Starting phenix.real_space_refine on Wed Mar 4 09:39:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hc5_34652/03_2026/8hc5_34652.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hc5_34652/03_2026/8hc5_34652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hc5_34652/03_2026/8hc5_34652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hc5_34652/03_2026/8hc5_34652.map" model { file = "/net/cci-nas-00/data/ceres_data/8hc5_34652/03_2026/8hc5_34652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hc5_34652/03_2026/8hc5_34652.cif" } resolution = 3.43 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= 0.002 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1488 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 7218 2.51 5 N 1906 2.21 5 O 2231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11400 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4948 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain breaks: 2 Chain: "H" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1588 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Chain breaks: 1 Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 203} Chain: "D" Number of atoms: 1665 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1690 Chain: "E" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.86, per 1000 atoms: 0.25 Number of scatterers: 11400 At special positions: 0 Unit cell: (99.552, 171.288, 161.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 2231 8.00 N 1906 7.00 C 7218 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 143 " - pdb=" SG CYS H 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 219 " - pdb=" SG CYS L 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 151 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 701 " - " ASN C 343 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 501.6 milliseconds 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2748 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 34 sheets defined 4.8% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.986A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.928A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.596A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 409 through 411 No H-bonds generated for 'chain 'C' and resid 409 through 411' Processing helix chain 'H' and resid 86 through 90 removed outlier: 4.049A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 161 No H-bonds generated for 'chain 'H' and resid 159 through 161' Processing helix chain 'H' and resid 188 through 192 removed outlier: 3.524A pdb=" N SER H 191 " --> pdb=" O PRO H 188 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU H 192 " --> pdb=" O SER H 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 188 through 192' Processing helix chain 'L' and resid 122 through 127 removed outlier: 3.612A pdb=" N LYS L 127 " --> pdb=" O GLU L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 188 removed outlier: 3.566A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 188' Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.962A pdb=" N GLU E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 removed outlier: 3.872A pdb=" N GLN E 131 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN E 133 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.142A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR C 279 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 63 through 67 removed outlier: 3.509A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.504A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.490A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.555A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.504A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 312 through 313 removed outlier: 3.710A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.708A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA C 435 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.737A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.087A pdb=" N ARG C 466 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY D 104 " --> pdb=" O ARG C 466 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE C 468 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 102 " --> pdb=" O ILE C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.750A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 664 through 667 removed outlier: 3.670A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 672 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.189A pdb=" N TYR H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.129A pdb=" N ARG H 97 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 123 through 127 removed outlier: 4.202A pdb=" N GLY H 142 " --> pdb=" O LEU H 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER H 183 " --> pdb=" O CYS H 143 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP H 147 " --> pdb=" O TYR H 179 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR H 179 " --> pdb=" O ASP H 147 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL H 184 " --> pdb=" O HIS