Starting phenix.real_space_refine on Sat Aug 8 06:37:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21wo_68056/08_2026/21wo_68056.cif Found real_map, /net/cci-nas-00/data/ceres_data/21wo_68056/08_2026/21wo_68056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21wo_68056/08_2026/21wo_68056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21wo_68056/08_2026/21wo_68056.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21wo_68056/08_2026/21wo_68056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21wo_68056/08_2026/21wo_68056.map" } resolution = 2.96 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= 0.001 sd= 0.015 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 87 residue(s): 0.03s 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: 18 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.86, per 1000 atoms: 0.23 Number of scatterers: 25860 At special positions: 0 Unit cell: (145.848, 137.608, 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: 2.15 Conformation dependent library (CDL) restraints added in 1.0 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: 165 helices and 12 sheets defined 61.4% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 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 Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 127 through 140 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 168 through 179 removed outlier: 3.906A pdb=" N ASN A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.949A pdb=" N LYS A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 231 removed outlier: 3.774A pdb=" N SER A 214 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 266 removed outlier: 4.139A pdb=" N TYR A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.843A pdb=" N SER A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 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 370 Proline residue: A 370 - end of helix Processing helix chain 'A' and resid 371 through 376 removed outlier: 4.210A pdb=" N LEU A 375 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 385 through 401 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 Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.783A pdb=" N ASP A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 127 through 140 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 168 Processing helix chain 'B' and resid 168 through 179 removed outlier: 3.912A pdb=" N ASN B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.932A pdb=" N LYS B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 231 removed outlier: 3.771A pdb=" N SER B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B 231 " --> pdb=" O ARG B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 265 Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.608A pdb=" N SER B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 295 " --> pdb=" O LEU B 291 " (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 removed outlier: 3.540A pdb=" N GLY B 373 " --> pdb=" O PRO B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 401 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 Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.781A pdb=" N ASP B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 96 through 103 removed outlier: 3.919A pdb=" N ARG C 100 " --> pdb=" O GLU C 97 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 140 Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 161 through 168 Processing helix chain 'C' and resid 168 through 179 removed outlier: 3.906A pdb=" N ASN C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 199 removed outlier: 3.942A pdb=" N LYS C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 231 removed outlier: 3.883A pdb=" N SER C 214 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA C 223 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP C 231 " --> pdb=" O ARG C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 266 removed outlier: 3.575A pdb=" N LYS C 265 " --> pdb=" O MET C 261 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.639A pdb=" N SER C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 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 370 Proline residue: C 370 - end of helix Processing helix chain 'C' and resid 371 through 376 removed outlier: 4.205A pdb=" N LEU C 375 " --> pdb=" O TYR C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 385 through 401 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 Processing helix chain 'C' and resid 447 through 462 removed outlier: 3.795A pdb=" N ASP C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'D' and resid 127 through 140 Processing helix chain 'D' and resid 158 through 160 No H-bonds generated for 'chain 'D' and resid 158 through 160' Processing helix chain 'D' and resid 161 through 168 Processing helix chain 'D' and resid 168 through 179 removed outlier: 3.924A pdb=" N ASN D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 199 removed outlier: 3.933A pdb=" N LYS D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.750A pdb=" N SER D 214 " --> pdb=" O PRO D 210 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL D 224 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 265 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.595A pdb=" N SER D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 309 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 removed outlier: 3.525A pdb=" N GLY D 373 " --> pdb=" O PRO D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 401 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 Processing helix chain 'D' and resid 447 through 462 removed outlier: 3.785A pdb=" N ASP