Starting phenix.real_space_refine on Sat Mar 7 13:42:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u65_26360/03_2026/7u65_26360.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u65_26360/03_2026/7u65_26360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u65_26360/03_2026/7u65_26360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u65_26360/03_2026/7u65_26360.map" model { file = "/net/cci-nas-00/data/ceres_data/7u65_26360/03_2026/7u65_26360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u65_26360/03_2026/7u65_26360.cif" } resolution = 2.8 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= 0.005 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 22812 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17154 2.51 5 N 4626 2.21 5 O 4716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26616 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 21, 'TRANS': 459} Chain breaks: 5 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 7, 'GLU:plan': 16, 'ASP:plan': 3, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLN%COO:plan1': 1} Unresolved non-hydrogen planarities: 144 Chain: "G" Number of atoms: 620 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 83, 615 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 82} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 69 Conformer: "B" Number of residues, atoms: 83, 615 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 82} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 69 bond proxies already assigned to first conformer: 623 Restraints were copied for chains: B, C, D, E, F, H, I, J, K, L Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ATHR G 36 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR G 36 " occ=0.50 residue: pdb=" N ATHR H 36 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR H 36 " occ=0.50 residue: pdb=" N ATHR I 36 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR I 36 " occ=0.50 residue: pdb=" N ATHR J 36 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR J 36 " occ=0.50 residue: pdb=" N ATHR K 36 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR K 36 " occ=0.50 residue: pdb=" N ATHR L 36 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR L 36 " occ=0.50 Time building chain proxies: 4.41, per 1000 atoms: 0.17 Number of scatterers: 26616 At special positions: 0 Unit cell: (131.412, 138.868, 135.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4716 8.00 N 4626 7.00 C 17154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.5 seconds 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6528 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 12 sheets defined 66.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 24 through 41 removed outlier: 3.559A pdb=" N ASN A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.700A pdb=" N ARG A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 91 removed outlier: 3.509A pdb=" N HIS A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 125 through 141 Processing helix chain 'A' and resid 142 through 145 Processing helix chain 'A' and resid 167 through 180 removed outlier: 3.869A pdb=" N GLU A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 239 through 250 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.556A pdb=" N SER A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 277 " --> pdb=" O CYS A 273 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.620A pdb=" N SER A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 355 removed outlier: 4.155A pdb=" N VAL A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 339 " --> pdb=" O TYR A 335 " (cutoff:3.500A) Proline residue: A 346 - end of helix Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.615A pdb=" N ASP A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 415 removed outlier: 3.506A pdb=" N GLU A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 421 through 431 removed outlier: 3.639A pdb=" N LYS A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 446 Processing helix chain 'A' and resid 448 through 461 removed outlier: 3.539A pdb=" N ARG A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 487 Processing helix chain 'A' and resid 489 through 501 Processing helix chain 'G' and resid 5 through 22 Processing helix chain 'G' and resid 62 through 82 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 24 through 41 removed outlier: 3.560A pdb=" N ASN B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.699A pdb=" N ARG B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 91 removed outlier: 3.509A pdb=" N HIS B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 125 through 141 Processing helix chain 'B' and resid 142 through 145 Processing helix chain 'B' and resid 167 through 180 removed outlier: 3.869A pdb=" N GLU B 171 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 195 Processing helix chain 'B' and resid 202 through 208 Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 239 through 250 Processing helix chain 'B' and resid 260 through 283 removed outlier: 3.556A pdb=" N SER B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 277 " --> pdb=" O CYS B 273 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 299 Processing helix chain 'B' and resid 309 through 319 removed outlier: 3.619A pdb=" N SER B 319 " --> pdb=" O ALA B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 355 removed outlier: 4.155A pdb=" N VAL B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN B 339 " --> pdb=" O TYR B 335 " (cutoff:3.500A) Proline residue: B 346 - end of helix Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 373 through 390 removed outlier: 3.616A pdb=" N ASP B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 415 removed outlier: 3.506A pdb=" N GLU B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 421 through 431 removed outlier: 3.640A pdb=" N LYS B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 446 Processing helix chain 'B' and resid 448 through 461 removed outlier: 3.539A pdb=" N ARG B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 487 Processing helix chain 'B' and resid 489 through 501 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 24 through 41 removed outlier: 3.559A pdb=" N ASN C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.700A pdb=" N ARG C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 91 removed outlier: 3.510A pdb=" N HIS C 69 " --> pdb=" O THR C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 125 through 141 Processing helix chain 'C' and resid 142 through 145 Processing helix chain 'C' and resid 167 through 180 removed outlier: 3.869A pdb=" N GLU C 171 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU C 172 " --> pdb=" O PRO C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 239 through 250 Processing helix chain 'C' and resid 260 through 283 removed outlier: 3.556A pdb=" N SER C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR C 272 " --> pdb=" O ASP C 268 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 277 " --> pdb=" O CYS C 273 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 299 Processing helix chain 'C' and resid 309 through 319 removed outlier: 3.620A pdb=" N SER C 319 " --> pdb=" O ALA C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 355 removed outlier: 4.155A pdb=" N VAL C 338 " --> pdb=" O