H 167 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 123 through 127 removed outlier: 4.202A pdb=" N GLY H 142 " --> pdb=" O LEU H 127 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER H 183 " --> pdb=" O CYS H 143 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP H 147 " --> pdb=" O TYR H 179 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR H 179 " --> pdb=" O ASP H 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 154 through 157 removed outlier: 3.559A pdb=" N THR H 154 " --> pdb=" O ASN H 202 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN H 202 " --> pdb=" O THR H 154 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS H 199 " --> pdb=" O LYS H 212 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS H 212 " --> pdb=" O CYS H 199 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL H 201 " --> pdb=" O VAL H 210 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL H 210 " --> pdb=" O VAL H 201 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.650A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.822A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.677A pdb=" N GLN L 90 " --> pdb=" O THR L 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 112 through 119 removed outlier: 7.156A pdb=" N ALA L 113 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE L 140 " --> pdb=" O ALA L 113 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN L 138 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL L 133 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU L 180 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N CYS L 135 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER L 178 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 154 through 155 removed outlier: 3.792A pdb=" N TYR L 193 " --> pdb=" O PHE L 210 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE L 210 " --> pdb=" O TYR L 193 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS L 195 " --> pdb=" O LYS L 208 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL L 197 " --> pdb=" O VAL L 206 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL L 206 " --> pdb=" O VAL L 197 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.034A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.670A pdb=" N ASN D 100 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE D 111 " --> pdb=" O ASN D 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 68 through 69 Processing sheet with id=AD1, first strand: chain 'D' and resid 131 through 135 removed outlier: 3.675A pdb=" N LYS D 154 " --> pdb=" O SER D 131 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE D 133 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU D 152 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY D 150 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 149 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 163 through 165 removed outlier: 3.690A pdb=" N SER D 164 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN D 208 " --> pdb=" O SER D 164 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR D 205 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS D 207 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS D 220 " --> pdb=" O CYS D 207 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL D 209 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL D 218 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR D 216 " --> pdb=" O HIS D 211 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.941A pdb=" N THR E 109 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR E 88 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP E 37 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.941A pdb=" N THR E 109 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR E 88 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 17 through 22 removed outlier: 4.166A pdb=" N VAL E 18 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE E 77 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE E 20 " --> pdb=" O LEU E 75 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 119 through 123 removed outlier: 3.586A pdb=" N SER E 181 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE E 141 " --> pdb=" O ALA E 179 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA E 179 " --> pdb=" O ILE E 141 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP E 143 " --> pdb=" O TYR E 177 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N TYR E 177 " --> pdb=" O ASP E 143 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 150 through 154 removed outlier: 4.277A pdb=" N THR E 150 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR E 201 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS E 154 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER E 197 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR E 196 " --> pdb=" O VAL E 211 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS E 198 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS E 209 " --> pdb=" O CYS E 198 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL E 200 