -0.021 2.00e-02 2.50e+03 pdb=" N1 DA J 7 " -0.028 2.00e-02 2.50e+03 pdb=" C2 DA J 7 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA J 7 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DA J 7 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA L 7 " 0.007 2.00e-02 2.50e+03 2.39e-02 1.57e+01 pdb=" N9 DA L 7 " -0.012 2.00e-02 2.50e+03 pdb=" C8 DA L 7 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA L 7 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DA L 7 " 0.018 2.00e-02 2.50e+03 pdb=" C6 DA L 7 " -0.066 2.00e-02 2.50e+03 pdb=" N6 DA L 7 " 0.020 2.00e-02 2.50e+03 pdb=" N1 DA L 7 " 0.028 2.00e-02 2.50e+03 pdb=" C2 DA L 7 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA L 7 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA L 7 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA K 7 " -0.007 2.00e-02 2.50e+03 2.38e-02 1.56e+01 pdb=" N9 DA K 7 " 0.012 2.00e-02 2.50e+03 pdb=" C8 DA K 7 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA K 7 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DA K 7 " -0.018 2.00e-02 2.50e+03 pdb=" C6 DA K 7 " 0.066 2.00e-02 2.50e+03 pdb=" N6 DA K 7 " -0.020 2.00e-02 2.50e+03 pdb=" N1 DA K 7 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DA K 7 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA K 7 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA K 7 " -0.001 2.00e-02 2.50e+03 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 206 2.67 - 3.23: 24460 3.23 - 3.79: 41880 3.79 - 4.34: 59454 4.34 - 4.90: 95752 Nonbonded interactions: 221752 Sorted by model distance: nonbonded pdb=" OD2 ASP D 240 " pdb="MG MG D 602 " model vdw 2.117 2.170 nonbonded pdb=" OD2 ASP E 240 " pdb="MG MG E 602 " model vdw 2.117 2.170 nonbonded pdb=" OD2 ASP F 240 " pdb="MG MG F 602 " model vdw 2.117 2.170 nonbonded pdb=" OD2 ASP C 240 " pdb="MG MG C 602 " model vdw 2.117 2.170 nonbonded pdb=" OD2 ASP B 240 " pdb="MG MG B 602 " model vdw 2.117 2.170 ... (remaining 221747 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' 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: 5.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 24.790 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.140 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:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 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 : 0.003 0.039 26538 Z= 0.192 Angle : 0.582 9.939 36078 Z= 0.348 Chirality : 0.044 0.278 3870 Planarity : 0.006 0.072 4494 Dihedral : 18.904 89.378 10104 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.29 % Allowed : 24.43 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.15), residues: 3042 helix: 1.37 (0.12), residues: 1638 sheet: -0.49 (0.36), residues: 246 loop : 0.06 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 16 TYR 0.043 0.003 TYR F 355 PHE 0.021 0.002 PHE D 140 TRP 0.023 0.003 TRP D 288 HIS 0.016 0.004 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.19 (26538) covalent geometry : angle 0.58225 / 0.35 (36078) hydrogen bonds : bond 0.15558 / 10.34 ( 1243) hydrogen bonds : angle 5.91574 / 4.22 ( 3603) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.8449 (mmm) cc_final: 0.8006 (mmt) REVERT: A 349 TYR cc_start: 0.7775 (m-10) cc_final: 0.7125 (m-10) REVERT: A 393 GLU cc_start: 0.8149 (tp30) cc_final: 0.7922 (mm-30) REVERT: A 459 ILE cc_start: 0.8402 (mt) cc_final: 0.8124 (mm) REVERT: B 54 ARG cc_start: 0.8565 (ttp80) cc_final: 0.8338 (ttp80) REVERT: B 69 ARG cc_start: 0.8169 (mtm-85) cc_final: 0.7780 (mtt180) REVERT: B 109 MET cc_start: 0.8464 (mmm) cc_final: 0.7984 (mmt) REVERT: B 349 TYR cc_start: 0.7662 (m-10) cc_final: 0.7196 (m-10) REVERT: B 400 GLU cc_start: 0.8299 (tp30) cc_final: 0.7747 (mt-10) REVERT: B 459 ILE cc_start: 0.8276 (mt) cc_final: 0.8028 (mm) REVERT: C 349 TYR cc_start: 0.7819 (m-10) cc_final: 0.7281 (m-10) REVERT: D 349 TYR cc_start: 0.7754 (m-10) cc_final: 0.7240 (m-10) REVERT: D 447 TYR cc_start: 0.8871 (m-80) cc_final: 0.8642 (m-80) REVERT: E 349 TYR cc_start: 0.7730 (m-10) cc_final: 0.7147 (m-10) REVERT: E 393 GLU cc_start: 0.8105 (tp30) cc_final: 