D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 96 through 103 removed outlier: 3.935A pdb=" N ARG E 100 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N PHE E 101 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 140 Processing helix chain 'E' and resid 152 through 157 Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 161 through 168 Processing helix chain 'E' and resid 168 through 179 removed outlier: 3.905A pdb=" N ASN E 177 " --> pdb=" O LYS E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 199 removed outlier: 3.943A pdb=" N LYS E 199 " --> pdb=" O GLN E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 231 removed outlier: 3.816A pdb=" N SER E 214 " --> pdb=" O PRO E 210 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA E 223 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 266 removed outlier: 3.575A pdb=" N LYS E 265 " --> pdb=" O MET E 261 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 removed outlier: 3.753A pdb=" N SER E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 309 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 370 Proline residue: E 370 - end of helix Processing helix chain 'E' and resid 371 through 376 removed outlier: 4.201A pdb=" N LEU E 375 " --> pdb=" O TYR E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 379 No H-bonds generated for 'chain 'E' and resid 377 through 379' Processing helix chain 'E' and resid 385 through 401 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 Processing helix chain 'E' and resid 447 through 462 removed outlier: 3.792A pdb=" N ASP E 462 " --> pdb=" O ILE E 458 " (cutoff:3.500A) 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 Processing helix chain 'F' and resid 95 through 100 Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'F' and resid 127 through 140 Processing helix chain 'F' and resid 152 through 157 Processing helix chain 'F' and resid 158 through 160 No H-bonds generated for 'chain 'F' and resid 158 through 160' Processing helix chain 'F' and resid 161 through 168 Processing helix chain 'F' and resid 168 through 179 removed outlier: 3.904A pdb=" N ASN F 177 " --> pdb=" O LYS F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 199 removed outlier: 3.948A pdb=" N LYS F 199 " --> pdb=" O GLN F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 231 removed outlier: 3.773A pdb=" N SER F 214 " --> pdb=" O PRO F 210 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA F 223 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL F 224 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 266 removed outlier: 4.139A pdb=" N TYR F 266 " --> pdb=" O GLU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 294 removed outlier: 3.825A pdb=" N SER F 290 " --> pdb=" O ASP F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 309 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 370 Proline residue: F 370 - end of helix Processing helix chain 'F' and resid 371 through 376 removed outlier: 4.216A pdb=" N LEU F 375 " --> pdb=" O TYR F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 379 No H-bonds generated for 'chain 'F' and resid 377 through 379' Processing helix chain 'F' and resid 385 through 401 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 Processing helix chain 'F' and resid 447 through 462 removed outlier: 3.787A pdb=" N ASP F 462 " --> pdb=" O ILE F 458 " (cutoff:3.500A) 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 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 235 through 237 Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 68 Processing sheet with id=AA4, first strand: chain 'B' and resid 235 through 237 Processing sheet with id=AA5, first strand: chain 'C' and resid 62 through 68 Processing sheet with id=AA6, first strand: chain 'C' and resid 235 through 237 Processing sheet with id=AA7, first strand: chain 'D' and resid 62 through 68 Processing sheet with id=AA8, first strand: chain 'D' and resid 235 through 237 Processing sheet with id=AA9, first strand: chain 'E' and resid 62 through 68 Processing sheet with id=AB1, first strand: chain 'E' and resid 235 through 237 Processing sheet with id=AB2, first strand: chain 'F' and resid 62 through 68 Processing sheet with id=AB3, first strand: chain 'F' and resid 235 through 237 1273 hydrogen bonds defined for protein. 3711 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: 4.80 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8279 1.34 - 1.46: 6636 1.46 - 1.58: 11359 1.58 - 1.70: 78 1.70 - 1.82: 186 Bond restraints: 26538 Sorted by residual: bond pdb=" C3' DA L 8 " pdb=" C2' DA L 8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.53e+00 bond pdb=" C3' DA G 8 " pdb=" C2' DA G 8 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.35e+00 bond pdb=" C3' DA K 8 " pdb=" C2' DA K 8 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.10e+00 bond pdb=" C3' DA H 8 " pdb=" C2' DA H 8 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.71e+00 bond pdb=" C3' DA I 8 " pdb=" C2' DA I 8 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.42e+00 ... (remaining 26533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 35837 2.24 - 4.47: 217 4.47 - 6.71: 16 6.71 - 8.94: 4 8.94 - 11.18: 4 Bond angle restraints: 36078 Sorted by residual: angle pdb=" N ILE C 446 " pdb=" CA ILE C 446 " pdb=" C ILE C 446 " ideal model delta sigma weight residual 113.20 109.54 3.66 9.60e-01 1.09e+00 1.46e+01 angle pdb=" N ILE D 446 " pdb=" CA ILE D 446 " pdb=" C ILE D 446 " ideal model delta sigma weight residual 113.20 109.55 3.65 9.60e-01 1.09e+00 1.44e+01 angle pdb=" CB MET D 109 " pdb=" CG MET D 109 " pdb=" SD MET D 109 " ideal model delta sigma weight residual 112.70 