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL E 207 " --> pdb=" O VAL E 200 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 768 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: 1.70 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3657 1.35 - 1.46: 2889 1.46 - 1.58: 5078 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 11678 Sorted by residual: bond pdb=" C1 NAG C 701 " pdb=" O5 NAG C 701 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" CB GLU D 89 " pdb=" CG GLU D 89 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CA PHE D 157 " pdb=" C PHE D 157 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.68e+00 bond pdb=" C5 NAG C 701 " pdb=" O5 NAG C 701 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.40e+00 bond pdb=" CA LYS H 213 " pdb=" C LYS H 213 " ideal model delta sigma weight residual 1.526 1.509 0.017 1.42e-02 4.96e+03 1.38e+00 ... (remaining 11673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 15694 2.06 - 4.11: 192 4.11 - 6.17: 11 6.17 - 8.23: 7 8.23 - 10.28: 1 Bond angle restraints: 15905 Sorted by residual: angle pdb=" CA GLU D 89 " pdb=" CB GLU D 89 " pdb=" CG GLU D 89 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA GLU D 159 " pdb=" C GLU D 159 " pdb=" N PRO D 160 " ideal model delta sigma weight residual 120.79 117.78 3.01 9.70e-01 1.06e+00 9.65e+00 angle pdb=" CA LEU H 181 " pdb=" CB LEU H 181 " pdb=" CG LEU H 181 " ideal model delta sigma weight residual 116.30 126.58 -10.28 3.50e+00 8.16e-02 8.63e+00 angle pdb=" N LYS H 204 " pdb=" CA LYS H 204 " pdb=" C LYS H 204 " ideal model delta sigma weight residual 109.81 116.20 -6.39 2.21e+00 2.05e-01 8.35e+00 angle pdb=" CB GLU D 89 " pdb=" CG GLU D 89 " pdb=" CD GLU D 89 " ideal model delta sigma weight residual 112.60 117.50 -4.90 1.70e+00 3.46e-01 8.31e+00 ... (remaining 15900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 6093 17.58 - 35.17: 656 35.17 - 52.75: 177 52.75 - 70.33: 21 70.33 - 87.91: 14 Dihedral angle restraints: 6961 sinusoidal: 2652 harmonic: 4309 Sorted by residual: dihedral pdb=" CB CYS H 143 " pdb=" SG CYS H 143 " pdb=" SG CYS H 199 " pdb=" CB CYS H 199 " ideal model delta sinusoidal sigma weight residual 93.00 165.28 -72.28 1 1.00e+01 1.00e-02 6.68e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 145.44 -52.44 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 63.78 29.22 1 1.00e+01 1.00e-02 1.22e+01 ... (remaining 6958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1360 0.043 - 0.086: 278 0.086 - 0.130: 147 0.130 - 0.173: 4 0.173 - 0.216: 1 Chirality restraints: 1790 Sorted by residual: chirality pdb=" CB THR H 90 " pdb=" CA THR H 90 " pdb=" OG1 THR H 90 " pdb=" CG2 THR H 90 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB VAL L 147 " pdb=" CA VAL L 147 " pdb=" CG1 VAL L 147 " pdb=" CG2 VAL L 147 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA VAL D 161 " pdb=" N VAL D 161 " pdb=" C VAL D 161 " pdb=" CB VAL D 161 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 1787 not shown) Planarity restraints: 2049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 112 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C GLY E 112 " 0.047 2.00e-02 2.50e+03 pdb=" O GLY E 112 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN E 113 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS H 204 " -0.045 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO H 205 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO H 205 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 205 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 133 " -0.010 2.00e-02 2.50e+03 1.46e-02 3.71e+00 pdb=" CG PHE D 133 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE D 133 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE D 133 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE D 133 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 133 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 133 " 0.000 2.00e-02 2.50e+03 ... (remaining 2046 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2089 2.78 - 3.31: 9272 3.31 - 3.84: 18298 3.84 - 4.37: 19741 4.37 - 4.90: 35658 Nonbonded interactions: 85058 Sorted by model distance: nonbonded pdb=" OD1 ASN L 92 " pdb=" N SER L 93 " model vdw 2.249 3.120 nonbonded pdb=" O LEU C 455 " pdb=" OH TYR H 33 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.300 3.040 nonbonded pdb=" O CYS D 151 " pdb=" OG SER D 191 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR E 33 " pdb=" OG SER E 95 " model vdw 2.337 3.040 ... (remaining 85053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.880 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 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 : 0.002 0.042 11697 Z= 0.112 Angle : 0.527 10.282 15946 Z= 0.275 Chirality : 0.043 0.216 1790 Planarity : 0.004 0.068 2048 Dihedral : 15.559 87.915 4156 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 23.19 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.21), residues: 1479 helix: -3.27 (0.45), residues: 57 sheet: 0.50 (0.25), residues: 460 loop : -0.89 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 