0.7876 (mm-30) REVERT: E 459 ILE cc_start: 0.8373 (mt) cc_final: 0.8129 (mm) REVERT: F 54 ARG cc_start: 0.8540 (ttp80) cc_final: 0.8314 (ttp80) REVERT: F 69 ARG cc_start: 0.8177 (mtm-85) cc_final: 0.7767 (mtt180) REVERT: F 109 MET cc_start: 0.8446 (mmm) cc_final: 0.7966 (mmt) REVERT: F 349 TYR cc_start: 0.7751 (m-10) cc_final: 0.7215 (m-10) REVERT: F 400 GLU cc_start: 0.8303 (tp30) cc_final: 0.7749 (mt-10) REVERT: F 459 ILE cc_start: 0.8281 (mt) cc_final: 0.8038 (mm) outliers start: 8 outliers final: 7 residues processed: 205 average time/residue: 0.7577 time to fit residues: 177.5889 Evaluate side-chains 196 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 189 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 494 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.0980 chunk 298 optimal weight: 4.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN A 257 HIS A 287 ASN A 324 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 287 ASN B 324 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 HIS C 287 ASN C 324 GLN D 124 ASN D 257 HIS D 287 ASN D 324 GLN E 124 ASN E 257 HIS E 287 ASN E 324 GLN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN F 287 ASN F 324 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.108138 restraints weight = 30194.719| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.68 r_work: 0.3076 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 26538 Z= 0.238 Angle : 0.526 6.457 36078 Z= 0.287 Chirality : 0.043 0.141 3870 Planarity : 0.005 0.045 4494 Dihedral : 13.307 79.983 3962 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.11 % Allowed : 21.89 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.83 (0.15), residues: 3042 helix: 1.15 (0.12), residues: 1704 sheet: -0.41 (0.35), residues: 246 loop : -0.02 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 54 TYR 0.021 0.002 TYR F 238 PHE 0.020 0.002 PHE B 154 TRP 0.005 0.001 TRP B 187 HIS 0.006 0.001 HIS E 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.24 (26538) covalent geometry : angle 0.52594 / 0.29 (36078) hydrogen bonds : bond 0.05380 / 3.63 ( 1243) hydrogen bonds : angle 4.92297 / 3.54 ( 3603) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 196 time to evaluate : 1.084 Fit side-chains REVERT: A 109 MET cc_start: 0.8894 (mmm) cc_final: 0.8572 (mmt) REVERT: A 349 TYR cc_start: 0.7758 (m-10) cc_final: 0.7254 (m-10) REVERT: A 393 GLU cc_start: 0.8376 (tp30) cc_final: 0.8145 (mm-30) REVERT: A 459 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8322 (mm) REVERT: B 69 ARG cc_start: 0.8300 (mtm-85) cc_final: 0.8053 (mtt180) REVERT: B 185 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7259 (mtmt) REVERT: B 349 TYR cc_start: 0.7544 (m-10) cc_final: 0.7190 (m-10) REVERT: C 185 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7173 (mtmt) REVERT: C 349 TYR cc_start: 0.7621 (m-10) cc_final: 0.7255 (m-10) REVERT: D 185 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7183 (mtmt) REVERT: D 349 TYR cc_start: 0.7594 (m-10) cc_final: 0.7239 (m-10) REVERT: E 109 MET cc_start: 0.8913 (mmm) cc_final: 0.8562 (mmt) REVERT: E 349 TYR cc_start: 0.7687 (m-10) cc_final: 0.7226 (m-10) REVERT: E 393 GLU cc_start: 0.8334 (tp30) cc_final: 0.8099 (mm-30) REVERT: E 459 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8336 (mm) REVERT: F 69 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.8105 (mtt180) REVERT: F 185 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7268 (mtmt) REVERT: F 349 TYR cc_start: 0.7570 (m-10) cc_final: 0.7201 (m-10) outliers start: 59 outliers final: 32 residues processed: 247 average time/residue: 0.6660 time to fit residues: 189.4612 Evaluate side-chains 223 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 312 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 204 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 153 optimal weight: 0.3980 chunk 180 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.131017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.111353 restraints weight = 29890.465| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.69 r_work: 