123.88 -11.18 3.00e+00 1.11e-01 1.39e+01 angle pdb=" O4' DA L 6 " pdb=" C4' DA L 6 " pdb=" C3' DA L 6 " ideal model delta sigma weight residual 106.00 103.88 2.12 6.00e-01 2.78e+00 1.24e+01 angle pdb=" O4' DA H 6 " pdb=" C4' DA H 6 " pdb=" C3' DA H 6 " ideal model delta sigma weight residual 106.00 103.90 2.10 6.00e-01 2.78e+00 1.22e+01 ... (remaining 36073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 13328 17.89 - 35.78: 1861 35.78 - 53.67: 583 53.67 - 71.56: 142 71.56 - 89.45: 34 Dihedral angle restraints: 15948 sinusoidal: 6864 harmonic: 9084 Sorted by residual: dihedral pdb=" CB MET C 495 " pdb=" CG MET C 495 " pdb=" SD MET C 495 " pdb=" CE MET C 495 " ideal model delta sinusoidal sigma weight residual -60.00 -0.24 -59.76 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ASN F 287 " pdb=" CA ASN F 287 " pdb=" CB ASN F 287 " pdb=" CG ASN F 287 " ideal model delta sinusoidal sigma weight residual -180.00 -120.54 -59.46 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ILE C 334 " pdb=" CB ILE C 334 " pdb=" CG1 ILE C 334 " pdb=" CD1 ILE C 334 " ideal model delta sinusoidal sigma weight residual 60.00 118.07 -58.07 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 15945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3087 0.046 - 0.091: 647 0.091 - 0.137: 133 0.137 - 0.182: 1 0.182 - 0.228: 2 Chirality restraints: 3870 Sorted by residual: chirality pdb=" CB VAL A 206 " pdb=" CA VAL A 206 " pdb=" CG1 VAL A 206 " pdb=" CG2 VAL A 206 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA VAL A 206 " pdb=" N VAL A 206 " pdb=" C VAL A 206 " pdb=" CB VAL A 206 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA VAL F 206 " pdb=" N VAL F 206 " pdb=" C VAL F 206 " pdb=" CB VAL F 206 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 3867 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 206 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO F 207 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 207 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 207 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 20 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO C 21 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 21 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 21 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 20 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO E 21 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 21 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 21 " -0.023 5.00e-02 4.00e+02 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 14 2.48 - 3.09: 18014 3.09 - 3.69: 39689 3.69 - 4.30: 60933 4.30 - 4.90: 101384 Nonbonded interactions: 220034 Sorted by model distance: nonbonded pdb=" OE1 GLU B 64 " pdb=" OH TYR B 66 " model vdw 1.881 3.040 nonbonded pdb=" O SER C 52 " pdb=" OD1 ASP C 489 " model vdw 1.924 3.040 nonbonded pdb=" O2B DTP D 601 " pdb="MG MG D 602 " model vdw 2.072 2.170 nonbonded pdb=" CA GLY C 53 " pdb=" OD1 ASP C 489 " model vdw 2.095 3.440 nonbonded pdb=" O2B DTP B 601 " pdb="MG MG B 602 " model vdw 2.098 2.170 ... (remaining 220029 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: 0.02 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: 3.760 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.460 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 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 0.031 26538 Z= 0.163 Angle : 0.484 11.180 36078 Z= 0.279 Chirality : 0.038 0.228 3870 Planarity : 0.004 0.045 4494 Dihedral : 18.728 89.450 10104 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.93 % Allowed : 25.14 % Favored : 73.93 % 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: 1.01 (0.15), residues: 3042 helix: 1.62 (0.13), residues: 1608 sheet: -0.49 (0.35), residues: 246 loop : -0.32 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 75 TYR 0.017 0.001 TYR F 475 PHE 0.005 0.001 PHE A 432 TRP 0.008 0.001 TRP B 187 HIS 0.003 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 (26538) covalent geometry : angle 0.48363 / 0.28 (36078) hydrogen bonds : bond 0.14931 / 9.91 ( 1273) hydrogen bonds : angle 6.24287 / 4.49 ( 3711) *********************** 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 210 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 324 GLN cc_start: 0.8624 (mt0) cc_final: 0.8391 (mt0) REVERT: B 37 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7157 (ptt180) REVERT: B 287 ASN cc_start: 0.8530 (m-40) cc_final: 0.8210 (m-40) REVERT: C 382 ASP cc_start: 0.9250 (t0) cc_final: 0.9023 (t0) REVERT: E 382 ASP cc_start: 0.9229 (t0) cc_final: 0.8999 (t0) REVERT: F 270 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8851 (pp) REVERT: F 382 ASP cc_start: 0.9203 (t0) cc_final: 0.8833 (p0) outliers start: 26 outliers final: 13 residues processed: 207 average time/residue: 0.7681 time to fit residues: 181.2160 Evaluate side-chains 172 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 489 ASP Chi-restraints excluded: chain E residue 489 ASP Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 328 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.094656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.075327 restraints weight = 52571.720| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.97 r_work: 0.2914 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26538 Z= 0.116 Angle : 0.457 7.382 36078 Z= 0.249 Chirality : 0.037 0.133 3870 Planarity : 0.004 0.045 4494 Dihedral : 12.680 88.322 3980 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.86 % Allowed : 23.35 % Favored : 73.78 % 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: 1.27 (0.15), residues: 3042 helix: 1.89 (0.13), residues: 