MET C 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) Proline residue: C 346 - end of helix Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 373 through 390 removed outlier: 3.615A pdb=" N ASP C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 415 removed outlier: 3.506A pdb=" N GLU C 397 " --> pdb=" O HIS C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 421 through 431 removed outlier: 3.638A pdb=" N LYS C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 446 Processing helix chain 'C' and resid 448 through 461 removed outlier: 3.539A pdb=" N ARG C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS C 461 " --> pdb=" O GLU C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 487 Processing helix chain 'C' and resid 489 through 501 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 24 through 41 removed outlier: 3.559A pdb=" N ASN D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 removed outlier: 3.699A pdb=" N ARG D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 91 removed outlier: 3.510A pdb=" N HIS D 69 " --> pdb=" O THR D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 Processing helix chain 'D' and resid 125 through 141 Processing helix chain 'D' and resid 142 through 145 Processing helix chain 'D' and resid 167 through 180 removed outlier: 3.868A pdb=" N GLU D 171 " --> pdb=" O GLU D 167 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU D 172 " --> pdb=" O PRO D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 195 Processing helix chain 'D' and resid 202 through 208 Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 239 through 250 Processing helix chain 'D' and resid 260 through 283 removed outlier: 3.555A pdb=" N SER D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASP D 276 " --> pdb=" O TYR D 272 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D 277 " --> pdb=" O CYS D 273 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 299 Processing helix chain 'D' and resid 309 through 319 removed outlier: 3.620A pdb=" N SER D 319 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 355 removed outlier: 4.155A pdb=" N VAL D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) Proline residue: D 346 - end of helix Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 373 through 390 removed outlier: 3.616A pdb=" N ASP D 377 " --> pdb=" O SER D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 415 removed outlier: 3.506A pdb=" N GLU D 397 " --> pdb=" O HIS D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 421 through 431 removed outlier: 3.639A pdb=" N LYS D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 446 Processing helix chain 'D' and resid 448 through 461 removed outlier: 3.539A pdb=" N ARG D 452 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 487 Processing helix chain 'D' and resid 489 through 501 Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.559A pdb=" N ASN E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 removed outlier: 3.699A pdb=" N ARG E 46 " --> pdb=" O SER E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 91 removed outlier: 3.509A pdb=" N HIS E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 116 Processing helix chain 'E' and resid 125 through 141 Processing helix chain 'E' and resid 142 through 145 Processing helix chain 'E' and resid 167 through 180 removed outlier: 3.869A pdb=" N GLU E 171 " --> pdb=" O GLU E 167 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU E 172 " --> pdb=" O PRO E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 195 Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 236 through 238 No H-bonds generated for 'chain 'E' and resid 236 through 238' Processing helix chain 'E' and resid 239 through 250 Processing helix chain 'E' and resid 260 through 283 removed outlier: 3.556A pdb=" N SER E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR E 272 " --> pdb=" O ASP E 268 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS E 273 " --> pdb=" O ASP E 269 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP E 276 " --> pdb=" O TYR E 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU E 277 " --> pdb=" O CYS E 273 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 299 Processing helix chain 'E' and resid 309 through 319 removed outlier: 3.619A pdb=" N SER E 319 " --> pdb=" O ALA E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 355 removed outlier: 4.155A pdb=" N VAL E 338 " --> pdb=" O MET E 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN E 339 " --> pdb=" O TYR E 335 " (cutoff:3.500A) Proline residue: E 346 - end of helix Processing helix chain 'E' and resid 355 through 362 Processing helix chain 'E' and resid 373 through 390 removed outlier: 3.615A pdb=" N ASP E 377 " --> pdb=" O SER E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 415 removed outlier: 3.506A pdb=" N GLU E 397 " --> pdb=" O HIS E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 419 Processing helix chain 'E' and resid 421 through 431 removed outlier: 3.638A pdb=" N LYS E 431 " --> pdb=" O GLU E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 446 Processing helix chain 'E' and resid 448 through 461 removed outlier: 3.540A pdb=" N ARG E 452 " --> pdb=" O SER E 448 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 487 Processing helix chain 'E' and resid 489 through 501 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 24 through 41 removed outlier: 3.558A pdb=" N ASN F 41 " --> pdb=" O GLY F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.699A pdb=" N ARG F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 91 removed outlier: 3.510A pdb=" N HIS F 69 " --> pdb=" O THR F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 116 Processing helix chain 'F' and resid 125 through 141 Processing helix chain 'F' and resid 142 through 145 Processing helix chain 'F' and resid 167 through 180 removed outlier: 3.869A pdb=" N GLU F 171 " --> pdb=" O GLU F 167 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU F 172 " --> pdb=" O PRO F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 195 Processing helix chain 'F' and resid 202 through 208 Processing helix chain 'F' and resid 236 through 238 No H-bonds generated for 'chain 'F' and resid 236 through 238' Processing helix chain 'F' and resid 239 through 250 Processing helix chain 'F' and resid 260 through 283 removed outlier: 3.555A pdb=" N SER F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR F 272 " --> pdb=" O ASP F 268 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS F 273 " --> pdb=" O ASP F 269 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL F 274 " --> pdb=" O ILE F 270 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP F 276 " --> pdb=" O TYR F 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU F 277 " --> pdb=" O CYS F 273 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 Processing helix chain 'F' and resid 309 through 319 removed outlier: 3.620A pdb=" N SER F 319 " --> pdb=" O ALA F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 355 removed outlier: 4.155A pdb=" N VAL F 338 " --> pdb=" O MET F 334 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN F 339 " --> pdb=" O TYR F 335 " (cutoff:3.500A) Proline residue: F 346 - end of helix Processing helix chain 'F' and resid 355 through 362 Processing helix chain 'F' and