Starting phenix.real_space_refine on Sat Oct 31 07:29:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10ri_75407/10_2026/10ri_75407.cif Found real_map, /net/cci-nas-00/data/ceres_data/10ri_75407/10_2026/10ri_75407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10ri_75407/10_2026/10ri_75407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10ri_75407/10_2026/10ri_75407.map" model { file = "/net/cci-nas-00/data/ceres_data/10ri_75407/10_2026/10ri_75407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10ri_75407/10_2026/10ri_75407.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 S 132 5.16 5 C 12834 2.51 5 N 3496 2.21 5 O 3858 1.98 5 H 19760 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40084 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2285 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 135} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 9389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 9389 Classifications: {'peptide': 604} Link IDs: {'PCIS': 6, 'PTRANS': 25, 'TRANS': 572} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 8324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 8324 Classifications: {'peptide': 537} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 503} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, D, F Time building chain proxies: 22.31, per 1000 atoms: 0.56 Number of scatterers: 40084 At special positions: 0 Unit cell: (135, 180.36, 238.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 132 16.00 O 3858 8.00 N 3496 7.00 C 12834 6.00 H 19760 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 93 " distance=2.02 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS B 85 " distance=2.03 Simple disulfide: pdb=" SG CYS A 82 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS B 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 162 " distance=2.02 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 171 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 93 " distance=2.02 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 160 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 162 " distance=2.02 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 171 " - pdb=" SG CYS B 185 " distance=2.03 Simple disulfide: pdb=" SG CYS C 152 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 248 " - pdb=" SG CYS C 309 " distance=2.03 Simple disulfide: pdb=" SG CYS C 447 " - pdb=" SG CYS C 528 " distance=2.03 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS C 480 " distance=2.03 Simple disulfide: pdb=" SG CYS C 569 " - pdb=" SG CYS C 640 " distance=2.03 Simple disulfide: pdb=" SG CYS C 686 " - pdb=" SG CYS C 735 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 54 " distance=2.03 Simple disulfide: pdb=" SG CYS E 82 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 206 " - pdb=" SG CYS E 228 " distance=2.03 Simple disulfide: pdb=" SG CYS E 275 " - pdb=" SG CYS E 424 " distance=2.03 Simple disulfide: pdb=" SG CYS E 431 " - pdb=" SG CYS E 583 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 54 " distance=2.03 Simple disulfide: pdb=" SG CYS F 82 " - pdb=" SG CYS F 104 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 206 " - pdb=" SG CYS F 228 " distance=2.03 Simple disulfide: pdb=" SG CYS F 275 " - pdb=" SG CYS F 424 " distance=2.03 Simple disulfide: pdb=" SG CYS F 431 " - pdb=" SG CYS F 583 " distance=2.03 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 248 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 447 " - pdb=" SG CYS D 528 " distance=2.03 Simple disulfide: pdb=" SG CYS D 468 " - pdb=" SG CYS D 480 " distance=2.03 Simple disulfide: pdb=" SG CYS D 569 " - pdb=" SG CYS D 640 " distance=2.03 Simple disulfide: pdb=" SG CYS D 686 " - pdb=" SG CYS D 735 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 743 " 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 801 " - " ASN C 247 " " NAG C 802 " - " ASN C 397 " " NAG D 801 " - " ASN D 247 " " NAG D 802 " - " ASN D 397 " " NAG E 901 " - " ASN E 150 " " NAG F 901 " - " ASN F 150 " Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4788 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 64 sheets defined 5.4% alpha, 49.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.700A pdb=" N PHE A 153 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.699A pdb=" N PHE B 153 " --> pdb=" O LYS B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'C' and resid 191 through 195 Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 391 through 395 removed outlier: 3.659A pdb=" N ALA C 395 " --> pdb=" O GLU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 430 Processing helix chain 'C' and resid 464 through 466 No H-bonds generated for 'chain 'C' and resid 464 through 466' Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 298 through 307 removed outlier: 7.191A pdb=" N VAL E 303 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU E 304 " --> pdb=" O TRP E 301 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG E 307 " --> pdb=" O GLU E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 463 removed outlier: 3.794A pdb=" N ILE E 462 " --> pdb=" O MET E 458 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG E 463 " --> pdb=" O PRO E 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 458 through 463' Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 298 through 307 removed outlier: 7.192A pdb=" N VAL F 303 " --> pdb=" O ASN F 300 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU F 304 " --> pdb=" O TRP F 301 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG F 307 " --> pdb=" O GLU F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 463 removed outlier: 3.794A pdb=" N ILE F 462 " --> pdb=" O MET F 458 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG F 463 " --> pdb=" O PRO F 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 458 through 463' Processing helix chain 'D' and resid 191 through 195 Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 391 through 395 removed outlier: 3.659A pdb=" N ALA D 395 " --> pdb=" O GLU D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 430 Processing helix chain 'D' and resid 464 through 466 No H-bonds generated for 'chain 'D' and resid 464 through 466' Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.707A pdb=" N GLN B 104 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.707A pdb=" N GLN B 104 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 91 " --> pdb=" O PRO B 131 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS B 93 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS B 129 " --> pdb=" O CYS B 93 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS B 127 " --> pdb=" O PRO B 95 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER B 97 " --> pdb=" O SER B 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 58 Processing sheet with id=AA4, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.547A pdb=" N LEU A 91 " --> pdb=" O PRO A 131 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS A 93 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS A 129 " --> pdb=" O CYS A 93 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS A 127 " --> pdb=" O PRO A 95 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER A 97 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 73 removed outlier: 9.802A pdb=" N ILE B 40 " --> pdb=" O ASN A 100 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N THR A 102 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'A' and resid 176 through 178 removed outlier: 4.018A pdb=" N LYS A 187 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 52 through 58 Processing sheet with id=AA9, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.018A pdb=" N LYS B 187 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 135 through 139 removed outlier: 6.701A pdb=" N GLY C 136 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL C 219 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL C 138 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 135 through 139 removed outlier: 6.701A pdb=" N GLY C 136 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL C 219 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL C 138 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 147 through 150 Processing sheet with id=AB5, first strand: chain 'C' and resid 225 through 231 removed outlier: 5.294A pdb=" N ASP C 227 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG C 251 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 250 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N MET C 289 " --> pdb=" O VAL C 279 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 236 through 239 removed outlier: 6.414A pdb=" N ILE C 236 " --> pdb=" O ARG C 325 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N HIS C 327 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU C 238 " --> pdb=" O HIS C 327 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 331 through 334 removed outlier: 3.552A pdb=" N PHE C 331 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 341 through 345 removed outlier: 6.645A pdb=" N VAL C 342 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASN C 420 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA C 344 " --> pdb=" O ASN C 420 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR C 450 " --> pdb=" O PRO C 423 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE C 425 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR C 448 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ALA C 451 " --> pdb=" O ASN C 509 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASN C 509 " --> pdb=" O ALA C 451 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 371 through 372 removed outlier: 3.558A pdb=" N ASP C 363 " --> pdb=" O THR C 403 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR C 450 " --> pdb=" O PRO C 423 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE C 425 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR C 448 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ALA C 451 " --> pdb=" O ASN C 509 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASN C 509 " --> pdb=" O ALA C 451 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 350 through 353 Processing sheet with id=AC2, first strand: chain 'C' and resid 437 through 438 removed outlier: 6.026A pdb=" N TYR C 437 " --> pdb=" O ILE C 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 484 through 485 Processing sheet with id=AC4, first strand: chain 'C' and resid 468 through 470 Processing sheet with id=AC5, first strand: chain 'C' and resid 550 through 554 Processing sheet with id=AC6, first strand: chain 'C' and resid 608 through 610 removed outlier: 3.563A pdb=" N TRP C 608 " --> pdb=" O LYS C 583 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TRP C 581 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN C 578 " --> pdb=" O GLN C 643 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 674 through 677 removed outlier: 3.822A pdb=" N GLN C 674 " --> pdb=" O LEU C 749 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 753 " --> pdb=" O THR C 676 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 681 through 685 Processing sheet with id=AC9, first strand: chain 'E' and resid 29 through 32 Processing sheet with id=AD1, first strand: chain 'E' and resid 37 through 40 Processing sheet with id=AD2, first strand: chain 'E' and resid 149 through 151 removed outlier: 6.472A pdb=" N LEU E 211 " --> pdb=" O ARG E 226 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG E 226 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE E 213 " --> pdb=" O ILE E 224 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 155 through 159 removed outlier: 6.754A pdb=" N GLY E 257 " --> pdb=" O PHE E 192 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE E 192 " --> pdb=" O GLY E 257 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER E 259 " --> pdb=" O GLU E 190 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 277 through 278 removed outlier: 6.812A pdb=" N CYS E 424 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL E 336 " --> pdb=" O CYS E 424 " (cutoff:3.500A) removed outlier: 12.656A pdb=" N ILE E 326 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N VAL E 409 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 12.614A pdb=" N VAL E 328 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N LYS E 407 " --> pdb=" O VAL E 328 " (cutoff:3.500A) removed outlier: 11.707A pdb=" N LEU E 330 " --> pdb=" O ARG E 405 " (cutoff:3.500A) removed outlier: 12.514A pdb=" N ARG E 405 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N LEU E 332 " --> pdb=" O PHE E 403 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE E 403 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA E 338 " --> pdb=" O LYS E 397 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N LYS E 397 " --> pdb=" O ALA E 338 " (cutoff:3.500A) removed outlier: 11.786A pdb=" N GLY E 340 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N PHE E 395 " --> pdb=" O GLY E 340 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR E 357 " --> pdb=" O VAL E 409 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 291 through 293 removed outlier: 12.656A pdb=" N ILE E 326 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N VAL E 409 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 12.614A pdb=" N VAL E 328 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N LYS E 407 " --> pdb=" O VAL E 328 " (cutoff:3.500A) removed outlier: 11.707A pdb=" N LEU E 330 " --> pdb=" O ARG E 405 " (cutoff:3.500A) removed outlier: 12.514A pdb=" N ARG E 405 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N LEU E 332 " --> pdb=" O PHE E 403 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE E 403 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA E 338 " --> pdb=" O LYS E 397 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N LYS E 397 " --> pdb=" O ALA E 338 " (cutoff:3.500A) removed outlier: 11.786A pdb=" N GLY E 340 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N PHE E 395 " --> pdb=" O GLY E 340 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR E 357 " --> pdb=" O VAL E 409 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 344 through 345 Processing sheet with id=AD7, first strand: chain 'E' and resid 373 through 374 removed outlier: 3.803A pdb=" N LYS E 377 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 447 through 449 removed outlier: 12.281A pdb=" N LEU E 485 " --> pdb=" O GLU E 567 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N GLU E 567 " --> pdb=" O LEU E 485 " (cutoff:3.500A) removed outlier: 12.549A pdb=" N VAL E 487 " --> pdb=" O TYR E 565 " (cutoff:3.500A) removed outlier: 11.410A pdb=" N TYR E 565 " --> pdb=" O VAL E 487 " (cutoff:3.500A) removed outlier: 11.553A pdb=" N LEU E 489 " --> pdb=" O ARG E 563 " (cutoff:3.500A) removed outlier: 12.260A pdb=" N ARG E 563 " --> pdb=" O LEU E 489 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N ASP E 491 " --> pdb=" O PHE E 561 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N PHE E 561 " --> pdb=" O ASP E 491 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS E 514 " --> pdb=" O GLU E 567 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA E 569 " --> pdb=" O MET E 512 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N MET E 512 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 471 through 473 removed outlier: 6.663A pdb=" N ARG E 577 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE E 500 " --> pdb=" O ARG E 577 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU E 579 " --> pdb=" O VAL E 498 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL E 498 " --> pdb=" O GLU E 579 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU E 581 " --> pdb=" O ARG E 496 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 503 through 505 Processing sheet with id=AE2, first strand: chain 'F' and resid 29 through 32 Processing sheet with id=AE3, first strand: chain 'F' and resid 37 through 40 Processing sheet with id=AE4, first strand: chain 'F' and resid 149 through 151 removed outlier: 6.472A pdb=" N LEU F 211 " --> pdb=" O ARG F 226 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG F 226 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE F 213 " --> pdb=" O ILE F 224 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 155 through 159 removed outlier: 6.754A pdb=" N GLY F 257 " --> pdb=" O PHE F 192 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE F 192 " --> pdb=" O GLY F 257 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER F 259 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 277 through 278 removed outlier: 6.812A pdb=" N CYS F 424 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL F 336 " --> pdb=" O CYS F 424 " (cutoff:3.500A) removed outlier: 12.656A pdb=" N ILE F 326 " --> pdb=" O VAL F 409 " (cutoff:3.500A) removed outlier: 10.797A pdb=" N VAL F 409 " --> pdb=" O ILE F 326 " (cutoff:3.500A) removed outlier: 12.613A pdb=" N VAL F 328 " --> pdb=" O LYS F 407 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N LYS F 407 " --> pdb=" O VAL F 328 " (cutoff:3.500A) removed outlier: 11.707A pdb=" N LEU F 330 " --> pdb=" O ARG F 405 " (cutoff:3.500A) removed outlier: 12.514A pdb=" N ARG F 405 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N LEU F 332 " --> pdb=" O PHE F 403 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE F 403 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA F 338 " --> pdb=" O LYS F 397 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N LYS F 397 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 11.787A pdb=" N GLY F 340 " --> pdb=" O PHE F 395 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N PHE F 395 " --> pdb=" O GLY F 340 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR F 357 " --> pdb=" O VAL F 409 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 291 through 293 removed outlier: 12.656A pdb=" N ILE F 326 " --> pdb=" O VAL F 409 " (cutoff:3.500A) removed outlier: 10.797A pdb=" N VAL F 409 " --> pdb=" O ILE F 326 " (cutoff:3.500A) removed outlier: 12.613A pdb=" N VAL F 328 " --> pdb=" O LYS F 407 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N LYS F 407 " --> pdb=" O VAL F 328 " (cutoff:3.500A) removed outlier: 11.707A pdb=" N LEU F 330 " --> pdb=" O ARG F 405 " (cutoff:3.500A) removed outlier: 12.514A pdb=" N ARG F 405 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N LEU F 332 " --> pdb=" O PHE F 403 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE F 403 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA F 338 " --> pdb=" O LYS F 397 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N LYS F 397 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 11.787A pdb=" N GLY F 340 " --> pdb=" O PHE F 395 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N PHE F 395 " --> pdb=" O GLY F 340 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR F 357 " --> pdb=" O VAL F 409 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 344 through 345 Processing sheet with id=AE9, first strand: chain 'F' and resid 373 through 374 removed outlier: 3.802A pdb=" N LYS F 377 " --> pdb=" O GLU F 374 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 447 through 449 removed outlier: 12.281A pdb=" N LEU F 485 " --> pdb=" O GLU F 567 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N GLU F 567 " --> pdb=" O LEU F 485 " (cutoff:3.500A) removed outlier: 12.548A pdb=" N VAL F 487 " --> pdb=" O TYR F 565 " (cutoff:3.500A) removed