1632 sheet: -0.15 (0.37), residues: 246 loop : -0.42 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 75 TYR 0.017 0.001 TYR A 475 PHE 0.009 0.001 PHE B 432 TRP 0.007 0.001 TRP B 187 HIS 0.003 0.001 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (26538) covalent geometry : angle 0.45721 / 0.25 (36078) hydrogen bonds : bond 0.04522 / 3.00 ( 1273) hydrogen bonds : angle 4.90240 / 3.50 ( 3711) *********************** 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 256 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 176 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 149 ASP cc_start: 0.8109 (p0) cc_final: 0.7124 (p0) REVERT: B 64 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8941 (mp0) REVERT: B 393 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8500 (tm-30) REVERT: C 64 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8833 (mp0) REVERT: C 254 GLU cc_start: 0.9035 (tp30) cc_final: 0.8726 (tp30) REVERT: C 287 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8319 (t0) REVERT: C 382 ASP cc_start: 0.9476 (t0) cc_final: 0.9180 (t0) REVERT: E 64 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8860 (mp0) REVERT: E 240 ASP cc_start: 0.9069 (OUTLIER) cc_final: 0.8844 (p0) REVERT: E 254 GLU cc_start: 0.9036 (tp30) cc_final: 0.8726 (tp30) REVERT: E 382 ASP cc_start: 0.9474 (t0) cc_final: 0.9159 (t0) REVERT: F 149 ASP cc_start: 0.8116 (p0) cc_final: 0.7126 (p0) REVERT: F 270 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8649 (pp) REVERT: F 382 ASP cc_start: 0.9460 (t0) cc_final: 0.8800 (p0) outliers start: 80 outliers final: 14 residues processed: 243 average time/residue: 0.7496 time to fit residues: 208.5475 Evaluate side-chains 188 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 489 ASP Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 407 MET Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 272 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 204 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 180 optimal weight: 0.0070 chunk 235 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 HIS ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.094370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.075070 restraints weight = 52587.671| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.97 r_work: 0.2902 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26538 Z= 0.140 Angle : 0.460 7.461 36078 Z= 0.248 Chirality : 0.038 0.134 3870 Planarity : 0.004 0.037 4494 Dihedral : 12.643 85.249 3958 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.86 % Allowed : 22.96 % Favored : 74.18 % 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: 1.33 (0.15), residues: 3042 helix: 1.97 (0.13), residues: 1644 sheet: -0.16 (0.36), residues: 246 loop : -0.45 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 75 TYR 0.016 0.001 TYR E 475 PHE 0.006 0.001 PHE C 318 TRP 0.006 0.001 TRP B 187 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (26538) covalent geometry : angle 0.46038 / 0.25 (36078) hydrogen bonds : bond 0.04213 / 2.80 ( 1273) hydrogen bonds : angle 4.57916 / 3.27 ( 3711) *********************** 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 250 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 170 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 149 ASP cc_start: 0.8012 (p0) cc_final: 0.7081 (p0) REVERT: B 64 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8942 (mp0) REVERT: B 393 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8487 (tm-30) REVERT: C 64 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8883 (mp0) REVERT: C 254 GLU cc_start: 0.9021 (tp30) cc_final: 0.8716 (tp30) REVERT: C 287 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8351 (t0) REVERT: C 382 ASP cc_start: 0.9478 (t0) cc_final: 0.9191 (t0) REVERT: D 37 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.6726 (ptt180) REVERT: E 64 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.8930 (mp0) REVERT: E 240 ASP cc_start: 0.9122 (OUTLIER) cc_final: 0.8900 (p0) REVERT: E 254 GLU cc_start: 0.9025 (tp30) cc_final: 0.8723 (tp30) REVERT: E 382 ASP cc_start: 0.9468 (t0) cc_final: 0.9155 (t0) REVERT: F 149 ASP cc_start: 0.8010 (p0) cc_final: 0.7038 (p0) REVERT: F 270 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8644 (pp) REVERT: F 382 ASP cc_start: 0.9460 (t0) cc_final: 0.8784 (p0) outliers start: 80 outliers final: 27 residues processed: 237 average time/residue: 0.7206 time to fit residues: 196.4956 Evaluate side-chains 196 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 489 ASP Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 489 ASP Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 407 MET Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain E residue 489 ASP Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 446 ILE 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: 5.9990 chunk 194 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 196 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN B 23 GLN C 23 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 HIS F 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.092343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.073048 restraints weight = 52647.108| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.96 r_work: 0.2862 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26538 Z= 0.217 Angle : 0.495 7.410 36078 Z= 0.265 Chirality : 0.040 0.150 3870 Planarity : 0.004 0.036 4494 Dihedral : 12.753 87.515 3958 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.93 % Allowed : 22.71 % Favored : 74.36 % 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: 1.31 (0.15), residues: 