0.3123 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 26538 Z= 0.110 Angle : 0.421 5.239 36078 Z= 0.233 Chirality : 0.038 0.129 3870 Planarity : 0.004 0.040 4494 Dihedral : 13.223 81.312 3960 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.43 % Allowed : 22.32 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.15), residues: 3042 helix: 1.41 (0.12), residues: 1710 sheet: -0.39 (0.36), residues: 246 loop : 0.08 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 54 TYR 0.012 0.001 TYR C 475 PHE 0.010 0.001 PHE B 154 TRP 0.006 0.001 TRP D 187 HIS 0.003 0.001 HIS E 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (26538) covalent geometry : angle 0.42096 / 0.23 (36078) hydrogen bonds : bond 0.04061 / 2.75 ( 1243) hydrogen bonds : angle 4.63302 / 3.34 ( 3603) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 1.057 Fit side-chains REVERT: A 109 MET cc_start: 0.8799 (mmm) cc_final: 0.8458 (mmt) REVERT: A 349 TYR cc_start: 0.7715 (m-10) cc_final: 0.7238 (m-10) REVERT: A 393 GLU cc_start: 0.8310 (tp30) cc_final: 0.8064 (mm-30) REVERT: A 459 ILE cc_start: 0.8531 (mt) cc_final: 0.8271 (mm) REVERT: B 69 ARG cc_start: 0.8244 (mtm-85) cc_final: 0.7860 (mtt180) REVERT: B 185 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7202 (mtmt) REVERT: B 349 TYR cc_start: 0.7483 (m-10) cc_final: 0.7133 (m-10) REVERT: B 385 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6556 (p0) REVERT: C 185 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7217 (mtmt) REVERT: C 349 TYR cc_start: 0.7613 (m-10) cc_final: 0.7248 (m-10) REVERT: D 185 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7237 (mtmt) REVERT: D 349 TYR cc_start: 0.7578 (m-10) cc_final: 0.7216 (m-10) REVERT: E 109 MET cc_start: 0.8805 (mmm) cc_final: 0.8453 (mmt) REVERT: E 349 TYR cc_start: 0.7639 (m-10) cc_final: 0.7227 (m-10) REVERT: E 393 GLU cc_start: 0.8320 (tp30) cc_final: 0.8069 (mm-30) REVERT: E 459 ILE cc_start: 0.8529 (mt) cc_final: 0.8283 (mm) REVERT: F 69 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.7869 (mtt180) REVERT: F 185 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7215 (mtmt) REVERT: F 349 TYR cc_start: 0.7522 (m-10) cc_final: 0.7161 (m-10) REVERT: F 385 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6572 (p0) outliers start: 40 outliers final: 16 residues processed: 243 average time/residue: 0.6626 time to fit residues: 186.0150 Evaluate side-chains 213 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 385 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 101 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.110828 restraints weight = 29921.880| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.60 r_work: 0.3109 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26538 Z= 0.136 Angle : 0.437 5.855 36078 Z= 0.240 Chirality : 0.039 0.132 3870 Planarity : 0.004 0.039 4494 Dihedral : 13.247 82.299 3960 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.82 % Allowed : 21.78 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.15), residues: 3042 helix: 1.46 (0.12), residues: 1704 sheet: -0.38 (0.36), residues: 246 loop : 0.06 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 54 TYR 0.012 0.001 TYR D 238 PHE 0.011 0.001 PHE F 154 TRP 0.007 0.001 TRP F 187 HIS 0.004 0.001 HIS F 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (26538) covalent geometry : angle 0.43713 / 0.24 (36078) hydrogen bonds : bond 0.04146 / 2.81 ( 1243) hydrogen bonds : angle 4.55282 / 3.28 ( 3603) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 1.068 Fit side-chains REVERT: A 109 MET cc_start: 0.8864 (mmm) cc_final: 0.8514 (mmt) REVERT: A 349 TYR cc_start: 0.7659 (m-10) cc_final: 0.7201 (m-10) REVERT: A 393 GLU cc_start: 0.8311 (tp30) cc_final: 0.8082 (mm-30) REVERT: A 459 ILE cc_start: 0.8576 (mt) cc_final: 0.8313 (mm) REVERT: B 69 ARG cc_start: 0.8268 (mtm-85) cc_final: 0.7873 (mtt180) REVERT: B 106 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: B 185 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7262 (mtmt) REVERT: B 349 TYR cc_start: 0.7453 (m-10) cc_final: 0.7131 (m-10) REVERT: B 