resid 373 through 390 removed outlier: 3.615A pdb=" N ASP F 377 " --> pdb=" O SER F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 415 removed outlier: 3.505A pdb=" N GLU F 397 " --> pdb=" O HIS F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 419 Processing helix chain 'F' and resid 421 through 431 removed outlier: 3.639A pdb=" N LYS F 431 " --> pdb=" O GLU F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 446 Processing helix chain 'F' and resid 448 through 461 removed outlier: 3.540A pdb=" N ARG F 452 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS F 461 " --> pdb=" O GLU F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 487 Processing helix chain 'F' and resid 489 through 501 Processing helix chain 'H' and resid 5 through 22 Processing helix chain 'H' and resid 62 through 82 Processing helix chain 'I' and resid 5 through 22 Processing helix chain 'I' and resid 62 through 82 Processing helix chain 'J' and resid 5 through 22 Processing helix chain 'J' and resid 62 through 82 Processing helix chain 'K' and resid 5 through 22 Processing helix chain 'K' and resid 62 through 82 Processing helix chain 'L' and resid 5 through 22 Processing helix chain 'L' and resid 62 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 215 removed outlier: 6.561A pdb=" N ARG A 214 " --> pdb=" O GLY A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'G' and resid 25 through 33 Processing sheet with id=AA3, first strand: chain 'B' and resid 214 through 215 removed outlier: 6.561A pdb=" N ARG B 214 " --> pdb=" O GLY B 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 214 through 215 removed outlier: 6.562A pdb=" N ARG C 214 " --> pdb=" O GLY C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 214 through 215 removed outlier: 6.561A pdb=" N ARG D 214 " --> pdb=" O GLY D 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 214 through 215 removed outlier: 6.561A pdb=" N ARG E 214 " --> pdb=" O GLY E 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 214 through 215 removed outlier: 6.561A pdb=" N ARG F 214 " --> pdb=" O GLY F 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 25 through 33 Processing sheet with id=AA9, first strand: chain 'I' and resid 25 through 33 Processing sheet with id=AB1, first strand: chain 'J' and resid 25 through 33 Processing sheet with id=AB2, first strand: chain 'K' and resid 25 through 33 Processing sheet with id=AB3, first strand: chain 'L' and resid 25 through 33 1584 hydrogen bonds defined for protein. 4644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4315 1.32 - 1.44: 7738 1.44 - 1.56: 15019 1.56 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 27264 Sorted by residual: bond pdb=" C ARG C 498 " pdb=" O ARG C 498 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.26e-02 6.30e+03 1.20e+01 bond pdb=" C ARG F 498 " pdb=" O ARG F 498 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.26e-02 6.30e+03 1.20e+01 bond pdb=" C ARG A 498 " pdb=" O ARG A 498 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.26e-02 6.30e+03 1.19e+01 bond pdb=" C ARG B 498 " pdb=" O ARG B 498 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.26e-02 6.30e+03 1.18e+01 bond pdb=" C ARG E 498 " pdb=" O ARG E 498 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.26e-02 6.30e+03 1.16e+01 ... (remaining 27259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 36025 1.62 - 3.24: 804 3.24 - 4.85: 155 4.85 - 6.47: 66 6.47 - 8.09: 12 Bond angle restraints: 37062 Sorted by residual: angle pdb=" C VAL C 429 " pdb=" CA VAL C 429 " pdb=" CB VAL C 429 " ideal model delta sigma weight residual 112.22 105.83 6.39 1.38e+00 5.25e-01 2.14e+01 angle pdb=" C VAL B 429 " pdb=" CA VAL B 429 " pdb=" CB VAL B 429 " ideal model delta sigma weight residual 112.22 105.84 6.38 1.38e+00 5.25e-01 2.14e+01 angle pdb=" C VAL A 429 " pdb=" CA VAL A 429 " pdb=" CB VAL A 429 " ideal model delta sigma weight residual 112.22 105.86 6.36 1.38e+00 5.25e-01 2.12e+01 angle pdb=" C VAL D 429 " pdb=" CA VAL D 429 " pdb=" CB VAL D 429 " ideal model delta sigma weight residual 112.22 105.86 6.36 1.38e+00 5.25e-01 2.12e+01 angle pdb=" C VAL E 429 " pdb=" CA VAL E 429 " pdb=" CB VAL E 429 " ideal model delta sigma weight residual 112.22 105.87 6.35 1.38e+00 5.25e-01 2.12e+01 ... (remaining 37057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 14736 16.82 - 33.65: 1143 33.65 - 50.47: 195 50.47 - 67.29: 42 67.29 - 84.11: 18 Dihedral angle restraints: 16134 sinusoidal: 6096 harmonic: 10038 Sorted by residual: dihedral pdb=" CA CYS E 273 " pdb=" C CYS E 273 " pdb=" N VAL E 274 " pdb=" CA VAL E 274 " ideal model delta harmonic sigma weight residual 180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA CYS C 273 " pdb=" C CYS C 273 " pdb=" N VAL C 274 " pdb=" CA VAL C 274 " ideal model delta harmonic sigma weight residual -180.00 -153.94 -26.06 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA CYS F 273 " pdb=" C CYS F 273 " pdb=" N VAL F 274 " pdb=" CA VAL F 274 " ideal model delta harmonic sigma weight residual -180.00 -153.95 -26.05 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 16131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3841 0.077 - 0.154: 245 0.154 - 0.231: 20 0.231 - 0.308: 11 0.308 - 0.385: 17 Chirality restraints: 4134 Sorted by residual: chirality pdb=" CA PHE E 127 " pdb=" N PHE E 127 " pdb=" C PHE E 127 " pdb=" CB PHE E 127 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA PHE F 127 " pdb=" N PHE F 127 " pdb=" C PHE F 127 " pdb=" CB PHE F 127 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA PHE B 127 " pdb=" N PHE B 127 " pdb=" C PHE B 127 " pdb=" CB PHE B 127 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 4131 not shown) Planarity restraints: 4716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 148 " -0.050 5.00e-02 4.00e+02 7.55e-02 9.12e+00 pdb=" N PRO C 149 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 148 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO A 149 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 148 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO F 149 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO F 149 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 149 " 0.041 5.00e-02 4.00e+02 ... (remaining 4713 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7465 2.82 - 3.34: 24186 3.34 - 3.86: 41801 3.86 - 4.38: 46972 4.38 - 4.90: 85366 Nonbonded interactions: 205790 Sorted by model distance: nonbonded pdb=" OD1 ASN A 41 " pdb=" OE2 GLU B 72 " model vdw 2.297 3.040 nonbonded pdb=" OE2 GLU E 72 " pdb=" OD1 ASN F 41 " model vdw 2.302 3.040 nonbonded pdb=" OE2 GLU C 72 " pdb=" OD1 ASN D 41 " model vdw 2.307 3.040 nonbonded pdb=" OD1 ASN C 41 " pdb=" OE2 GLU D 72 " model vdw 2.322 3.040 nonbonded pdb=" OD1 ASN E 41 " pdb=" OE2 GLU F 72 " model vdw 2.324 3.040 ... (remaining 205785 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 22.920 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.090 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:8.