3042 helix: 2.01 (0.13), residues: 1656 sheet: -0.23 (0.36), residues: 246 loop : -0.57 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 75 TYR 0.017 0.001 TYR B 475 PHE 0.006 0.001 PHE A 73 TRP 0.005 0.001 TRP B 471 HIS 0.003 0.001 HIS F 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (26538) covalent geometry : angle 0.49506 / 0.26 (36078) hydrogen bonds : bond 0.04438 / 2.94 ( 1273) hydrogen bonds : angle 4.47487 / 3.20 ( 3711) *********************** 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 246 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 164 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 149 ASP cc_start: 0.8097 (p0) cc_final: 0.7171 (p0) REVERT: B 37 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.6933 (ptt180) REVERT: B 64 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8924 (mp0) REVERT: B 393 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8476 (tm-30) REVERT: C 64 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8878 (mp0) REVERT: C 254 GLU cc_start: 0.9007 (tp30) cc_final: 0.8721 (tp30) REVERT: C 382 ASP cc_start: 0.9471 (t0) cc_final: 0.9181 (t0) REVERT: D 37 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.6903 (ptt180) REVERT: D 135 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7584 (mt-10) REVERT: E 64 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.8906 (mp0) REVERT: E 254 GLU cc_start: 0.9020 (tp30) cc_final: 0.8740 (tp30) REVERT: E 382 ASP cc_start: 0.9471 (t0) cc_final: 0.9171 (t0) REVERT: F 149 ASP cc_start: 0.8095 (p0) cc_final: 0.7163 (p0) REVERT: F 270 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8719 (pp) REVERT: F 382 ASP cc_start: 0.9456 (t0) cc_final: 0.8787 (p0) outliers start: 82 outliers final: 43 residues processed: 233 average time/residue: 0.7176 time to fit residues: 192.2948 Evaluate side-chains 206 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 156 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 489 ASP Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 489 ASP Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 407 MET Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain E residue 489 ASP Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 446 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 101 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 165 optimal weight: 0.0170 chunk 208 optimal weight: 3.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN B 364 HIS C 23 GLN C 324 GLN D 23 GLN D 364 HIS E 324 GLN F 58 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.093502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.074271 restraints weight = 52293.452| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.97 r_work: 0.2887 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26538 Z= 0.130 Angle : 0.449 6.882 36078 Z= 0.242 Chirality : 0.038 0.132 3870 Planarity : 0.003 0.036 4494 Dihedral : 12.751 88.016 3958 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.40 % Allowed : 23.18 % Favored : 74.43 % 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: 2.05 (0.13), residues: 1662 sheet: -0.25 (0.36), residues: 246 loop : -0.48 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 75 TYR 0.015 0.001 TYR E 475 PHE 0.005 0.001 PHE C 318 TRP 0.006 0.001 TRP B 187 HIS 0.003 0.000 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (26538) covalent geometry : angle 0.44865 / 0.24 (36078) hydrogen bonds : bond 0.03946 / 2.61 ( 1273) hydrogen bonds : angle 4.32186 / 3.09 ( 3711) *********************** 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 237 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 170 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: B 37 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.6892 (ptt180) REVERT: B 64 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8902 (mp0) REVERT: B 393 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8675 (tm-30) REVERT: C 64 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.8849 (mp0) REVERT: C 135 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7524 (mt-10) REVERT: C 254 GLU cc_start: 0.9002 (tp30) cc_final: 0.8710 (tp30) REVERT: C 382 ASP cc_start: 0.9465 (t0) cc_final: 0.9170 (t0) REVERT: D 37 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.6861 (ptt180) REVERT: D 135 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7634 (mt-10) REVERT: D 254 GLU cc_start: 0.8994 (tp30) cc_final: 0.8674 (tp30) REVERT: E 64 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8879 (mp0) REVERT: E 254 GLU cc_start: 0.9017 (tp30) cc_final: 0.8729 (tp30) REVERT: E 382 ASP cc_start: 0.9459 (t0) cc_final: 0.9139 (t0) REVERT: F 270 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8714 (pp) REVERT: F 382 ASP cc_start: 0.9450 (t0) cc_final: 0.8793 (p0) outliers start: 67 outliers final: 38 residues processed: 229 average time/residue: 0.6776 time to fit residues: 177.8754 Evaluate side-chains 206 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 489 ASP Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 407 MET Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 311 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 153 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 286 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 278 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 287 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN C 23 GLN E 23 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.091660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.072414 restraints weight = 52996.133| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.95 r_work: 0.2848 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 