outlier: 11.410A pdb=" N TYR F 565 " --> pdb=" O VAL F 487 " (cutoff:3.500A) removed outlier: 11.552A pdb=" N LEU F 489 " --> pdb=" O ARG F 563 " (cutoff:3.500A) removed outlier: 12.260A pdb=" N ARG F 563 " --> pdb=" O LEU F 489 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N ASP F 491 " --> pdb=" O PHE F 561 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N PHE F 561 " --> pdb=" O ASP F 491 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS F 514 " --> pdb=" O GLU F 567 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA F 569 " --> pdb=" O MET F 512 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N MET F 512 " --> pdb=" O ALA F 569 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 471 through 473 removed outlier: 6.662A pdb=" N ARG F 577 " --> pdb=" O ILE F 500 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE F 500 " --> pdb=" O ARG F 577 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU F 579 " --> pdb=" O VAL F 498 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL F 498 " --> pdb=" O GLU F 579 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU F 581 " --> pdb=" O ARG F 496 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 503 through 505 Processing sheet with id=AF4, first strand: chain 'D' and resid 135 through 139 removed outlier: 6.702A pdb=" N GLY D 136 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL D 219 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL D 138 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 135 through 139 removed outlier: 6.702A pdb=" N GLY D 136 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL D 219 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL D 138 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 147 through 150 Processing sheet with id=AF7, first strand: chain 'D' and resid 225 through 231 removed outlier: 5.295A pdb=" N ASP D 227 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG D 251 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 250 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N MET D 289 " --> pdb=" O VAL D 279 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 236 through 239 removed outlier: 6.413A pdb=" N ILE D 236 " --> pdb=" O ARG D 325 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N HIS D 327 " --> pdb=" O ILE D 236 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU D 238 " --> pdb=" O HIS D 327 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 331 through 334 removed outlier: 3.552A pdb=" N PHE D 331 " --> pdb=" O TYR D 359 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 341 through 345 removed outlier: 6.644A pdb=" N VAL D 342 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASN D 420 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA D 344 " --> pdb=" O ASN D 420 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR D 450 " --> pdb=" O PRO D 423 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE D 425 " --> pdb=" O THR D 448 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR D 448 " --> pdb=" O ILE D 425 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA D 451 " --> pdb=" O ASN D 509 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ASN D 509 " --> pdb=" O ALA D 451 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 371 through 372 removed outlier: 3.559A pdb=" N ASP D 363 " --> pdb=" O THR D 403 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR D 450 " --> pdb=" O PRO D 423 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE D 425 " --> pdb=" O THR D 448 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR D 448 " --> pdb=" O ILE D 425 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA D 451 " --> pdb=" O ASN D 509 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ASN D 509 " --> pdb=" O ALA D 451 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 350 through 353 Processing sheet with id=AG4, first strand: chain 'D' and resid 437 through 438 removed outlier: 6.026A pdb=" N TYR D 437 " --> pdb=" O ILE D 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'D' and resid 484 through 485 Processing sheet with id=AG6, first strand: chain 'D' and resid 468 through 470 Processing sheet with id=AG7, first strand: chain 'D' and resid 550 through 554 Processing sheet with id=AG8, first strand: chain 'D' and resid 608 through 610 removed outlier: 3.562A pdb=" N TRP D 608 " --> pdb=" O LYS D 583 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TRP D 581 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN D 578 " --> pdb=" O GLN D 643 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 674 through 677 removed outlier: 3.822A pdb=" N GLN D 674 " --> pdb=" O LEU D 749 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 753 " --> pdb=" O THR D 676 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 681 through 685 730 hydrogen bonds defined for protein. 1809 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: 10.13 Time building geometry restraints manager: 5.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 19756 1.02 - 1.22: 12 1.22 - 1.42: 8740 1.42 - 1.62: 11864 1.62 - 1.82: 178 Bond restraints: 40550 Sorted by residual: bond pdb=" CB ASN B 87 " pdb=" CG ASN B 87 " ideal model delta sigma weight residual 1.516 1.642 -0.126 2.50e-02 1.60e+03 2.54e+01 bond pdb=" CB ASN A 87 " pdb=" CG ASN A 87 " ideal model delta sigma weight residual 1.516 1.641 -0.125 2.50e-02 1.60e+03 2.50e+01 bond pdb=" CG PRO A 110 " pdb=" CD PRO A 110 " ideal model delta sigma weight residual 1.503 1.411 0.092 3.40e-02 8.65e+02 7.34e+00 bond pdb=" CG PRO B 110 " pdb=" CD PRO B 110 " ideal model delta sigma weight residual 1.503 1.412 0.091 3.40e-02 8.65e+02 7.16e+00 bond pdb=" CA PHE B 153 " pdb=" CB PHE B 153 " ideal model delta sigma weight residual 1.535 1.489 0.046 2.09e-02 2.29e+03 4.90e+00 ... (remaining 40545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 72509 3.79 - 7.58: 536 7.58 - 11.37: 74 11.37 - 15.16: 21 15.16 - 18.95: 4 Bond angle restraints: 73144 Sorted by residual: angle pdb=" CG ASP A 186 " pdb=" CB ASP A 186 " pdb=" HB3 ASP A 186 " ideal model delta sigma weight residual 108.00 126.95 -18.95 3.00e+00 1.11e-01 3.99e+01 angle pdb=" CG ASP B 186 " pdb=" CB ASP B 186 " pdb=" HB3 ASP B 186 " ideal model delta sigma weight residual 108.00 126.90 -18.90 3.00e+00 1.11e-01 3.97e+01 angle pdb=" CG ASP B 186 " pdb=" CB ASP B 186 " pdb=" HB2 ASP B 186 " ideal model delta sigma weight residual 108.00 90.37 17.63 3.00e+00 1.11e-01 3.45e+01 angle pdb=" CG ASP A 