385 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6603 (p0) REVERT: C 185 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7330 (mtmt) REVERT: C 349 TYR cc_start: 0.7608 (m-10) cc_final: 0.7279 (m-10) REVERT: D 349 TYR cc_start: 0.7595 (m-10) cc_final: 0.7256 (m-10) REVERT: E 109 MET cc_start: 0.8866 (mmm) cc_final: 0.8485 (mmt) REVERT: E 349 TYR cc_start: 0.7651 (m-10) cc_final: 0.7253 (m-10) REVERT: E 393 GLU cc_start: 0.8331 (tp30) cc_final: 0.8100 (mm-30) REVERT: E 459 ILE cc_start: 0.8565 (mt) cc_final: 0.8316 (mm) REVERT: F 69 ARG cc_start: 0.8276 (mtm-85) cc_final: 0.7875 (mtt180) REVERT: F 106 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7174 (pm20) REVERT: F 185 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7271 (mtmt) REVERT: F 349 TYR cc_start: 0.7538 (m-10) cc_final: 0.7193 (m-10) REVERT: F 385 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6614 (p0) outliers start: 51 outliers final: 24 residues processed: 238 average time/residue: 0.6923 time to fit residues: 189.7205 Evaluate side-chains 218 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 385 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 101 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 162 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 227 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.130952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.111870 restraints weight = 29903.292| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.59 r_work: 0.3186 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 26538 Z= 0.114 Angle : 0.419 5.615 36078 Z= 0.231 Chirality : 0.038 0.131 3870 Planarity : 0.004 0.038 4494 Dihedral : 13.256 82.120 3960 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.04 % Allowed : 22.03 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.15), residues: 3042 helix: 1.52 (0.12), residues: 1710 sheet: -0.33 (0.37), residues: 246 loop : 0.13 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 54 TYR 0.011 0.001 TYR C 475 PHE 0.010 0.001 PHE B 154 TRP 0.007 0.001 TRP F 187 HIS 0.003 0.001 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (26538) covalent geometry : angle 0.41924 / 0.23 (36078) hydrogen bonds : bond 0.03866 / 2.62 ( 1243) hydrogen bonds : angle 4.47244 / 3.23 ( 3603) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 193 time to evaluate : 0.743 Fit side-chains REVERT: A 106 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: A 109 MET cc_start: 0.8850 (mmm) cc_final: 0.8476 (mmt) REVERT: A 349 TYR cc_start: 0.7633 (m-10) cc_final: 0.7202 (m-10) REVERT: A 393 GLU cc_start: 0.8321 (tp30) cc_final: 0.8085 (mm-30) REVERT: A 459 ILE cc_start: 0.8565 (mt) cc_final: 0.8313 (mm) REVERT: B 69 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.7873 (mtt180) REVERT: B 185 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7272 (mtmt) REVERT: B 290 SER cc_start: 0.8254 (OUTLIER) cc_final: 0.8007 (m) REVERT: B 349 TYR cc_start: 0.7418 (m-10) cc_final: 0.7095 (m-10) REVERT: B 385 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6598 (p0) REVERT: C 349 TYR cc_start: 0.7610 (m-10) cc_final: 0.7283 (m-10) REVERT: D 349 TYR cc_start: 0.7585 (m-10) cc_final: 0.7257 (m-10) REVERT: E 109 MET cc_start: 0.8865 (mmm) cc_final: 0.8499 (mmt) REVERT: E 349 TYR cc_start: 0.7625 (m-10) cc_final: 0.7252 (m-10) REVERT: E 393 GLU cc_start: 0.8329 (tp30) cc_final: 0.8093 (mm-30) REVERT: E 459 ILE cc_start: 0.8545 (mt) cc_final: 0.8307 (mm) REVERT: F 69 ARG cc_start: 0.8273 (mtm-85) cc_final: 0.7881 (mtt180) REVERT: F 185 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7263 (mtmt) REVERT: F 349 TYR cc_start: 0.7501 (m-10) cc_final: 0.7165 (m-10) REVERT: F 385 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6603 (p0) outliers start: 57 outliers final: 27 residues processed: 245 average time/residue: 0.6200 time to fit residues: 176.0474 Evaluate side-chains 222 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 385 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 153 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 0.0070 chunk 286 