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 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 : 0.005 0.064 27264 Z= 0.285 Angle : 0.648 8.092 37062 Z= 0.400 Chirality : 0.048 0.385 4134 Planarity : 0.006 0.076 4716 Dihedral : 12.920 84.114 9606 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.46 % Allowed : 0.80 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.15), residues: 3318 helix: 1.68 (0.12), residues: 1998 sheet: 1.40 (0.44), residues: 156 loop : -0.90 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 38 TYR 0.012 0.001 TYR E 79 PHE 0.027 0.002 PHE B 127 TRP 0.013 0.002 TRP C 217 HIS 0.004 0.001 HIS E 69 Details of bonding type rmsd covalent geometry : bond 0.00471 (27264) covalent geometry : angle 0.64838 (37062) hydrogen bonds : bond 0.18575 ( 1584) hydrogen bonds : angle 5.81317 ( 4644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 634 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7456 (m-30) cc_final: 0.7254 (m-30) REVERT: B 217 TRP cc_start: 0.8620 (p-90) cc_final: 0.8207 (p90) REVERT: B 251 ASN cc_start: 0.8015 (m-40) cc_final: 0.7799 (m110) REVERT: B 440 GLU cc_start: 0.6817 (mp0) cc_final: 0.6572 (mp0) REVERT: B 491 LEU cc_start: 0.8152 (mt) cc_final: 0.7942 (mm) REVERT: B 498 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7278 (mtm180) REVERT: C 137 ARG cc_start: 0.7998 (ttm110) cc_final: 0.7793 (ttp-110) REVERT: C 217 TRP cc_start: 0.8772 (p-90) cc_final: 0.8265 (p90) REVERT: C 421 SER cc_start: 0.8384 (m) cc_final: 0.8087 (p) REVERT: C 422 LEU cc_start: 0.8503 (tp) cc_final: 0.8272 (tp) REVERT: C 469 PHE cc_start: 0.7712 (t80) cc_final: 0.7393 (t80) REVERT: C 486 SER cc_start: 0.8365 (t) cc_final: 0.8110 (p) REVERT: D 192 LEU cc_start: 0.8154 (tp) cc_final: 0.7911 (tt) REVERT: D 197 MET cc_start: 0.7708 (mmm) cc_final: 0.7461 (mmm) REVERT: D 217 TRP cc_start: 0.8708 (p-90) cc_final: 0.8345 (p90) REVERT: D 237 LEU cc_start: 0.8581 (tp) cc_final: 0.8353 (tt) REVERT: D 251 ASN cc_start: 0.8195 (m-40) cc_final: 0.7965 (m-40) REVERT: D 268 ASP cc_start: 0.6992 (t0) cc_final: 0.6662 (t0) REVERT: D 337 ARG cc_start: 0.5540 (mtt-85) cc_final: 0.5301 (mtt-85) REVERT: D 421 SER cc_start: 0.8321 (m) cc_final: 0.8087 (p) REVERT: D 469 PHE cc_start: 0.7631 (t80) cc_final: 0.7362 (t80) REVERT: E 71 MET cc_start: 0.7465 (mtp) cc_final: 0.7249 (mtp) REVERT: E 121 ASN cc_start: 0.8210 (m110) cc_final: 0.7988 (m-40) REVERT: E 154 ARG cc_start: 0.8246 (mtp180) cc_final: 0.8027 (mtm-85) REVERT: E 217 TRP cc_start: 0.8602 (p-90) cc_final: 0.8289 (p90) REVERT: E 230 MET cc_start: 0.8284 (mtp) cc_final: 0.8047 (mtp) REVERT: E 440 GLU cc_start: 0.6765 (mp0) cc_final: 0.6533 (mp0) REVERT: E 446 LYS cc_start: 0.8128 (tppp) cc_final: 0.7762 (tppp) REVERT: E 491 LEU cc_start: 0.8137 (mt) cc_final: 0.7363 (mm) REVERT: E 495 ASP cc_start: 0.6894 (m-30) cc_final: 0.6613 (m-30) REVERT: F 10 ILE cc_start: 0.8399 (mt) cc_final: 0.8141 (mp) REVERT: F 134 ASP cc_start: 0.7392 (m-30) cc_final: 0.7150 (m-30) REVERT: I 71 THR cc_start: 0.8017 (m) cc_final: 0.7796 (m) outliers start: 12 outliers final: 0 residues processed: 644 average time/residue: 0.7984 time to fit residues: 578.0320 Evaluate side-chains 607 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 607 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 53 GLN A 121 ASN A 342 ASN B 53 GLN B 342 ASN B 365 ASN C 11 ASN C 49 GLN C 53 GLN C 342 ASN C 365 ASN D 53 GLN E 11 ASN E 53 GLN E 350 GLN E 365 ASN F 11 ASN F 41 ASN F 49 GLN F 53 GLN F 342 ASN I 75 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.144790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.122039 restraints weight = 33660.340| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.69 r_work: 0.3393 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 27264 Z= 0.123 Angle : 0.482 5.655 37062 Z= 0.262 Chirality : 0.036 0.138 4134 Planarity : 0.005 0.059 4716 Dihedral : 3.672 16.438 3732 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.30 % Allowed : 8.26 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.08 (0.15), residues: 3318 helix: 2.24 (0.12), residues: 2100 sheet: 1.52 (0.45), residues: 168 loop : -0.45 (0.21), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 498 TYR 0.018 0.001 TYR D 292 PHE 0.016 0.001 PHE B 127 TRP 0.010 0.001 TRP C 262 HIS 0.005 0.001 HIS F 126 Details of bonding type rmsd covalent geometry : bond 0.00238 (27264) covalent geometry : angle 0.48204 (37062) hydrogen bonds : bond 0.05352 ( 1584) hydrogen bonds : angle 4.09990 ( 4644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 601 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7983 (m-30) cc_final: 0.7702 (m-30) REVERT: A 232 LYS cc_start: 0.8436 (mtpm) cc_final: 0.8124 (mtpt) REVERT: A 286 PHE cc_start: 0.8377 (p90) cc_final: 0.8131 (p90) REVERT: A 365 ASN cc_start: 0.8489 (t0) cc_final: 0.8242 (t0) REVERT: A 415 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7063 (ttp80) REVERT: A 498 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7725 (mtm-85) REVERT: B 53 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.6939 (tm130) REVERT: B 217 TRP cc_start: 0.8785 (p-90) cc_final: 0.8466 (p90) REVERT: B 354 ASP cc_start: 0.7318 (t0) cc_final: 0.7088 (t0) REVERT: B 440 GLU cc_start: 0.7576 (mp0) cc_final: 0.7329 (mp0) REVERT: C 38 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8124 (mtt90) REVERT: C 421 SER cc_start: 0.8461 (m) cc_final: 0.8136 (p) REVERT: C 459 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8131 (t) REVERT: C 469 PHE cc_start: 0.7822 (t80) cc_final: 0.7518 (t80) REVERT: C 498 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.7649 (mtm-85) REVERT: D 172 LEU cc_start: 0.8322 (tp) cc_final: 0.8114 (tt) REVERT: D 192 LEU cc_start: 0.8395 (tp) cc_final: 0.8157 (tt) REVERT: D 217 TRP cc_start: 0.8821 (p-90) cc_final: 0.8494 (p90) REVERT: D 369 LEU cc_start: 0.8411 (mp) cc_final: 0.8210 (mm) REVERT: D 415 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7363 (ttp80) REVERT: D 421 SER cc_start: 0.8493 (m) cc_final: 0.8169 (p) REVERT: D 469 PHE cc_start: 0.7639 (t80) cc_final: 0.7287 (t80) REVERT: D 473 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6848 (tm-30) REVERT: D 498 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.7544 (mtm-85) REVERT: E 148 GLN cc_start: 0.7912 (pm20) cc_final: 0.7508 (pm20) REVERT: E 154 ARG cc_start: 0.8303 (mtp180) cc_final: 0.8099 (mtm-85) REVERT: E 440 GLU cc_start: 0.7515 (mp0) cc_final: 0.7293 (mp0) REVERT: E 446 LYS cc_start: 0.8494 (tppp) cc_final: 0.8261 (tppp) REVERT: E 491 LEU cc_start: 0.8498 (mt) cc_final: 0.8029 (mm) REVERT: E 495 ASP cc_start: 0.8060 (m-30) cc_final: 0.7827 (m-30) REVERT: F 117 HIS cc_start: 0.8170 (t70) cc_final: 0.7806 (t70) REVERT: F 415 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7267 (ttp80) REVERT: F 498 ARG cc_start: 0.8181 (mtm180) cc_final: 0.7840 (mtm180) REVERT: I 71 THR cc_start: 0.8325 (m) cc_final: 0.8035 (m) outliers start: 34 outliers final: 17 residues processed: 607 average time/residue: 0.8080 time to fit residues: 550.2953 Evaluate side-chains 620 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 597 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 464 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 68 optimal weight: 4.9990 chunk 333 optimal weight: 0.0000 chunk 227 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 173 optimal weight: 0.6980 chunk 330 optimal weight: 10.0000 chunk 249 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 49 GLN A 53 GLN A 121 ASN A 342 ASN B 11 ASN B 41 ASN B 53 GLN B 342 ASN C 11 ASN C 49 GLN C 53 GLN C 121 ASN D 49 GLN D 53 GLN E 53 GLN E 342 