87 TYR 0.027 0.001 TYR L 141 PHE 0.033 0.001 PHE D 133 TRP 0.018 0.001 TRP C 104 HIS 0.003 0.000 HIS H 203 Details of bonding type rmsd covalent geometry : bond 0.00216 (11678) covalent geometry : angle 0.52694 (15905) SS BOND : bond 0.00177 ( 18) SS BOND : angle 0.45530 ( 38) hydrogen bonds : bond 0.31730 ( 275) hydrogen bonds : angle 10.81994 ( 768) link_NAG-ASN : bond 0.00152 ( 1) link_NAG-ASN : angle 0.84712 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: D 89 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7870 (tm-30) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0781 time to fit residues: 9.4228 Evaluate side-chains 65 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS H 39 GLN ** H 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 HIS L 38 GLN D 210 ASN E 39 GLN E 81 GLN E 189 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.246306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.200610 restraints weight = 20957.045| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 7.45 r_work: 0.3625 rms_B_bonded: 6.40 restraints_weight: 2.0000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.094 11697 Z= 0.364 Angle : 0.777 8.883 15946 Z= 0.410 Chirality : 0.051 0.232 1790 Planarity : 0.006 0.063 2048 Dihedral : 4.530 29.569 1628 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.54 % Allowed : 19.97 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.21), residues: 1479 helix: -2.74 (0.62), residues: 48 sheet: 0.19 (0.24), residues: 520 loop : -0.98 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 466 TYR 0.034 0.003 TYR C 396 PHE 0.036 0.003 PHE H 67 TRP 0.025 0.002 TRP C 436 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00861 (11678) covalent geometry : angle 0.77477 (15905) SS BOND : bond 0.00730 ( 18) SS BOND : angle 1.33391 ( 38) hydrogen bonds : bond 0.04779 ( 275) hydrogen bonds : angle 7.52717 ( 768) link_NAG-ASN : bond 0.00395 ( 1) link_NAG-ASN : angle 1.76253 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 77 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: C 59 PHE cc_start: 0.3441 (m-10) cc_final: 0.3201 (m-10) REVERT: C 433 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8709 (m) REVERT: H 120 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7560 (tppt) REVERT: L 77 SER cc_start: 0.7545 (OUTLIER) cc_final: 0.7257 (p) REVERT: D 51 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8243 (tt) REVERT: D 181 LEU cc_start: 0.5374 (OUTLIER) cc_final: 0.5139 (tp) REVERT: E 81 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6217 (mm110) REVERT: E 83 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.7014 (tt0) outliers start: 45 outliers final: 20 residues processed: 118 average time/residue: 0.0837 time to fit residues: 15.3536 Evaluate side-chains 90 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 143 CYS Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 149 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 109 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 145 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.252396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.215605 restraints weight = 14752.560| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 4.22 r_work: 0.4071 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3876 r_free = 0.3876 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3876 r_free = 0.3876 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11697 Z= 0.120 Angle : 0.529 6.721 15946 Z= 0.272 Chirality : 0.044 0.169 1790 Planarity : 0.004 0.059 2048 Dihedral : 3.836 26.052 1628 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.28 % Allowed : 21.23 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.22), residues: 1479 helix: -2.33 (0.68), residues: 48 sheet: 0.16 (0.23), residues: 536 loop : -0.73 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 97 TYR 0.013 0.001 TYR C 423 PHE 0.013 0.001 PHE D 157 TRP 0.014 0.001 TRP D 36 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00273 (11678) covalent geometry : angle 0.52486 (15905) SS BOND : bond 0.00391 ( 18) SS BOND : angle 1.34134 ( 38) hydrogen bonds : bond 0.03711 ( 275) hydrogen bonds : angle 6.51842 ( 768) link_NAG-ASN : bond 0.00056 ( 1) link_NAG-ASN : angle 1.65535 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: C 59 PHE cc_start: 0.2983 (m-10) cc_final: 0.2723 (m-10) REVERT: C 377 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.6703 (m-80) REVERT: H 124 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7883 (m) outliers start: 29 outliers final: 17 residues processed: 102 average time/residue: 0.0848 time to fit residues: 13.1308 Evaluate side-chains 87 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 138 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 146 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 12 optimal weight: 50.