26538 Z= 0.246 Angle : 0.512 7.095 36078 Z= 0.272 Chirality : 0.041 0.127 3870 Planarity : 0.004 0.036 4494 Dihedral : 12.839 89.841 3958 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.93 % Allowed : 22.96 % Favored : 74.11 % 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: 1.33 (0.15), residues: 3042 helix: 2.05 (0.13), residues: 1656 sheet: -0.27 (0.36), residues: 246 loop : -0.61 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 75 TYR 0.017 0.001 TYR B 475 PHE 0.006 0.001 PHE A 140 TRP 0.006 0.001 TRP C 288 HIS 0.003 0.001 HIS F 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.25 (26538) covalent geometry : angle 0.51236 / 0.27 (36078) hydrogen bonds : bond 0.04403 / 2.92 ( 1273) hydrogen bonds : angle 4.36714 / 3.12 ( 3711) *********************** 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 240 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 158 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: A 149 ASP cc_start: 0.8358 (p0) cc_final: 0.7258 (p0) REVERT: B 37 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.6938 (ptt180) REVERT: B 64 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8927 (mp0) REVERT: B 314 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8468 (mp0) REVERT: B 393 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8631 (tm-30) REVERT: C 64 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.8862 (mp0) REVERT: C 135 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7595 (mt-10) REVERT: C 254 GLU cc_start: 0.9011 (tp30) cc_final: 0.8725 (tp30) REVERT: C 382 ASP cc_start: 0.9471 (t0) cc_final: 0.9186 (t0) REVERT: D 37 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.6908 (ptt180) REVERT: E 64 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8879 (mp0) REVERT: E 254 GLU cc_start: 0.9029 (tp30) cc_final: 0.8749 (tp30) REVERT: E 382 ASP cc_start: 0.9470 (t0) cc_final: 0.9157 (t0) REVERT: F 270 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8755 (pp) outliers start: 82 outliers final: 46 residues processed: 229 average time/residue: 0.6882 time to fit residues: 181.8172 Evaluate side-chains 209 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 156 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 489 ASP Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 489 ASP Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 407 MET Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain E residue 489 ASP Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 446 ILE Chi-restraints excluded: chain F residue 491 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 214 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 271 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 227 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 231 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 chunk 251 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN A 378 HIS C 23 GLN C 324 GLN E 23 GLN F 58 GLN F 378 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.093587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.074357 restraints weight = 52294.687| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.97 r_work: 0.2895 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26538 Z= 0.113 Angle : 0.454 8.268 36078 Z= 0.243 Chirality : 0.038 0.136 3870 Planarity : 0.003 0.036 4494 Dihedral : 12.804 89.933 3958 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.61 % Allowed : 23.64 % Favored : 73.75 % 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: 1.41 (0.15), residues: 3042 helix: 2.07 (0.13), residues: 1668 sheet: -0.26 (0.36), residues: 246 loop : -0.50 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 75 TYR 0.015 0.001 TYR E 475 PHE 0.008 0.001 PHE E 432 TRP 0.007 0.001 TRP B 187 HIS 0.004 0.000 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (26538) covalent geometry : angle 0.45400 / 0.24 (36078) hydrogen bonds : bond 0.03840 / 2.54 ( 1273) hydrogen bonds : angle 4.24000 / 3.03 ( 3711) *********************** 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 239 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 166 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: B 37 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.6833 (ptt180) REVERT: B 64 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8907 (mp0) REVERT: B 314 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8483 (mp0) REVERT: B 393 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8704 (tm-30) REVERT: C 64 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.8839 (mp0) REVERT: C 135 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7447 (mt-10) REVERT: C 254 GLU cc_start: 0.9011 (tp30) cc_final: 0.8717 (tp30) REVERT: C 382 ASP cc_start: 0.9467 (t0) cc_final: 0.9164 (t0) REVERT: C 393 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8694 (mm-30) REVERT: D 37 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.6816 (ptt180) REVERT: D 254 GLU cc_start: 0.8982 (tp30) cc_final: 0.8654 (tp30) REVERT: E 64 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8902 (mp0) REVERT: E 254 GLU cc_start: 0.9019 (tp30) cc_final: 0.8729 (tp30) REVERT: E 382 ASP cc_start: 0.9473 (t0) cc_final: 0.9153 (t0) REVERT: E 393 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8703 (mm-30) REVERT: F 149 ASP cc_start: 0.8266 (p0) cc_final: 0.7174 (p0) REVERT: F 270 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8657 (pp) REVERT: F 382 ASP cc_start: 0.9452 (t0) cc_final: 0.8784 (p0) outliers start: 73 outliers final: 39 residues processed: 227 average time/residue: 0.6316 time to fit residues: 164.2034 Evaluate side-chains 204 