186 " pdb=" CB ASP A 186 " pdb=" HB2 ASP A 186 " ideal model delta sigma weight residual 108.00 90.37 17.63 3.00e+00 1.11e-01 3.45e+01 angle pdb=" CD LYS A 132 " pdb=" CG LYS A 132 " pdb=" HG2 LYS A 132 " ideal model delta sigma weight residual 108.00 93.13 14.87 3.00e+00 1.11e-01 2.46e+01 ... (remaining 73139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 17438 17.66 - 35.31: 1379 35.31 - 52.97: 405 52.97 - 70.63: 130 70.63 - 88.29: 40 Dihedral angle restraints: 19392 sinusoidal: 10618 harmonic: 8774 Sorted by residual: dihedral pdb=" CA LYS B 109 " pdb=" C LYS B 109 " pdb=" N PRO B 110 " pdb=" CA PRO B 110 " ideal model delta harmonic sigma weight residual -180.00 -155.44 -24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA LYS A 109 " pdb=" C LYS A 109 " pdb=" N PRO A 110 " pdb=" CA PRO A 110 " ideal model delta harmonic sigma weight residual -180.00 -155.47 -24.53 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA SER C 375 " pdb=" C SER C 375 " pdb=" N ASN C 376 " pdb=" CA ASN C 376 " ideal model delta harmonic sigma weight residual 180.00 161.24 18.76 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 19389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2446 0.054 - 0.108: 465 0.108 - 0.162: 176 0.162 - 0.215: 15 0.215 - 0.269: 4 Chirality restraints: 3106 Sorted by residual: chirality pdb=" CB VAL C 400 " pdb=" CA VAL C 400 " pdb=" CG1 VAL C 400 " pdb=" CG2 VAL C 400 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB VAL D 400 " pdb=" CA VAL D 400 " pdb=" CG1 VAL D 400 " pdb=" CG2 VAL D 400 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA VAL D 200 " pdb=" N VAL D 200 " pdb=" C VAL D 200 " pdb=" CB VAL D 200 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 3103 not shown) Planarity restraints: 6056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 181 " 0.018 9.50e-02 1.11e+02 6.00e-02 8.03e+01 pdb=" NE ARG A 181 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 181 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 181 " 0.042 2.00e-02 2.50e+03 pdb=" NH2 ARG A 181 " -0.004 2.00e-02 2.50e+03 pdb="HH11 ARG A 181 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 181 " -0.092 2.00e-02 2.50e+03 pdb="HH21 ARG A 181 " -0.090 2.00e-02 2.50e+03 pdb="HH22 ARG A 181 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 181 " -0.017 9.50e-02 1.11e+02 6.00e-02 8.02e+01 pdb=" NE ARG B 181 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 181 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 181 " -0.042 2.00e-02 2.50e+03 pdb=" NH2 ARG B 181 " 0.003 2.00e-02 2.50e+03 pdb="HH11 ARG B 181 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 181 " 0.092 2.00e-02 2.50e+03 pdb="HH21 ARG B 181 " 0.090 2.00e-02 2.50e+03 pdb="HH22 ARG B 181 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 107 " 0.259 9.50e-02 1.11e+02 9.12e-02 2.64e+01 pdb=" NE ARG A 107 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG A 107 " -0.062 2.00e-02 2.50e+03 pdb=" NH1 ARG A 107 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 107 " 0.018 2.00e-02 2.50e+03 pdb="HH11 ARG A 107 " -0.034 2.00e-02 2.50e+03 pdb="HH12 ARG A 107 " 0.038 2.00e-02 2.50e+03 pdb="HH21 ARG A 107 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 107 " -0.008 2.00e-02 2.50e+03 ... (remaining 6053 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1321 2.13 - 2.75: 73283 2.75 - 3.37: 111005 3.37 - 3.98: 145484 3.98 - 4.60: 223130 Nonbonded interactions: 554223 Sorted by model distance: nonbonded pdb=" OE1 GLN A 47 " pdb=" HH TYR C 167 " model vdw 1.514 2.450 nonbonded pdb="HD22 ASN A 87 " pdb=" H GLY C 198 " model vdw 1.535 2.100 nonbonded pdb="HD22 ASN B 87 " pdb=" H GLY D 198 " model vdw 1.541 2.100 nonbonded pdb=" H ASP D 701 " pdb=" O LEU D 732 " model vdw 1.547 2.450 nonbonded pdb=" H ASP C 701 " pdb=" O LEU C 732 " model vdw 1.548 2.450 ... (remaining 554218 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 52.400 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 0.004 0.126 20838 Z= 0.178 Angle : 0.719 11.180 28298 Z= 0.389 Chirality : 0.051 0.269 3106 Planarity : 0.008 0.107 3642 Dihedral : 13.931 86.689 7796 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.65 % Favored : 95.23 % Rotamer: Outliers : 0.18 % Allowed : 8.54 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.57 (0.16), residues: 2538 helix: -4.11 (0.47), residues: 44 sheet: 0.59 (0.15), residues: 1058 loop : -1.04 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.002 ARG A 107 TYR 0.064 0.003 TYR C 216 PHE 0.029 0.002 PHE C 331 TRP 0.035 0.001 TRP D 181 HIS 0.022 0.003 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (20790) covalent geometry : angle 0.71692 / 0.39 (28196) SS BOND : bond 0.00296 / 0.20 ( 42) SS BOND : angle 1.01577 / 0.75 ( 84) hydrogen bonds : bond 0.21587 / 14.26 ( 679) hydrogen bonds : angle 10.42042 / 7.27 ( 1809) link_NAG-ASN : bond 0.00097 / 0.05 ( 6) link_NAG-ASN : angle 1.69607 / 1.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 319 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8051 (ptp90) REVERT: D 319 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8012 (ptp90) REVERT: D 646 LYS cc_start: 0.6478 (pptt) cc_final: 0.6160 (pttm) outliers start: 4 outliers final: 2 residues processed: 101 average time/residue: 0.3244 time to fit residues: 52.4337 Evaluate side-chains 101 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain D residue 319 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: [216, 98, 194, 227, 107, 10, 66, 247, 130, 124, 103] chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 50.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN D 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.128045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.079849 restraints weight = 186798.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.082052 restraints weight = 76210.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.081979 restraints weight = 47885.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.082415 restraints weight = 48393.