ASN F 41 ASN F 49 GLN F 53 GLN F 121 ASN F 126 HIS F 342 ASN K 75 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.140127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.117438 restraints weight = 33439.184| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.70 r_work: 0.3311 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27264 Z= 0.196 Angle : 0.541 6.943 37062 Z= 0.288 Chirality : 0.040 0.182 4134 Planarity : 0.005 0.054 4716 Dihedral : 3.811 15.556 3732 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.61 % Allowed : 10.13 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.15), residues: 3318 helix: 2.13 (0.11), residues: 2136 sheet: 2.25 (0.46), residues: 156 loop : -0.59 (0.21), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 161 TYR 0.019 0.002 TYR D 292 PHE 0.019 0.002 PHE A 106 TRP 0.013 0.001 TRP C 262 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00462 (27264) covalent geometry : angle 0.54099 (37062) hydrogen bonds : bond 0.07368 ( 1584) hydrogen bonds : angle 4.12727 ( 4644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 608 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 PHE cc_start: 0.8389 (p90) cc_final: 0.8183 (p90) REVERT: A 365 ASN cc_start: 0.8502 (t0) cc_final: 0.8224 (t0) REVERT: A 415 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7505 (ttp80) REVERT: A 498 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.7836 (mtm-85) REVERT: B 175 LYS cc_start: 0.8428 (mtmm) cc_final: 0.8198 (mtpt) REVERT: B 217 TRP cc_start: 0.8758 (p-90) cc_final: 0.8499 (p90) REVERT: B 440 GLU cc_start: 0.7566 (mp0) cc_final: 0.7328 (mp0) REVERT: B 495 ASP cc_start: 0.8015 (m-30) cc_final: 0.7772 (m-30) REVERT: C 38 ARG cc_start: 0.8423 (mtt90) cc_final: 0.8166 (mtt90) REVERT: C 397 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: C 459 VAL cc_start: 0.8460 (OUTLIER) cc_final: 0.8194 (t) REVERT: D 172 LEU cc_start: 0.8306 (tp) cc_final: 0.8104 (tt) REVERT: D 217 TRP cc_start: 0.8831 (p-90) cc_final: 0.8472 (p90) REVERT: D 415 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7833 (ttp80) REVERT: D 421 SER cc_start: 0.8582 (m) cc_final: 0.8255 (p) REVERT: D 498 ARG cc_start: 0.8340 (mtm-85) cc_final: 0.7427 (mtm-85) REVERT: E 148 GLN cc_start: 0.8001 (pm20) cc_final: 0.7501 (pm20) REVERT: E 186 ASN cc_start: 0.8177 (m-40) cc_final: 0.7967 (m-40) REVERT: E 440 GLU cc_start: 0.7526 (mp0) cc_final: 0.7292 (mp0) REVERT: E 446 LYS cc_start: 0.8565 (tppp) cc_final: 0.8209 (tppp) REVERT: E 491 LEU cc_start: 0.8528 (mt) cc_final: 0.8082 (mm) REVERT: E 495 ASP cc_start: 0.8126 (m-30) cc_final: 0.7870 (m-30) REVERT: F 134 ASP cc_start: 0.7980 (m-30) cc_final: 0.7749 (m-30) REVERT: F 286 PHE cc_start: 0.8302 (p90) cc_final: 0.8075 (p90) REVERT: F 415 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7500 (ttp80) REVERT: F 498 ARG cc_start: 0.8248 (mtm180) cc_final: 0.7860 (mtm180) REVERT: K 4 LEU cc_start: 0.8309 (tp) cc_final: 0.8104 (tp) outliers start: 42 outliers final: 28 residues processed: 614 average time/residue: 0.8211 time to fit residues: 564.7647 Evaluate side-chains 638 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 605 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 464 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 80 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 291 optimal weight: 0.7980 chunk 181 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 53 GLN A 121 ASN A 342 ASN B 11 ASN B 41 ASN B 53 GLN C 50 GLN C 53 GLN C 121 ASN C 342 ASN D 11 ASN D 49 GLN D 53 GLN E 41 ASN E 53 GLN E 342 ASN F 41 ASN F 49 GLN F 53 GLN F 126 HIS F 342 ASN I 75 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.143013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120479 restraints weight = 33305.068| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.69 r_work: 0.3360 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 27264 Z= 0.127 Angle : 0.471 6.785 37062 Z= 0.251 Chirality : 0.037 0.155 4134 Planarity : 0.004 0.048 4716 Dihedral : 3.678 15.067 3732 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.80 % Allowed : 11.05 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.27 (0.15), residues: 3318 helix: 2.32 (0.11), residues: 2136 sheet: 2.47 (0.47), residues: 156 loop : -0.43 (0.21), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 498 TYR 0.020 0.001 TYR D 292 PHE 0.015 0.001 PHE A 106 TRP 0.008 0.001 TRP D 135 HIS 0.004 0.001 HIS F 126 Details of bonding type rmsd covalent geometry : bond 0.00273 (27264) covalent geometry : angle 0.47102 (37062) hydrogen bonds : bond 0.05526 ( 1584) hydrogen bonds : angle 3.88976 ( 4644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 605 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.8014 (m-30) cc_final: 0.7805 (m-30) REVERT: A 365 ASN cc_start: 0.8504 (t0) cc_final: 0.8224 (t0) REVERT: A 415 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7166 (ttp80) REVERT: A 498 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.7853 (mtm-85) REVERT: B 175 LYS cc_start: 0.8426 (mtmm) cc_final: 0.8222 (mtmm) REVERT: B 217 TRP cc_start: 0.8756 (p-90) cc_final: 0.8510 (p90) REVERT: B 440 GLU cc_start: 0.7564 (mp0) cc_final: 0.7313 (mp0) REVERT: B 495 ASP cc_start: 0.8040 (m-30) cc_final: 0.7810 (m-30) REVERT: C 38 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8150 (mtt90) REVERT: C 118 ASP cc_start: 0.7649 (m-30) cc_final: 0.7402 (t0) REVERT: C 397 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.7044 (mt-10) REVERT: C 459 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.8070 (t) REVERT: C 498 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.7629 (mtm-85) REVERT: D 172 LEU cc_start: 0.8255 (tp) cc_final: 0.8053 (tt) REVERT: D 217 TRP cc_start: 0.8828 (p-90) cc_final: 0.8482 (p90) REVERT: D 415 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7604 (ttp80) REVERT: D 421 SER cc_start: 0.8573 (m) cc_final: 0.8237 (p) REVERT: D 498 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.7545 (mtm-85) REVERT: E 118 ASP cc_start: 0.7483 (m-30) cc_final: 0.7213 (t0) REVERT: E 148 GLN cc_start: 0.7981 (pm20) cc_final: 0.7513 (pm20) REVERT: E 440 GLU cc_start: 0.7554 (mp0) cc_final: 0.7326 (mp0) REVERT: E 446 LYS cc_start: 0.8490 (tppp) cc_final: 0.8126 (tppp) REVERT: E 491 LEU cc_start: 0.8492 (mt) cc_final: 0.8087 (mm) REVERT: E 495 ASP cc_start: 0.8177 (m-30) cc_final: 0.7926 (m-30) REVERT: F 117 HIS cc_start: 0.8375 (t-90) cc_final: 0.7977 (t70) REVERT: F 134 ASP cc_start: 0.7965 (m-30) cc_final: 0.7679 (m-30) REVERT: F 415 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7344 (ttp80) REVERT: F 498 ARG cc_start: 0.8208 (mtm180) cc_final: 0.7845 (mtm180) outliers start: 47 outliers final: 25 residues processed: 614 average time/residue: 0.8084 time to fit residues: 556.1354 Evaluate side-chains 633 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 602 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 461 LYS Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 464 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 289 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 309 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 267 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 28 optimal weight: 0.0020 chunk 261 optimal weight: 0.9980 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 49 GLN A 