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 278 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 287 optimal weight: 0.0370 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.131188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.112038 restraints weight = 29924.009| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.61 r_work: 0.3186 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 26538 Z= 0.112 Angle : 0.417 5.686 36078 Z= 0.229 Chirality : 0.038 0.138 3870 Planarity : 0.004 0.038 4494 Dihedral : 13.266 82.327 3960 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.11 % Allowed : 21.96 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.15), residues: 3042 helix: 1.57 (0.12), residues: 1710 sheet: -0.31 (0.37), residues: 246 loop : 0.15 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 54 TYR 0.012 0.001 TYR D 475 PHE 0.009 0.001 PHE B 154 TRP 0.007 0.001 TRP F 187 HIS 0.003 0.001 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (26538) covalent geometry : angle 0.41727 / 0.23 (36078) hydrogen bonds : bond 0.03786 / 2.57 ( 1243) hydrogen bonds : angle 4.42299 / 3.19 ( 3603) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 190 time to evaluate : 1.039 Fit side-chains REVERT: A 106 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: A 109 MET cc_start: 0.8825 (mmm) cc_final: 0.8445 (mmt) REVERT: A 349 TYR cc_start: 0.7627 (m-10) cc_final: 0.7204 (m-10) REVERT: A 393 GLU cc_start: 0.8321 (tp30) cc_final: 0.8089 (mm-30) REVERT: A 459 ILE cc_start: 0.8558 (mt) cc_final: 0.8311 (mm) REVERT: B 69 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7863 (mtt180) REVERT: B 106 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7097 (pm20) REVERT: B 185 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7298 (mtmt) REVERT: B 290 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.7999 (m) REVERT: B 349 TYR cc_start: 0.7425 (m-10) cc_final: 0.7105 (m-10) REVERT: B 385 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.6612 (p0) REVERT: C 349 TYR cc_start: 0.7606 (m-10) cc_final: 0.7279 (m-10) REVERT: E 106 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: E 109 MET cc_start: 0.8834 (mmm) cc_final: 0.8478 (mmt) REVERT: E 349 TYR cc_start: 0.7617 (m-10) cc_final: 0.7251 (m-10) REVERT: E 393 GLU cc_start: 0.8333 (tp30) cc_final: 0.8097 (mm-30) REVERT: E 459 ILE cc_start: 0.8534 (mt) cc_final: 0.8298 (mm) REVERT: F 69 ARG cc_start: 0.8251 (mtm-85) cc_final: 0.7866 (mtt180) REVERT: F 106 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7134 (pm20) REVERT: F 185 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7200 (mtmt) REVERT: F 349 TYR cc_start: 0.7484 (m-10) cc_final: 0.7164 (m-10) REVERT: F 385 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6601 (p0) outliers start: 59 outliers final: 29 residues processed: 243 average time/residue: 0.6615 time to fit residues: 186.0412 Evaluate side-chains 224 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 459 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 214 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 227 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 286 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.128908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.109741 restraints weight = 30171.603| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.60 r_work: 0.3091 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26538 Z= 0.171 Angle : 0.464 5.991 36078 Z= 0.254 Chirality : 0.041 0.138 3870 Planarity : 0.004 0.040 4494 Dihedral : 13.359 81.811 3960 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.04 % Allowed : 22.17 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.15), residues: 3042 helix: 1.46 (0.12), residues: 1704 sheet: -0.30 (0.37), residues: 246 loop : 0.02 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 54 TYR 0.015 0.001 TYR F 238 PHE 0.013 0.001 PHE F 154 TRP 0.006 0.001 TRP F 187 HIS 0.004 0.001 HIS F 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (26538) covalent geometry : angle 0.46391 / 0.25 (36078) hydrogen bonds : bond 0.04349 / 2.94 ( 1243) hydrogen bonds : angle 4.51242 / 3.25 ( 3603) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 0.865 Fit side-chains REVERT: A 106 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7312 (pm20) REVERT: A 349 TYR cc_start: 0.7651 (m-10) cc_final: 0.7226 (m-10) REVERT: A 393 GLU cc_start: 0.8331 (tp30) cc_final: 0.8105 (mm-30) REVERT: A 459 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8316 (mm) REVERT: B 69 ARG cc_start: 0.8252 (mtm-85) cc_final: 0.7946 (mtt180) REVERT: B 106 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7184 (pm20) REVERT: B 185 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7337 (mtmt) REVERT: B 290 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.8027 (m) REVERT: B 349 TYR cc_start: 0.7413 (m-10) cc_final: 0.7120 (m-10) REVERT: B 385 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6606 (p0) REVERT: E 106 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: E 349 TYR cc_start: 0.7619 (m-10) cc_final: 0.7253 (m-10) REVERT: E 393 GLU cc_start: 0.8333 (tp30) cc_final: 0.8101 (mm-30) REVERT: E 459 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8301 (mm) REVERT: F 69 ARG cc_start: 0.8257 (mtm-85) cc_final: 0.7862 (mtt180) REVERT: F 106 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7191 (pm20) REVERT: F 185 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7331 (mtmt) REVERT: F 349 TYR cc_start: 0.7479 (m-10) cc_final: 0.7160 (m-10) REVERT: F 385 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6601 (p0) outliers start: 57 outliers final: 33 residues processed: 243 average time/residue: 0.6943 time to fit residues: 194.5101 Evaluate side-chains 229 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 459 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 32 optimal weight: 2.9990 chunk 233 optimal weight: 0.9980 chunk 284 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 209 optimal weight: 5.9990 chunk 211 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 299 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.130234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.111136 restraints weight = 30103.906| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.60 r_work: 0.3177 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 26538 Z= 0.123 Angle : 0.429 5.643 36078 Z= 0.236 Chirality : 0.039 0.135 3870 Planarity : 0.004 0.040 4494 Dihedral : 13.361 80.839 3960 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.68 % Allowed : 22.75 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.15), residues: 3042 helix: 1.52 (0.12), residues: 1710 sheet: -0.37 (0.37), residues: 246 loop : 0.10 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 54 TYR 0.013 0.001 TYR C 475 PHE 0.010 0.001 PHE F 154 TRP 0.008 0.001 TRP F 187 HIS 0.003 0.001 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (26538) covalent geometry : angle 0.42949 / 0.24 (36078) hydrogen bonds : bond 0.03898 / 2.64 ( 1243) hydrogen bonds : angle 4.45144 / 3.21 ( 3603) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 0.967 Fit side-chains REVERT: A 106 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7284 (pm20) REVERT: A 349 TYR cc_start: 0.7598 (m-10) cc_final: 0.7212 (m-10) REVERT: A 393 GLU cc_start: 0.8325 (tp30) cc_final: 0.8094 (mm-30) REVERT: A 459 ILE cc_start: 0.8569 (mt) cc_final: 0.8298 (mm) REVERT: B 69 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.7861 (mtt180) REVERT: B 106 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7170 (pm20) REVERT: B 185 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7333 (mtmt) REVERT: B 290 SER cc_start: 0.8234 (OUTLIER) cc_final: 0.8015 (m) REVERT: B 349 TYR cc_start: 0.7428 (m-10) cc_final: 0.7131 (m-10) REVERT: B 385 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6566 (p0) REVERT: C 106 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7425 (pm20) REVERT: E 106 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: E 109 MET cc_start: 0.8868 (mmm) cc_final: 0.8472 (mmt) REVERT: E 349 TYR cc_start: 0.7620 (m-10) cc_final: 0.7251 (m-10) REVERT: E 393 GLU cc_start: 0.8329 (tp30) cc_final: 