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.082733 restraints weight = 42490.848| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20838 Z= 0.182 Angle : 0.550 4.686 28298 Z= 0.294 Chirality : 0.048 0.153 3106 Planarity : 0.004 0.045 3642 Dihedral : 4.999 23.808 2946 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.31 % Allowed : 8.54 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.39 (0.16), residues: 2538 helix: -2.82 (0.57), residues: 50 sheet: 0.58 (0.16), residues: 1054 loop : -0.81 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 305 TYR 0.012 0.001 TYR D 359 PHE 0.012 0.001 PHE E 419 TRP 0.006 0.001 TRP F 214 HIS 0.005 0.001 HIS C 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (20790) covalent geometry : angle 0.54695 / 0.29 (28196) SS BOND : bond 0.00219 / 0.15 ( 42) SS BOND : angle 0.94676 / 0.67 ( 84) hydrogen bonds : bond 0.04111 / 2.72 ( 679) hydrogen bonds : angle 7.09500 / 4.95 ( 1809) link_NAG-ASN : bond 0.00362 / 0.21 ( 6) link_NAG-ASN : angle 1.66304 / 1.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 MET cc_start: 0.8824 (ttt) cc_final: 0.8612 (ttm) outliers start: 7 outliers final: 5 residues processed: 107 average time/residue: 0.2788 time to fit residues: 49.6359 Evaluate side-chains 103 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: [234, 92, 187, 7, 17, 192, 181, 31, 91, 218, 245] chunk 234 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 218 optimal weight: 0.9990 chunk 245 optimal weight: 30.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.127813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.079699 restraints weight = 186533.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.082533 restraints weight = 77131.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.082081 restraints weight = 46036.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.082665 restraints weight = 46772.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.082941 restraints weight = 40715.734| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 20838 Z= 0.113 Angle : 0.481 4.356 28298 Z= 0.254 Chirality : 0.047 0.145 3106 Planarity : 0.003 0.041 3642 Dihedral : 4.564 19.829 2932 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.67 % Allowed : 8.50 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.29 (0.17), residues: 2538 helix: -2.10 (0.66), residues: 50 sheet: 0.62 (0.16), residues: 1046 loop : -0.74 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 418 TYR 0.011 0.001 TYR D 359 PHE 0.009 0.001 PHE F 403 TRP 0.004 0.001 TRP F 471 HIS 0.009 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (20790) covalent geometry : angle 0.47893 / 0.25 (28196) SS BOND : bond 0.00160 / 0.11 ( 42) SS BOND : angle 0.74609 / 0.54 ( 84) hydrogen bonds : bond 0.03303 / 2.18 ( 679) hydrogen bonds : angle 6.17240 / 4.29 ( 1809) link_NAG-ASN : bond 0.00111 / 0.06 ( 6) link_NAG-ASN : angle 1.36706 / 0.89 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.8457 (m-80) cc_final: 0.8075 (p90) REVERT: B 106 MET cc_start: 0.8791 (ttt) cc_final: 0.8589 (ttm) REVERT: E 245 MET cc_start: 0.7777 (mtp) cc_final: 0.7447 (mtp) outliers start: 15 outliers final: 9 residues processed: 117 average time/residue: 0.2556 time to fit residues: 50.9986 Evaluate side-chains 111 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 378 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: [173, 203, 20, 100, 177, 196, 244, 175, 144, 115, 35] chunk 173 optimal weight: 20.0000 chunk 203 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 196 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 144 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.127960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.079113 restraints weight = 186368.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.082139 restraints weight = 89392.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.082921 restraints weight = 51498.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.082963 restraints weight = 50265.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.083173 restraints weight = 47206.915| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20838 Z= 0.183 Angle : 0.512 4.818 28298 Z= 0.270 Chirality : 0.046 0.148 3106 Planarity : 0.004 0.044 3642 Dihedral : 4.646 23.085 2932 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.67 % Allowed : 9.26 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.34 (0.17), residues: 2538 helix: -1.86 (0.68), residues: 50 sheet: 0.60 (0.16), residues: 1034 loop : -0.78 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 305 TYR 0.016 0.001 TYR D 359 PHE 0.008 0.001 PHE E 247 TRP 0.005 0.001 TRP D 181 HIS 0.005 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (20790) covalent geometry : angle 0.50943 / 0.27 (28196) SS BOND : bond 0.00217 / 0.13 ( 42) SS BOND : angle 0.80273 / 0.56 ( 84) hydrogen bonds : bond 0.02997 / 1.97 ( 679) hydrogen bonds : angle 5.85946 / 4.07 ( 1809) link_NAG-ASN : bond 0.00248 / 0.15 ( 6) link_NAG-ASN : angle 1.75751 / 1.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 111 average time/residue: 0.2843 time to fit residues: 52.9807 Evaluate side-chains 111 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 544 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 391 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: [39, 88, 253, 72, 138, 247, 41, 80, 51, 114, 214] chunk 39 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 253 optimal weight: 40.0000 chunk 72 optimal weight: 0.5980 chunk 138 optimal weight: 10.0000 chunk 247 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 80 optimal weight: 50.0000 chunk 51 optimal weight: 0.9990 chunk 114 optimal weight: 30.0000 chunk 214 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN ** C 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.128156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.080260 restraints weight = 186933.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.082627 restraints weight = 98584.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.083286 restraints weight = 52965.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.083352 restraints weight = 50245.