53 GLN A 121 ASN B 41 ASN B 53 GLN B 342 ASN C 11 ASN C 41 ASN C 49 GLN C 121 ASN C 342 ASN D 11 ASN D 49 GLN D 53 GLN E 41 ASN E 53 GLN E 342 ASN F 11 ASN F 41 ASN F 53 GLN F 121 ASN F 126 HIS F 342 ASN I 75 ASN K 75 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.141346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118835 restraints weight = 33362.669| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.69 r_work: 0.3339 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 27264 Z= 0.159 Angle : 0.499 6.482 37062 Z= 0.264 Chirality : 0.038 0.167 4134 Planarity : 0.004 0.046 4716 Dihedral : 3.705 15.484 3732 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.29 % Allowed : 11.47 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.28 (0.16), residues: 3318 helix: 2.32 (0.11), residues: 2136 sheet: 2.21 (0.47), residues: 162 loop : -0.39 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 498 TYR 0.024 0.001 TYR D 292 PHE 0.019 0.002 PHE A 106 TRP 0.010 0.001 TRP D 135 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00366 (27264) covalent geometry : angle 0.49900 (37062) hydrogen bonds : bond 0.06374 ( 1584) hydrogen bonds : angle 3.93394 ( 4644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 608 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 PHE cc_start: 0.8378 (p90) cc_final: 0.8145 (p90) REVERT: A 365 ASN cc_start: 0.8543 (t0) cc_final: 0.8260 (t0) REVERT: A 415 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7251 (ttp80) REVERT: A 471 LEU cc_start: 0.7934 (mt) cc_final: 0.7640 (mt) REVERT: A 498 ARG cc_start: 0.8377 (mtm-85) cc_final: 0.7898 (mtm-85) REVERT: B 217 TRP cc_start: 0.8740 (p-90) cc_final: 0.8490 (p90) REVERT: B 440 GLU cc_start: 0.7579 (mp0) cc_final: 0.7321 (mp0) REVERT: B 495 ASP cc_start: 0.8046 (m-30) cc_final: 0.7811 (m-30) REVERT: C 118 ASP cc_start: 0.7680 (m-30) cc_final: 0.7387 (t0) REVERT: C 459 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8083 (t) REVERT: D 217 TRP cc_start: 0.8827 (p-90) cc_final: 0.8433 (p90) REVERT: D 277 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7603 (mp) REVERT: D 415 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7733 (ttp80) REVERT: D 421 SER cc_start: 0.8597 (m) cc_final: 0.8251 (p) REVERT: D 469 PHE cc_start: 0.7435 (t80) cc_final: 0.7171 (t80) REVERT: E 71 MET cc_start: 0.7892 (mtp) cc_final: 0.7652 (mtt) REVERT: E 148 GLN cc_start: 0.7953 (pm20) cc_final: 0.7497 (pm20) REVERT: E 440 GLU cc_start: 0.7548 (mp0) cc_final: 0.7304 (mp0) REVERT: E 446 LYS cc_start: 0.8538 (tppp) cc_final: 0.8168 (tppp) REVERT: E 491 LEU cc_start: 0.8504 (mt) cc_final: 0.8091 (mm) REVERT: E 495 ASP cc_start: 0.8126 (m-30) cc_final: 0.7868 (m-30) REVERT: F 134 ASP cc_start: 0.7986 (m-30) cc_final: 0.7752 (m-30) REVERT: F 286 PHE cc_start: 0.8308 (p90) cc_final: 0.8100 (p90) REVERT: F 415 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7427 (ttp80) REVERT: F 498 ARG cc_start: 0.8261 (mtm180) cc_final: 0.7865 (mtm180) REVERT: I 71 THR cc_start: 0.8315 (m) cc_final: 0.7969 (m) outliers start: 60 outliers final: 32 residues processed: 622 average time/residue: 0.8001 time to fit residues: 559.0376 Evaluate side-chains 640 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 603 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 461 LYS Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain L residue 4 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 189 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 203 optimal weight: 0.0970 chunk 188 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 316 optimal weight: 20.0000 chunk 294 optimal weight: 4.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 53 GLN A 121 ASN B 41 ASN B 53 GLN B 342 ASN C 11 ASN C 41 ASN C 53 GLN C 121 ASN D 11 ASN D 49 GLN D 53 GLN E 41 ASN E 53 GLN E 342 ASN F 11 ASN F 41 ASN F 53 GLN F 121 ASN F 126 HIS F 342 ASN I 75 ASN K 75 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.139226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116763 restraints weight = 33342.658| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.69 r_work: 0.3292 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 27264 Z= 0.212 Angle : 0.556 8.045 37062 Z= 0.294 Chirality : 0.041 0.191 4134 Planarity : 0.005 0.049 4716 Dihedral : 3.892 15.240 3732 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.41 % Allowed : 11.70 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.11 (0.15), residues: 3318 helix: 2.17 (0.11), residues: 2136 sheet: 2.31 (0.47), residues: 162 loop : -0.42 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 498 TYR 0.014 0.002 TYR A 292 PHE 0.021 0.002 PHE A 106 TRP 0.011 0.001 TRP C 135 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00508 (27264) covalent geometry : angle 0.55555 (37062) hydrogen bonds : bond 0.07590 ( 1584) hydrogen bonds : angle 4.09339 ( 4644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 616 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8252 (p90) REVERT: A 415 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7393 (ttp80) REVERT: A 471 LEU cc_start: 0.7984 (mt) cc_final: 0.7731 (mt) REVERT: A 498 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.7920 (mtm-85) REVERT: B 217 TRP cc_start: 0.8755 (p-90) cc_final: 0.8496 (p90) REVERT: B 440 GLU cc_start: 0.7584 (mp0) cc_final: 0.7355 (mp0) REVERT: B 495 ASP cc_start: 0.8017 (m-30) cc_final: 0.7762 (m-30) REVERT: C 118 ASP cc_start: 0.7684 (m-30) cc_final: 0.7386 (t0) REVERT: C 446 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8073 (mtpp) REVERT: C 459 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8105 (t) REVERT: D 118 ASP cc_start: 0.7648 (m-30) cc_final: 0.7302 (t0) REVERT: D 217 TRP cc_start: 0.8847 (p-90) cc_final: 0.8431 (p90) REVERT: D 415 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7880 (ttp80) REVERT: D 421 SER cc_start: 0.8594 (m) cc_final: 0.8251 (p) REVERT: D 469 PHE cc_start: 0.7496 (t80) cc_final: 0.7242 (t80) REVERT: D 498 ARG cc_start: 0.8390 (mtm-85) cc_final: 0.7541 (mtm-85) REVERT: E 118 ASP cc_start: 0.7479 (m-30) cc_final: 0.7251 (t0) REVERT: E 148 GLN cc_start: 0.7941 (pm20) cc_final: 0.7505 (pm20) REVERT: E 440 GLU cc_start: 0.7535 (mp0) cc_final: 0.7326 (mp0) REVERT: E 446 LYS cc_start: 0.8574 (tppp) cc_final: 0.8184 (tppp) REVERT: E 491 LEU cc_start: 0.8525 (mt) cc_final: 0.8133 (mm) REVERT: E 495 ASP cc_start: 0.8116 (m-30) cc_final: 0.7885 (m-30) REVERT: F 198 ARG cc_start: 0.7789 (mtp85) cc_final: 0.7486 (mtp85) REVERT: F 415 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7549 (ttp80) REVERT: F 498 ARG cc_start: 0.8288 (mtm180) cc_final: 0.7897 (mtm180) outliers start: 63 outliers final: 33 residues processed: 634 average time/residue: 0.8027 time to fit residues: 569.9768 Evaluate side-chains 647 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 608 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 494 TRP Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 494 TRP Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 501 MET Chi-restraints excluded: chain L residue 4 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 328 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 155 optimal weight: 0.0270 chunk 126 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 216 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 288 