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.242552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.204373 restraints weight = 20591.003| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 4.42 r_work: 0.4035 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 11697 Z= 0.282 Angle : 0.678 9.797 15946 Z= 0.350 Chirality : 0.048 0.190 1790 Planarity : 0.005 0.060 2048 Dihedral : 4.539 29.461 1628 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.69 % Allowed : 21.23 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.21), residues: 1479 helix: -2.43 (0.69), residues: 48 sheet: -0.08 (0.23), residues: 544 loop : -0.90 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 212 TYR 0.033 0.002 TYR C 396 PHE 0.019 0.002 PHE C 429 TRP 0.015 0.002 TRP C 436 HIS 0.008 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00673 (11678) covalent geometry : angle 0.67421 (15905) SS BOND : bond 0.00500 ( 18) SS BOND : angle 1.50939 ( 38) hydrogen bonds : bond 0.03995 ( 275) hydrogen bonds : angle 6.64085 ( 768) link_NAG-ASN : bond 0.00042 ( 1) link_NAG-ASN : angle 2.12184 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 71 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: C 377 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: C 441 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7321 (mp) REVERT: H 190 SER cc_start: 0.4418 (OUTLIER) cc_final: 0.4000 (p) REVERT: L 193 TYR cc_start: 0.5231 (p90) cc_final: 0.4748 (p90) outliers start: 47 outliers final: 31 residues processed: 115 average time/residue: 0.0880 time to fit residues: 15.4829 Evaluate side-chains 94 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 60 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 149 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 52 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 30.0000 chunk 17 optimal weight: 40.0000 chunk 107 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 25 optimal weight: 50.0000 chunk 114 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.246899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.204892 restraints weight = 12523.470| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 4.31 r_work: 0.3808 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11697 Z= 0.130 Angle : 0.534 7.036 15946 Z= 0.274 Chirality : 0.044 0.152 1790 Planarity : 0.004 0.053 2048 Dihedral : 4.000 25.922 1628 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.91 % Allowed : 21.93 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.22), residues: 1479 helix: -2.12 (0.73), residues: 48 sheet: -0.12 (0.23), residues: 529 loop : -0.74 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 212 TYR 0.012 0.001 TYR C 396 PHE 0.012 0.001 PHE D 157 TRP 0.013 0.001 TRP D 36 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00307 (11678) covalent geometry : angle 0.53116 (15905) SS BOND : bond 0.00424 ( 18) SS BOND : angle 1.07320 ( 38) hydrogen bonds : bond 0.03174 ( 275) hydrogen bonds : angle 6.05357 ( 768) link_NAG-ASN : bond 0.00013 ( 1) link_NAG-ASN : angle 2.02023 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: C 377 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7541 (m-80) REVERT: C 441 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7414 (mp) REVERT: H 56 SER cc_start: 0.7936 (OUTLIER) cc_final: 0.7486 (t) REVERT: L 193 TYR cc_start: 0.4713 (p90) cc_final: 0.4094 (p90) outliers start: 37 outliers final: 25 residues processed: 100 average time/residue: 0.0962 time to fit residues: 14.5071 Evaluate side-chains 92 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 78 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 6 optimal weight: 50.0000 chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 chunk 49 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.244514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.190905 restraints weight = 24405.756| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 10.09 r_work: 0.3553 rms_B_bonded: 5.19 restraints_weight: 2.0000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11697 Z= 0.177 Angle : 0.566 8.393 15946 Z= 0.293 Chirality : 0.045 0.167 1790 Planarity : 0.004 0.050 2048 Dihedral : 4.059 25.926 1628 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.38 % Allowed : 21.86 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.22), residues: 1479 helix: -1.74 (0.79), residues: 43 sheet: -0.05 (0.23), residues: 547 loop : -0.80 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 212 TYR 0.020 0.001 TYR C 396 PHE 0.012 0.001 PHE L 99 TRP 0.013 0.001 TRP C 436 HIS 0.004 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00420 (11678) covalent geometry : angle 0.56375 (15905) SS BOND : bond 0.00466 ( 18) SS BOND : angle 1.14662 ( 38) hydrogen bonds : bond 0.03311 ( 275) hydrogen bonds : angle 5.99267 ( 768) link_NAG-ASN : bond 0.00018 ( 1) link_NAG-ASN : angle 2.04857 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 66 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: C 377 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7423 (m-80) REVERT: C 441 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7543 (mp) REVERT: L 4 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8824 (mtm) REVERT: L 92 ASN cc_start: 0.7692 (t0) cc_final: 0.7324 (t0) REVERT: L 193 TYR