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.083593 restraints weight = 47471.879| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20838 Z= 0.128 Angle : 0.480 5.552 28298 Z= 0.253 Chirality : 0.046 0.156 3106 Planarity : 0.003 0.043 3642 Dihedral : 4.485 20.521 2932 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.58 % Allowed : 9.35 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.30 (0.17), residues: 2538 helix: -1.55 (0.73), residues: 50 sheet: 0.55 (0.16), residues: 1042 loop : -0.71 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 305 TYR 0.015 0.001 TYR D 359 PHE 0.012 0.001 PHE C 543 TRP 0.005 0.001 TRP D 181 HIS 0.005 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (20790) covalent geometry : angle 0.47797 / 0.25 (28196) SS BOND : bond 0.00258 / 0.15 ( 42) SS BOND : angle 0.71885 / 0.50 ( 84) hydrogen bonds : bond 0.02759 / 1.81 ( 679) hydrogen bonds : angle 5.63950 / 3.91 ( 1809) link_NAG-ASN : bond 0.00109 / 0.06 ( 6) link_NAG-ASN : angle 1.52151 / 1.01 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 13 residues processed: 112 average time/residue: 0.2635 time to fit residues: 49.9469 Evaluate side-chains 110 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 544 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 378 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: [101, 18, 11, 47, 133, 105, 80, 87, 68, 235, 240] chunk 101 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 30.0000 chunk 87 optimal weight: 50.0000 chunk 68 optimal weight: 7.9990 chunk 235 optimal weight: 0.6980 chunk 240 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN C 544 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.127395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.078325 restraints weight = 186055.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.081434 restraints weight = 86832.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.081794 restraints weight = 49939.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.081998 restraints weight = 42885.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.082249 restraints weight = 43315.964| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20838 Z= 0.208 Angle : 0.517 4.900 28298 Z= 0.272 Chirality : 0.046 0.146 3106 Planarity : 0.004 0.044 3642 Dihedral : 4.643 23.262 2932 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.07 % Allowed : 9.30 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.49 (0.17), residues: 2538 helix: -1.56 (0.73), residues: 50 sheet: 0.28 (0.15), residues: 1066 loop : -0.74 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 305 TYR 0.016 0.001 TYR D 359 PHE 0.009 0.001 PHE C 323 TRP 0.006 0.001 TRP C 181 HIS 0.009 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (20790) covalent geometry : angle 0.51240 / 0.27 (28196) SS BOND : bond 0.00225 / 0.14 ( 42) SS BOND : angle 1.03518 / 0.71 ( 84) hydrogen bonds : bond 0.02903 / 1.91 ( 679) hydrogen bonds : angle 5.59358 / 3.88 ( 1809) link_NAG-ASN : bond 0.00292 / 0.18 ( 6) link_NAG-ASN : angle 1.97761 / 1.34 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 21 residues processed: 117 average time/residue: 0.2678 time to fit residues: 52.3947 Evaluate side-chains 118 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 391 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: [238, 159, 4, 110, 8, 79, 214, 246, 39, 44, 5] chunk 238 optimal weight: 30.0000 chunk 159 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 chunk 246 optimal weight: 50.0000 chunk 39 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 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 = 0.4387 r_free = 0.4387 target = 0.128123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.080211 restraints weight = 187290.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.082808 restraints weight = 99345.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.083273 restraints weight = 52040.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.083576 restraints weight = 51227.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.083754 restraints weight = 47791.989| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 20838 Z= 0.108 Angle : 0.497 10.725 28298 Z= 0.258 Chirality : 0.046 0.167 3106 Planarity : 0.003 0.042 3642 Dihedral : 4.641 46.138 2932 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.67 % Allowed : 9.75 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.36 (0.17), residues: 2538 helix: -1.33 (0.77), residues: 50 sheet: 0.44 (0.16), residues: 1036 loop : -0.69 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 305 TYR 0.015 0.001 TYR D 359 PHE 0.009 0.001 PHE E 403 TRP 0.006 0.001 TRP C 181 HIS 0.003 0.001 HIS C 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (20790) covalent geometry : angle 0.48819 / 0.25 (28196) SS BOND : bond 0.00250 / 0.14 ( 42) SS BOND : angle 1.65240 / 1.05 ( 84) hydrogen bonds : bond 0.02550 / 1.67 ( 679) hydrogen bonds : angle 5.39489 / 3.75 ( 1809) link_NAG-ASN : bond 0.00055 / 0.03 ( 6) link_NAG-ASN : angle 1.49612 / 1.01 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 MET cc_start: 0.8798 (mmm) cc_final: 0.8468 (mmt) REVERT: C 517 ILE cc_start: 0.9164 (mt) cc_final: 0.8456 (tt) outliers start: 15 outliers final: 12 residues processed: 115 average time/residue: 0.2756 time to fit residues: 53.4668 Evaluate side-chains 112 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 364 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: [155, 190, 240, 39, 183, 66, 113, 29, 22, 188, 235] chunk 155 optimal weight: 0.9990 chunk 190 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 39 optimal weight: 0.4980 chunk 183 optimal weight: 10.0000 chunk 66 optimal weight: 0.2980 chunk 113 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.128169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.079816 restraints weight = 186370.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.083184 restraints weight = 86497.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.083625 restraints weight = 47369.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.084081 restraints weight = 42362.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.084196 restraints weight = 40939.192| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 20838 Z= 0.116 Angle : 0.485 10.808 28298 Z= 0.251 Chirality : 0.046 0.144 3106 Planarity : 0.003 0.042 3642 Dihedral : 4.416 33.747 2932 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.67 % Allowed : 9.75 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.33 (0.17), residues: 2538 helix: -1.21 (0.78), residues: 50 sheet: 0.40 (0.16), residues: 1050 loop : -0.62 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 305 TYR 0.015 0.001 TYR D 359 PHE 0.008 0.001 PHE E 403 TRP 0.008 0.001 TRP C 181 HIS 0.003 0.001 HIS C 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (20790) covalent geometry : angle 0.47467 / 0.25 (28196) SS BOND : bond 0.00177 / 0.11 ( 42) SS BOND : angle 1.80062 / 1.15 ( 84) hydrogen bonds : bond 0.02464 / 1.61 ( 679) hydrogen bonds : angle 5.20664 / 3.62 ( 1809) link_NAG-ASN : bond 0.00090 / 0.05 ( 6) link_NAG-ASN : angle 1.54244 / 1.