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 53 GLN A 121 ASN A 227 HIS B 41 ASN B 53 GLN B 342 ASN B 350 GLN C 11 ASN C 41 ASN C 49 GLN C 121 ASN D 11 ASN D 49 GLN D 53 GLN E 41 ASN E 53 GLN F 11 ASN F 41 ASN F 53 GLN F 121 ASN F 126 HIS F 342 ASN I 75 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116950 restraints weight = 33272.012| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.70 r_work: 0.3316 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 27264 Z= 0.197 Angle : 0.545 10.324 37062 Z= 0.288 Chirality : 0.040 0.186 4134 Planarity : 0.005 0.051 4716 Dihedral : 3.896 17.751 3732 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.41 % Allowed : 12.04 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.10 (0.15), residues: 3318 helix: 2.14 (0.11), residues: 2136 sheet: 2.41 (0.47), residues: 162 loop : -0.41 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 398 TYR 0.014 0.002 TYR A 292 PHE 0.021 0.002 PHE A 106 TRP 0.011 0.001 TRP A 217 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00471 (27264) covalent geometry : angle 0.54517 (37062) hydrogen bonds : bond 0.07199 ( 1584) hydrogen bonds : angle 4.05409 ( 4644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 614 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7303 (ttp80) REVERT: A 471 LEU cc_start: 0.7976 (mt) cc_final: 0.7724 (mt) REVERT: A 498 ARG cc_start: 0.8410 (mtm-85) cc_final: 0.7933 (mtm-85) REVERT: B 217 TRP cc_start: 0.8743 (p-90) cc_final: 0.8488 (p90) REVERT: B 440 GLU cc_start: 0.7554 (mp0) cc_final: 0.7338 (mp0) REVERT: B 495 ASP cc_start: 0.8026 (m-30) cc_final: 0.7769 (m-30) REVERT: C 118 ASP cc_start: 0.7691 (m-30) cc_final: 0.7348 (t0) REVERT: C 446 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7881 (mtpp) REVERT: C 459 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8075 (t) REVERT: D 217 TRP cc_start: 0.8830 (p-90) cc_final: 0.8411 (p90) REVERT: D 415 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7799 (ttp80) REVERT: D 469 PHE cc_start: 0.7496 (t80) cc_final: 0.7236 (t80) REVERT: E 118 ASP cc_start: 0.7486 (m-30) cc_final: 0.7152 (t0) REVERT: E 148 GLN cc_start: 0.7966 (pm20) cc_final: 0.7521 (pm20) REVERT: E 440 GLU cc_start: 0.7527 (mp0) cc_final: 0.7320 (mp0) REVERT: E 446 LYS cc_start: 0.8569 (tppp) cc_final: 0.8176 (tppp) REVERT: E 491 LEU cc_start: 0.8498 (mt) cc_final: 0.8143 (mm) REVERT: E 495 ASP cc_start: 0.8103 (m-30) cc_final: 0.7894 (m-30) REVERT: F 134 ASP cc_start: 0.7926 (m-30) cc_final: 0.7678 (m-30) REVERT: F 198 ARG cc_start: 0.7805 (mtp85) cc_final: 0.7504 (mtp85) REVERT: F 415 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7499 (ttp80) REVERT: F 498 ARG cc_start: 0.8306 (mtm180) cc_final: 0.7907 (mtm180) outliers start: 63 outliers final: 31 residues processed: 631 average time/residue: 0.7978 time to fit residues: 564.1273 Evaluate side-chains 645 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 609 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 494 TRP Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 494 TRP Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain F residue 464 SER Chi-restraints excluded: chain L residue 4 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 130 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 249 optimal weight: 0.9990 chunk 67 optimal weight: 0.0060 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 53 GLN A 121 ASN ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 53 GLN B 342 ASN B 350 GLN C 11 ASN C 41 ASN C 121 ASN D 11 ASN D 49 GLN D 53 GLN E 41 ASN E 53 GLN F 11 ASN F 41 ASN F 53 GLN F 121 ASN F 126 HIS F 342 ASN I 75 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.140588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118217 restraints weight = 33535.048| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.69 r_work: 0.3330 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 27264 Z= 0.158 Angle : 0.511 10.005 37062 Z= 0.270 Chirality : 0.038 0.171 4134 Planarity : 0.005 0.051 4716 Dihedral : 3.806 17.469 3732 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.91 % Allowed : 12.81 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.25 (0.15), residues: 3318 helix: 2.26 (0.11), residues: 2136 sheet: 2.52 (0.47), residues: 162 loop : -0.35 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 38 TYR 0.012 0.001 TYR D 292 PHE 0.019 0.002 PHE A 106 TRP 0.012 0.001 TRP A 217 HIS 0.005 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00364 (27264) covalent geometry : angle 0.51085 (37062) hydrogen bonds : bond 0.06393 ( 1584) hydrogen bonds : angle 3.94708 ( 4644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 604 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7467 (mpp-170) REVERT: A 415 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7261 (ttp80) REVERT: A 498 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.7930 (mtm-85) REVERT: B 217 TRP cc_start: 0.8745 (p-90) cc_final: 0.8491 (p90) REVERT: B 440 GLU cc_start: 0.7545 (mp0) cc_final: 0.7325 (mp0) REVERT: B 495 ASP cc_start: 0.8025 (m-30) cc_final: 0.7770 (m-30) REVERT: C 118 ASP cc_start: 0.7684 (m-30) cc_final: 0.7344 (t0) REVERT: C 265 GLU cc_start: 0.7922 (tt0) cc_final: 0.7584 (tt0) REVERT: C 459 VAL cc_start: 0.8297 (OUTLIER) cc_final: 0.8043 (t) REVERT: D 217 TRP cc_start: 0.8825 (p-90) cc_final: 0.8406 (p90) REVERT: D 265 GLU cc_start: 0.7867 (tt0) cc_final: 0.7523 (tt0) REVERT: D 415 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7684 (ttp80) REVERT: D 469 PHE cc_start: 0.7450 (t80) cc_final: 0.7211 (t80) REVERT: D 498 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.7523 (mtm-85) REVERT: E 118 ASP cc_start: 0.7486 (m-30) cc_final: 0.7153 (t0) REVERT: E 148 GLN cc_start: 0.7942 (pm20) cc_final: 0.7512 (pm20) REVERT: E 440 GLU cc_start: 0.7504 (mp0) cc_final: 0.7299 (mp0) REVERT: E 446 LYS cc_start: 0.8538 (tppp) cc_final: 0.8172 (tppp) REVERT: E 491 LEU cc_start: 0.8484 (mt) cc_final: 0.8151 (mm) REVERT: F 198 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7506 (mtp85) REVERT: F 415 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7430 (ttp80) REVERT: F 498 ARG cc_start: 0.8302 (mtm180) cc_final: 0.7913 (mtm180) outliers start: 50 outliers final: 34 residues processed: 618 average time/residue: 0.7941 time to fit residues: 550.4256 Evaluate side-chains 638 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 599 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 494 TRP Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 494 TRP Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain L residue 4 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 72 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 14 optimal weight: 0.1980 chunk 112 optimal weight: 4.9990 chunk 280 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 267 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 251 optimal weight: 0.0670 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 53 GLN A 121 ASN ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 53 GLN B 350 GLN C 11 ASN C 41 ASN C 49 GLN C 121 ASN D 11 ASN D 49 GLN D 53 GLN D 126 HIS E 41 ASN E 53 GLN F 11 ASN F 41 ASN F 53 GLN F 121 ASN F 126 HIS F 342 ASN I 75 ASN K 75 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.140519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118206 