cc_start: 0.4629 (p90) cc_final: 0.4033 (p90) outliers start: 43 outliers final: 31 residues processed: 107 average time/residue: 0.0860 time to fit residues: 14.2359 Evaluate side-chains 97 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 149 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 75 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 30.0000 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.243977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.199700 restraints weight = 20636.904| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 5.95 r_work: 0.3780 rms_B_bonded: 5.32 restraints_weight: 2.0000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11697 Z= 0.178 Angle : 0.565 7.986 15946 Z= 0.291 Chirality : 0.045 0.159 1790 Planarity : 0.004 0.049 2048 Dihedral : 4.097 26.132 1628 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.46 % Allowed : 21.46 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.22), residues: 1479 helix: -1.70 (0.79), residues: 43 sheet: -0.04 (0.23), residues: 555 loop : -0.84 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 212 TYR 0.020 0.001 TYR C 396 PHE 0.012 0.001 PHE H 67 TRP 0.014 0.001 TRP C 436 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00426 (11678) covalent geometry : angle 0.56261 (15905) SS BOND : bond 0.00506 ( 18) SS BOND : angle 1.17043 ( 38) hydrogen bonds : bond 0.03232 ( 275) hydrogen bonds : angle 5.87867 ( 768) link_NAG-ASN : bond 0.00053 ( 1) link_NAG-ASN : angle 2.03530 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 61 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: C 377 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7314 (m-80) REVERT: C 441 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7397 (mp) REVERT: H 83 ASN cc_start: 0.5815 (m-40) cc_final: 0.5329 (m-40) REVERT: L 4 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8594 (mtm) REVERT: L 193 TYR cc_start: 0.4983 (p90) cc_final: 0.4425 (p90) outliers start: 44 outliers final: 33 residues processed: 103 average time/residue: 0.0820 time to fit residues: 13.3791 Evaluate side-chains 94 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 58 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 149 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 30.0000 chunk 27 optimal weight: 40.0000 chunk 73 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 0.0270 chunk 69 optimal weight: 0.0870 chunk 110 optimal weight: 2.9990 chunk 3 optimal weight: 50.0000 chunk 64 optimal weight: 0.5980 chunk 8 optimal weight: 50.0000 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.249277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.242741 restraints weight = 14360.803| |-----------------------------------------------------------------------------| r_work (start): 0.4692 rms_B_bonded: 0.57 r_work: 0.4593 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.4548 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.4548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4552 r_free = 0.4552 target_work(ls_wunit_k1) = 0.226 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4552 r_free = 0.4552 target_work(ls_wunit_k1) = 0.226 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11697 Z= 0.100 Angle : 0.508 6.852 15946 Z= 0.259 Chirality : 0.043 0.148 1790 Planarity : 0.004 0.048 2048 Dihedral : 3.736 23.202 1628 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.52 % Allowed : 22.64 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.22), residues: 1479 helix: -1.71 (0.78), residues: 45 sheet: 0.04 (0.23), residues: 556 loop : -0.80 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 212 TYR 0.016 0.001 TYR L 141 PHE 0.010 0.001 PHE D 157 TRP 0.014 0.001 TRP D 36 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00232 (11678) covalent geometry : angle 0.50586 (15905) SS BOND : bond 0.00361 ( 18) SS BOND : angle 1.02372 ( 38) hydrogen bonds : bond 0.02789 ( 275) hydrogen bonds : angle 5.52570 ( 768) link_NAG-ASN : bond 0.00012 ( 1) link_NAG-ASN : angle 1.93416 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: C 377 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6727 (m-80) REVERT: C 441 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7372 (mp) REVERT: L 193 TYR cc_start: 0.5075 (p90) cc_final: 0.4768 (p90) REVERT: E 28 ASN cc_start: 0.8086 (p0) cc_final: 0.7496 (p0) outliers start: 32 outliers final: 25 residues processed: 94 average time/residue: 0.0808 time to fit residues: 12.0856 Evaluate side-chains 88 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 149 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 133 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 14 optimal weight: 50.0000 chunk 130 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.242173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.199819 restraints weight = 19347.164| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 5.17 r_work: 0.3929 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3932 r_free = 0.3932 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3932 r_free = 0.3932 