0.8093 (mm-30) REVERT: E 459 ILE cc_start: 0.8545 (mt) cc_final: 0.8279 (mm) REVERT: F 69 ARG cc_start: 0.8239 (mtm-85) cc_final: 0.7855 (mtt180) REVERT: F 106 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7202 (pm20) REVERT: F 185 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7328 (mtmt) REVERT: F 349 TYR cc_start: 0.7503 (m-10) cc_final: 0.7171 (m-10) REVERT: F 385 ASP cc_start: 0.7222 (OUTLIER) cc_final: 0.6521 (p0) outliers start: 47 outliers final: 26 residues processed: 234 average time/residue: 0.6836 time to fit residues: 183.8323 Evaluate side-chains 222 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 385 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 293 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 249 optimal weight: 5.9990 chunk 60 optimal weight: 0.0060 chunk 218 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN F 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.131821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.112744 restraints weight = 29880.950| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.61 r_work: 0.3136 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 26538 Z= 0.099 Angle : 0.412 5.639 36078 Z= 0.226 Chirality : 0.038 0.129 3870 Planarity : 0.004 0.039 4494 Dihedral : 13.315 80.662 3960 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.61 % Allowed : 22.68 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.15), residues: 3042 helix: 1.63 (0.12), residues: 1710 sheet: -0.28 (0.37), residues: 246 loop : 0.15 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 54 TYR 0.011 0.001 TYR C 475 PHE 0.008 0.001 PHE B 154 TRP 0.008 0.001 TRP F 187 HIS 0.003 0.001 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (26538) covalent geometry : angle 0.41155 / 0.23 (36078) hydrogen bonds : bond 0.03598 / 2.44 ( 1243) hydrogen bonds : angle 4.36968 / 3.16 ( 3603) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7269 (pm20) REVERT: A 349 TYR cc_start: 0.7581 (m-10) cc_final: 0.7199 (m-10) REVERT: A 393 GLU cc_start: 0.8316 (tp30) cc_final: 0.8090 (mm-30) REVERT: A 459 ILE cc_start: 0.8555 (mt) cc_final: 0.8309 (mm) REVERT: B 69 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7858 (mtt180) REVERT: B 106 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7183 (pm20) REVERT: B 185 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7215 (mtmt) REVERT: B 349 TYR cc_start: 0.7467 (m-10) cc_final: 0.7170 (m-10) REVERT: B 385 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6547 (p0) REVERT: C 106 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7471 (pm20) REVERT: C 349 TYR cc_start: 0.7634 (m-10) cc_final: 0.7293 (m-10) REVERT: D 106 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: D 349 TYR cc_start: 0.7607 (m-10) cc_final: 0.7264 (m-10) REVERT: E 106 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7254 (pm20) REVERT: E 349 TYR cc_start: 0.7605 (m-10) cc_final: 0.7240 (m-10) REVERT: E 393 GLU cc_start: 0.8314 (tp30) cc_final: 0.8082 (mm-30) REVERT: E 459 ILE cc_start: 0.8513 (mt) cc_final: 0.8273 (mm) REVERT: F 69 ARG cc_start: 0.8221 (mtm-85) cc_final: 0.7855 (mtt180) REVERT: F 106 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7203 (pm20) REVERT: F 185 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7201 (mtmt) REVERT: F 349 TYR cc_start: 0.7505 (m-10) cc_final: 0.7183 (m-10) REVERT: F 385 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6547 (p0) outliers start: 45 outliers final: 24 residues processed: 243 average time/residue: 0.6567 time to fit residues: 183.8356 Evaluate side-chains 224 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 385 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 294 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.0670 chunk 191 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 251 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.131741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.112679 restraints weight = 29782.269| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.61 r_work: 0.3166 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 