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 MET cc_start: 0.8999 (mmm) cc_final: 0.8600 (mmt) REVERT: B 51 CYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7318 (t) REVERT: C 517 ILE cc_start: 0.9195 (mt) cc_final: 0.8509 (tt) REVERT: F 437 MET cc_start: 0.8812 (tpp) cc_final: 0.8588 (tpp) outliers start: 15 outliers final: 12 residues processed: 114 average time/residue: 0.2750 time to fit residues: 52.9278 Evaluate side-chains 111 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 364 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: [96, 83, 11, 172, 199, 104, 152, 15, 112, 28, 159] chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 50.0000 chunk 11 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 112 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN B 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.127566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.078188 restraints weight = 187518.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.081892 restraints weight = 81105.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.082090 restraints weight = 49259.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.082534 restraints weight = 41460.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.082632 restraints weight = 38977.425| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 20838 Z= 0.202 Angle : 0.527 10.945 28298 Z= 0.274 Chirality : 0.046 0.144 3106 Planarity : 0.004 0.044 3642 Dihedral : 4.653 35.875 2932 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.72 % Allowed : 10.02 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.44 (0.17), residues: 2538 helix: -1.55 (0.73), residues: 50 sheet: 0.24 (0.16), residues: 1074 loop : -0.63 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 418 TYR 0.017 0.001 TYR D 359 PHE 0.009 0.001 PHE E 403 TRP 0.007 0.001 TRP C 181 HIS 0.004 0.001 HIS D 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (20790) covalent geometry : angle 0.51568 / 0.27 (28196) SS BOND : bond 0.00256 / 0.15 ( 42) SS BOND : angle 1.86671 / 1.18 ( 84) hydrogen bonds : bond 0.02775 / 1.82 ( 679) hydrogen bonds : angle 5.28357 / 3.66 ( 1809) link_NAG-ASN : bond 0.00263 / 0.16 ( 6) link_NAG-ASN : angle 1.90649 / 1.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 MET cc_start: 0.9045 (mmm) cc_final: 0.8658 (mmt) REVERT: C 199 MET cc_start: 0.5393 (ttt) cc_final: 0.4911 (ttt) outliers start: 16 outliers final: 15 residues processed: 113 average time/residue: 0.2762 time to fit residues: 52.1238 Evaluate side-chains 110 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 391 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: [166, 80, 127, 43, 213, 114, 117, 206, 3, 209, 205] chunk 166 optimal weight: 2.9990 chunk 80 optimal weight: 50.0000 chunk 127 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 206 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 209 optimal weight: 0.0870 chunk 205 optimal weight: 1.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.127946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.080868 restraints weight = 186131.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.083152 restraints weight = 95994.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.082790 restraints weight = 57381.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.083364 restraints weight = 58944.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.083494 restraints weight = 51803.043| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20838 Z= 0.119 Angle : 0.500 10.466 28298 Z= 0.259 Chirality : 0.046 0.200 3106 Planarity : 0.004 0.066 3642 Dihedral : 4.554 36.060 2932 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.67 % Allowed : 10.02 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.41 (0.17), residues: 2538 helix: -1.40 (0.75), residues: 50 sheet: 0.31 (0.16), residues: 1056 loop : -0.65 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 305 TYR 0.017 0.001 TYR D 359 PHE 0.010 0.001 PHE E 403 TRP 0.009 0.001 TRP D 181 HIS 0.018 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (20790) covalent geometry : angle 0.49188 / 0.26 (28196) SS BOND : bond 0.00202 / 0.12 ( 42) SS BOND : angle 1.59413 / 1.02 ( 84) hydrogen bonds : bond 0.02572 / 1.67 ( 679) hydrogen bonds : angle 5.20167 / 3.60 ( 1809) link_NAG-ASN : bond 0.00040 / 0.02 ( 6) link_NAG-ASN : angle 1.65693 / 1.13 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 MET cc_start: 0.8981 (mmm) cc_final: 0.8586 (mmt) REVERT: B 51 CYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7172 (t) outliers start: 15 outliers final: 12 residues processed: 114 average time/residue: 0.2780 time to fit residues: 52.1263 Evaluate side-chains 110 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 391 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: [223, 249, 73, 103, 42, 231, 95, 2, 144, 18, 184] chunk 223 optimal weight: 0.9990 chunk 249 optimal weight: 0.3980 chunk 73 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 231 optimal weight: 9.9990 chunk 95 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 184 optimal weight: 8.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.131267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.084048 restraints weight = 196657.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.087299 restraints weight = 76785.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.088880 restraints weight = 47361.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.090294 restraints weight = 37998.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.090784 restraints weight = 33514.994| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 20838 Z= 0.081 Angle : 0.472 10.158 28298 Z= 0.242 Chirality : 0.046 0.142 3106 Planarity : 0.003 0.041 3642 Dihedral : 4.238 33.536 2932 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.49 % Allowed : 10.24 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.29 (0.17), residues: 2538 helix: -1.27 (0.75), residues: 50 sheet: 0.38 (0.16), residues: 1050 loop : -0.56 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 650 TYR 0.014 0.001 TYR C 470 PHE 0.008 0.001 PHE D 331 TRP 0.009 0.001 TRP E 56 HIS 0.005 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.08 (20790) covalent geometry : angle 0.46618 / 0.24 (28196) SS BOND : bond 0.00160 / 0.10 ( 42) SS BOND : angle 1.24390 / 0.80 ( 84) hydrogen bonds : bond 0.02268 / 1.48 ( 679) hydrogen bonds : angle 4.93958 / 3.43 ( 1809) link_NAG-ASN : bond 0.00069 / 0.04 ( 6) link_NAG-ASN : angle 1.36512 / 0.90 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6492.86 seconds wall clock time: 111 minutes 8.80 seconds (6668.80 seconds total)