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 11697 Z= 0.239 Angle : 0.620 9.736 15946 Z= 0.320 Chirality : 0.047 0.185 1790 Planarity : 0.005 0.048 2048 Dihedral : 4.216 24.509 1628 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.75 % Allowed : 22.56 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.22), residues: 1479 helix: -2.14 (0.69), residues: 50 sheet: -0.06 (0.23), residues: 540 loop : -0.81 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 212 TYR 0.029 0.002 TYR C 396 PHE 0.015 0.002 PHE H 67 TRP 0.015 0.002 TRP C 436 HIS 0.006 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00571 (11678) covalent geometry : angle 0.61617 (15905) SS BOND : bond 0.00567 ( 18) SS BOND : angle 1.42417 ( 38) hydrogen bonds : bond 0.03448 ( 275) hydrogen bonds : angle 5.93168 ( 768) link_NAG-ASN : bond 0.00039 ( 1) link_NAG-ASN : angle 2.07533 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 60 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: C 377 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: C 441 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7363 (mp) REVERT: C 506 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8258 (mt0) REVERT: L 4 MET cc_start: 0.8351 (mtp) cc_final: 0.8018 (mtp) REVERT: L 193 TYR cc_start: 0.5171 (p90) cc_final: 0.4823 (p90) REVERT: D 102 TYR cc_start: 0.8483 (p90) cc_final: 0.8222 (p90) outliers start: 35 outliers final: 30 residues processed: 94 average time/residue: 0.0915 time to fit residues: 13.4061 Evaluate side-chains 92 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 30.0000 chunk 35 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 67 optimal weight: 0.5980 chunk 138 optimal weight: 30.0000 chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 117 optimal weight: 0.0020 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.247947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.204558 restraints weight = 19421.552| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 5.72 r_work: 0.3750 rms_B_bonded: 5.54 restraints_weight: 2.0000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11697 Z= 0.113 Angle : 0.527 7.608 15946 Z= 0.270 Chirality : 0.044 0.151 1790 Planarity : 0.004 0.048 2048 Dihedral : 3.856 22.177 1628 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.28 % Allowed : 22.96 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.22), residues: 1479 helix: -1.34 (0.82), residues: 43 sheet: 0.06 (0.23), residues: 534 loop : -0.80 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 212 TYR 0.017 0.001 TYR L 141 PHE 0.010 0.001 PHE D 157 TRP 0.014 0.001 TRP D 36 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00263 (11678) covalent geometry : angle 0.52424 (15905) SS BOND : bond 0.00451 ( 18) SS BOND : angle 1.07045 ( 38) hydrogen bonds : bond 0.02854 ( 275) hydrogen bonds : angle 5.57578 ( 768) link_NAG-ASN : bond 0.00037 ( 1) link_NAG-ASN : angle 2.00733 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: C 340 GLU cc_start: 0.8155 (tp30) cc_final: 0.7878 (tp30) REVERT: C 377 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: C 441 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7420 (mp) REVERT: L 4 MET cc_start: 0.8621 (mtp) cc_final: 0.8297 (mtp) REVERT: L 92 ASN cc_start: 0.7589 (t0) cc_final: 0.7302 (t0) REVERT: L 193 TYR cc_start: 0.5176 (p90) cc_final: 0.4767 (p90) REVERT: D 102 TYR cc_start: 0.8519 (p90) cc_final: 0.8308 (p90) REVERT: E 28 ASN cc_start: 0.8299 (p0) cc_final: 0.8097 (p0) outliers start: 29 outliers final: 24 residues processed: 90 average time/residue: 0.0878 time to fit residues: 12.4803 Evaluate side-chains 85 residues out of total 1271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 38 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 119 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 50.0000 chunk 21 optimal weight: 50.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.242574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.203186 restraints weight = 20954.505| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 4.92 r_work: 0.3981 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11697 Z= 0.205 Angle : 0.601 9.122 15946 Z= 0.309 Chirality : 0.046 0.181 1790 Planarity : 0.004 0.047 2048 Dihedral : 4.152 23.468 1628 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.59 % Allowed : 22.56 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.22), residues: 1479 helix: -1.45 (0.79), residues: 43 sheet: -0.06 (0.23), residues: 538 loop : -0.80 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 212 TYR 0.025 0.002 TYR C 396 PHE 0.014 0.002 PHE H 67 TRP 0.014 0.001 TRP C 436 HIS 0.005 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00489 (11678) covalent geometry : angle 0.59778 (15905) SS BOND : bond 0.00537 ( 18) SS BOND : angle 1.29974 ( 38) hydrogen bonds : bond 0.03308 ( 275) hydrogen bonds : angle 5.83299 ( 768) link_NAG-ASN : bond 0.00012 ( 1) link_NAG-ASN : angle 2.07371 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2589.08 seconds wall clock time: 45 minutes 5.22 seconds (2705.22 seconds total)