26538 Z= 0.106 Angle : 0.415 5.590 36078 Z= 0.228 Chirality : 0.038 0.133 3870 Planarity : 0.004 0.038 4494 Dihedral : 13.318 80.877 3960 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.39 % Allowed : 23.00 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.15), residues: 3042 helix: 1.65 (0.12), residues: 1710 sheet: -0.26 (0.37), residues: 246 loop : 0.17 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 54 TYR 0.011 0.001 TYR D 475 PHE 0.009 0.001 PHE F 154 TRP 0.008 0.001 TRP F 187 HIS 0.003 0.001 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (26538) covalent geometry : angle 0.41507 / 0.23 (36078) hydrogen bonds : bond 0.03658 / 2.48 ( 1243) hydrogen bonds : angle 4.35590 / 3.15 ( 3603) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 0.912 Fit side-chains REVERT: A 106 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7271 (pm20) REVERT: A 349 TYR cc_start: 0.7591 (m-10) cc_final: 0.7207 (m-10) REVERT: A 393 GLU cc_start: 0.8313 (tp30) cc_final: 0.8087 (mm-30) REVERT: A 459 ILE cc_start: 0.8547 (mt) cc_final: 0.8298 (mm) REVERT: B 69 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7860 (mtt180) REVERT: B 106 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7179 (pm20) REVERT: B 185 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7211 (mtmt) REVERT: B 349 TYR cc_start: 0.7442 (m-10) cc_final: 0.7146 (m-10) REVERT: B 385 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6625 (p0) REVERT: C 106 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: C 349 TYR cc_start: 0.7633 (m-10) cc_final: 0.7290 (m-10) REVERT: D 106 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7409 (pm20) REVERT: D 349 TYR cc_start: 0.7596 (m-10) cc_final: 0.7256 (m-10) REVERT: E 106 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7254 (pm20) REVERT: E 349 TYR cc_start: 0.7604 (m-10) cc_final: 0.7241 (m-10) REVERT: E 393 GLU cc_start: 0.8328 (tp30) cc_final: 0.8094 (mm-30) REVERT: E 459 ILE cc_start: 0.8521 (mt) cc_final: 0.8283 (mm) REVERT: F 69 ARG cc_start: 0.8227 (mtm-85) cc_final: 0.7863 (mtt180) REVERT: F 106 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7209 (pm20) REVERT: F 185 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7219 (mtmt) REVERT: F 349 TYR cc_start: 0.7457 (m-10) cc_final: 0.7159 (m-10) REVERT: F 385 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6553 (p0) outliers start: 39 outliers final: 28 residues processed: 232 average time/residue: 0.7177 time to fit residues: 191.4829 Evaluate side-chains 228 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 62 CYS Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 62 CYS Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 367 MET Chi-restraints excluded: chain F residue 385 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 201 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 47 optimal weight: 0.0370 chunk 169 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 267 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.132747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113807 restraints weight = 29700.446| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.60 r_work: 0.3164 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 26538 Z= 0.096 Angle : 0.404 5.444 36078 Z= 0.222 Chirality : 0.038 0.129 3870 Planarity : 0.004 0.038 4494 Dihedral : 13.299 80.561 3960 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.29 % Allowed : 23.18 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.15), residues: 3042 helix: 1.70 (0.12), residues: 1710 sheet: -0.23 (0.37), residues: 246 loop : 0.18 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 54 TYR 0.011 0.001 TYR D 475 PHE 0.007 0.001 PHE F 154 TRP 0.009 0.001 TRP F 187 HIS 0.003 0.001 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (26538) covalent geometry : angle 0.40440 / 0.22 (36078) hydrogen bonds : bond 0.03470 / 2.35 ( 1243) hydrogen bonds : angle 4.30829 / 3.11 ( 3603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6765.17 seconds wall clock time: 116 minutes 41.15 seconds (7001.15 seconds total)