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 489 ASP Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 407 MET Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 491 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 32 optimal weight: 6.9990 chunk 233 optimal weight: 0.7980 chunk 284 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 209 optimal weight: 0.3980 chunk 211 optimal weight: 3.9990 chunk 67 optimal weight: 0.0980 chunk 184 optimal weight: 5.9990 chunk 299 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN C 23 GLN E 23 GLN E 324 GLN F 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.094051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.074863 restraints weight = 52317.922| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.97 r_work: 0.2899 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26538 Z= 0.107 Angle : 0.459 8.623 36078 Z= 0.243 Chirality : 0.038 0.139 3870 Planarity : 0.003 0.037 4494 Dihedral : 12.773 89.587 3958 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.43 % Allowed : 23.86 % Favored : 73.71 % 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: 2.09 (0.13), residues: 1668 sheet: -0.19 (0.36), residues: 246 loop : -0.46 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 75 TYR 0.015 0.001 TYR E 475 PHE 0.006 0.001 PHE C 318 TRP 0.008 0.001 TRP E 187 HIS 0.004 0.000 HIS F 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (26538) covalent geometry : angle 0.45917 / 0.24 (36078) hydrogen bonds : bond 0.03667 / 2.43 ( 1273) hydrogen bonds : angle 4.16541 / 2.97 ( 3711) *********************** 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 236 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 168 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 382 ASP cc_start: 0.9399 (t0) cc_final: 0.8797 (p0) REVERT: B 37 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.6855 (ptt180) REVERT: B 64 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8904 (mp0) REVERT: B 314 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8528 (mp0) REVERT: B 393 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8717 (tm-30) REVERT: C 64 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8816 (mp0) REVERT: C 135 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7512 (mt-10) REVERT: C 254 GLU cc_start: 0.9025 (tp30) cc_final: 0.8728 (tp30) REVERT: C 382 ASP cc_start: 0.9458 (t0) cc_final: 0.9157 (t0) REVERT: C 393 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8697 (mm-30) REVERT: D 37 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.6884 (ptt180) REVERT: D 254 GLU cc_start: 0.8993 (tp30) cc_final: 0.8680 (tp30) REVERT: D 314 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8498 (mp0) REVERT: E 64 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8868 (mp0) REVERT: E 254 GLU cc_start: 0.9030 (tp30) cc_final: 0.8735 (tp30) REVERT: E 382 ASP cc_start: 0.9456 (t0) cc_final: 0.9135 (t0) REVERT: E 393 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8720 (mm-30) REVERT: F 270 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8716 (pp) REVERT: F 382 ASP cc_start: 0.9446 (t0) cc_final: 0.8785 (p0) outliers start: 68 outliers final: 38 residues processed: 227 average time/residue: 0.6621 time to fit residues: 172.6586 Evaluate side-chains 210 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 446 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 293 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 249 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 218 optimal weight: 0.1980 chunk 147 optimal weight: 3.9990 chunk 288 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN C 23 GLN ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN E 324 GLN F 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.094027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.074864 restraints weight = 52233.915| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.97 r_work: 0.2907 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26538 Z= 0.118 Angle : 0.470 9.079 36078 Z= 0.248 Chirality : 0.038 0.131 3870 Planarity : 0.003 0.036 4494 Dihedral : 12.765 89.606 3954 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.22 % Allowed : 24.11 % Favored : 73.68 % 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: 1.47 (0.15), residues: 3042 helix: 2.10 (0.13), residues: 1668 sheet: -0.18 (0.36), residues: 246 loop : -0.45 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 75 TYR 0.018 0.001 TYR C 11 PHE 0.005 0.001 PHE A 318 TRP 0.008 0.001 TRP D 187 HIS 0.003 0.000 HIS F 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (26538) covalent geometry : angle 0.47017 / 0.25 (36078) hydrogen bonds : bond 0.03666 / 2.43 ( 1273) hydrogen bonds : angle 4.14978 / 2.96 ( 3711) *********************** 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 229 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 167 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 ASP cc_start: 0.9402 (t0) cc_final: 0.8791 (p0) REVERT: B 37 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.6808 (ptt180) REVERT: B 64 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8921 (mp0) REVERT: B 314 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8505 (mp0) REVERT: B 393 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8709 (tm-30) REVERT: C 64 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8852 (mp0) REVERT: C 135 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7477 (mt-10) REVERT: C 254 GLU cc_start: 0.9013 (tp30) cc_final: 0.8709 (tp30) REVERT: C 382 ASP cc_start: 0.9462 (t0) cc_final: 0.9162 (t0) REVERT: C 393 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8675 (mm-30) REVERT: D 37 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.6835 (ptt180) REVERT: D 254 GLU cc_start: 0.8997 (tp30) cc_final: 0.8674 (tp30) REVERT: E 64 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8860 (mp0) REVERT: E 254 GLU cc_start: 0.9027 (tp30) cc_final: 0.8725 (tp30) REVERT: E 382 ASP cc_start: 0.9447 (t0) cc_final: 0.9126 (t0) REVERT: E 393 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8700 (mm-30) REVERT: F 270 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8649 (pp) REVERT: F 382 ASP cc_start: 0.9452 (t0) cc_final: 0.8772 (p0) outliers start: 62 outliers final: 44 residues processed: 220 average time/residue: 0.6993 time to fit residues: 176.2460 Evaluate side-chains 212 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 161 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 449 GLU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain E residue 489 ASP Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 446 ILE Chi-restraints excluded: chain F residue 491 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 294 optimal weight: 0.7980 chunk 289 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 191 optimal weight: 0.1980 chunk 129 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 251 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN C 23 GLN D 23 GLN E 23 GLN F 58 GLN ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.095572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.076478 restraints weight = 51979.828| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.97 r_work: 0.2925 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26538 Z= 0.095 Angle : 0.461 10.336 36078 Z= 0.242 Chirality : 0.037 0.133 3870 Planarity : 0.003 0.036 4494 Dihedral : 12.710 88.845 3954 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.93 % Allowed : 24.50 % Favored : 73.57 % 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: 1.50 (0.15), residues: 3042 helix: 2.11 (0.12), residues: 1668 sheet: -0.14 (0.36), residues: 246 loop : -0.41 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 75 TYR 0.014 0.001 TYR C 349 PHE 0.005 0.001 PHE E 101 TRP 0.010 0.001 TRP A 187 HIS 0.004 0.000 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (26538) covalent geometry : angle 0.46133 / 0.24 (36078) hydrogen bonds : bond 0.03406 / 2.25 ( 1273) hydrogen bonds : angle 4.07464 / 2.90 ( 3711) ********************** 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 226 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 ASP cc_start: 0.9399 (t0) cc_final: 0.8778 (p0) REVERT: B 37 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.6838 (ptt180) REVERT: B 64 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8892 (mp0) REVERT: B 254 GLU cc_start: 0.8988 (tp30) cc_final: 0.8666 (tp30) REVERT: B 393 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8690 (tm-30) REVERT: C 64 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8861 (mp0) REVERT: C 135 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7495 (mt-10) REVERT: C 254 GLU cc_start: 0.9030 (tp30) cc_final: 0.8729 (tp30) REVERT: C 382 ASP cc_start: 0.9455 (t0) cc_final: 0.9155 (t0) REVERT: C 393 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8678 (mm-30) REVERT: D 37 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.6812 (ptt180) REVERT: D 254 GLU cc_start: 0.8987 (tp30) cc_final: 0.8668 (tp30) REVERT: D 393 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8757 (mm-30) REVERT: E 64 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8865 (mp0) REVERT: E 254 GLU cc_start: 0.9035 (tp30) cc_final: 0.8737 (tp30) REVERT: E 393 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8682 (mm-30) REVERT: F 261 MET cc_start: 0.8054 (mtp) cc_final: 0.7518 (mtt) REVERT: F 270 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8683 (pp) REVERT: F 382 ASP cc_start: 0.9444 (t0) cc_final: 0.8782 (p0) outliers start: 54 outliers final: 39 residues processed: 220 average time/residue: 0.6895 time to fit residues: 173.7921 Evaluate side-chains 218 residues out of total 2796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 491 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 201 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 169 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 233 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 267 optimal weight: 0.1980 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 0.0470 overall best weight: 0.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN C 23 GLN ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.095634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.076563 restraints weight = 51944.648| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.97 r_work: 0.2938 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26538 Z= 0.098 Angle : 0.472 11.366 36078 Z= 0.246 Chirality : 0.037 0.148 3870 Planarity : 0.003 0.036 4494 Dihedral : 12.690 88.631 3954 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.86 % Allowed : 24.57 % Favored : 73.57 % 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: 1.54 (0.15), residues: 3042 helix: 2.14 (0.12), residues: 1668 sheet: -0.11 (0.36), residues: 246 loop : -0.40 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 75 TYR 0.020 0.001 TYR C 11 PHE 0.005 0.001 PHE A 318 TRP 0.009 0.001 TRP D 187 HIS 0.003 0.000 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (26538) covalent geometry : angle 0.47173 / 0.25 (36078) hydrogen bonds : bond 0.03414 / 2.27 ( 1273) hydrogen bonds : angle 4.05077 / 2.89 ( 3711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5732.37 seconds wall clock time: 99 minutes 26.62 seconds (5966.62 seconds total)