restraints weight = 33406.855| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.69 r_work: 0.3330 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 27264 Z= 0.160 Angle : 0.517 10.900 37062 Z= 0.272 Chirality : 0.039 0.172 4134 Planarity : 0.005 0.051 4716 Dihedral : 3.791 18.033 3732 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.99 % Allowed : 13.19 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.29 (0.15), residues: 3318 helix: 2.28 (0.11), residues: 2136 sheet: 2.51 (0.47), residues: 162 loop : -0.33 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 38 TYR 0.012 0.001 TYR B 292 PHE 0.019 0.002 PHE A 106 TRP 0.013 0.001 TRP A 217 HIS 0.005 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00370 (27264) covalent geometry : angle 0.51661 (37062) hydrogen bonds : bond 0.06417 ( 1584) hydrogen bonds : angle 3.93293 ( 4644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 601 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7467 (mpp-170) REVERT: A 184 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7130 (tp30) REVERT: A 415 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7272 (ttp80) REVERT: A 498 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.7928 (mtm-85) REVERT: B 217 TRP cc_start: 0.8746 (p-90) cc_final: 0.8488 (p90) REVERT: B 440 GLU cc_start: 0.7540 (mp0) cc_final: 0.7314 (mp0) REVERT: B 495 ASP cc_start: 0.8022 (m-30) cc_final: 0.7768 (m-30) REVERT: C 118 ASP cc_start: 0.7699 (m-30) cc_final: 0.7361 (t0) REVERT: C 446 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8048 (mtpp) REVERT: C 459 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.8034 (t) REVERT: D 265 GLU cc_start: 0.7849 (tt0) cc_final: 0.7539 (tt0) REVERT: D 397 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: D 415 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7689 (ttp80) REVERT: D 469 PHE cc_start: 0.7445 (t80) cc_final: 0.7154 (t80) REVERT: D 498 ARG cc_start: 0.8318 (mtm-85) cc_final: 0.7515 (mtm-85) REVERT: E 148 GLN cc_start: 0.7936 (pm20) cc_final: 0.7512 (pm20) REVERT: E 446 LYS cc_start: 0.8533 (tppp) cc_final: 0.8165 (tppp) REVERT: F 137 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7938 (ttp-170) REVERT: F 198 ARG cc_start: 0.7800 (mtp85) cc_final: 0.7501 (mtp85) REVERT: F 415 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7425 (ttp80) REVERT: F 498 ARG cc_start: 0.8295 (mtm180) cc_final: 0.7910 (mtm180) outliers start: 52 outliers final: 37 residues processed: 615 average time/residue: 0.7379 time to fit residues: 509.7712 Evaluate side-chains 643 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 599 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 494 TRP Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 494 TRP Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain L residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 59 optimal weight: 0.0670 chunk 101 optimal weight: 1.9990 chunk 315 optimal weight: 30.0000 chunk 170 optimal weight: 4.9990 chunk 256 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 53 GLN A 121 ASN ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 53 GLN B 342 ASN B 350 GLN C 11 ASN C 49 GLN C 121 ASN C 355 ASN D 11 ASN D 49 GLN D 53 GLN D 126 HIS D 355 ASN E 41 ASN E 53 GLN F 11 ASN F 41 ASN F 53 GLN F 121 ASN F 126 HIS F 342 ASN I 75 ASN K 75 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.143270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.121081 restraints weight = 33474.521| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.68 r_work: 0.3383 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 27264 Z= 0.112 Angle : 0.465 9.258 37062 Z= 0.246 Chirality : 0.036 0.147 4134 Planarity : 0.004 0.050 4716 Dihedral : 3.640 16.528 3732 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.49 % Allowed : 13.76 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.51 (0.16), residues: 3318 helix: 2.44 (0.12), residues: 2142 sheet: 2.55 (0.47), residues: 162 loop : -0.19 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.015 0.001 TYR D 292 PHE 0.014 0.001 PHE D 106 TRP 0.013 0.001 TRP A 217 HIS 0.005 0.001 HIS F 126 Details of bonding type rmsd covalent geometry : bond 0.00230 (27264) covalent geometry : angle 0.46496 (37062) hydrogen bonds : bond 0.04954 ( 1584) hydrogen bonds : angle 3.77344 ( 4644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 601 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7515 (tpp-160) REVERT: A 184 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6945 (tp30) REVERT: A 415 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7049 (ttp80) REVERT: A 498 ARG cc_start: 0.8362 (mtm-85) cc_final: 0.7894 (mtm-85) REVERT: B 217 TRP cc_start: 0.8746 (p-90) cc_final: 0.8498 (p90) REVERT: B 382 TYR cc_start: 0.7284 (m-80) cc_final: 0.6938 (m-80) REVERT: B 440 GLU cc_start: 0.7511 (mp0) cc_final: 0.7299 (mp0) REVERT: B 495 ASP cc_start: 0.8039 (m-30) cc_final: 0.7792 (m-30) REVERT: C 118 ASP cc_start: 0.7771 (m-30) cc_final: 0.7425 (t0) REVERT: C 265 GLU cc_start: 0.7738 (tt0) cc_final: 0.7484 (tt0) REVERT: C 446 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8021 (mtpp) REVERT: C 459 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7926 (t) REVERT: C 498 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.7658 (mtm-85) REVERT: D 265 GLU cc_start: 0.7745 (tt0) cc_final: 0.7481 (tt0) REVERT: D 412 GLU cc_start: 0.8051 (tp30) cc_final: 0.7770 (tp30) REVERT: D 415 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7341 (ttp80) REVERT: D 469 PHE cc_start: 0.7389 (t80) cc_final: 0.7168 (t80) REVERT: D 498 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.7546 (mtm-85) REVERT: E 148 GLN cc_start: 0.7927 (pm20) cc_final: 0.7520 (pm20) REVERT: E 421 SER cc_start: 0.8618 (m) cc_final: 0.8204 (p) REVERT: E 446 LYS cc_start: 0.8455 (tppp) cc_final: 0.8098 (tppp) REVERT: F 198 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7590 (mtp85) REVERT: F 415 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7252 (ttp80) REVERT: F 498 ARG cc_start: 0.8266 (mtm180) cc_final: 0.7914 (mtm180) REVERT: I 71 THR cc_start: 0.8319 (m) cc_final: 0.7988 (m) REVERT: K 69 MET cc_start: 0.8128 (mtp) cc_final: 0.7919 (mtm) outliers start: 39 outliers final: 19 residues processed: 610 average time/residue: 0.6572 time to fit residues: 450.6306 Evaluate side-chains 623 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 598 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 494 TRP Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 415 ARG Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain F residue 415 ARG Chi-restraints excluded: chain F residue 453 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 235 optimal weight: 10.0000 chunk 221 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 256 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 41 ASN A 49 GLN A 53 GLN A 121 ASN ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN B 41 ASN B 53 GLN C 11 ASN C 121 ASN D 11 ASN D 49 GLN D 53 GLN E 41 ASN E 53 GLN E 342 ASN F 41 ASN F 49 GLN F 53 GLN F 121 ASN F 126 HIS F 342 ASN I 75 ASN K 75 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.140688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.118360 restraints weight = 33389.871| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.68 r_work: 0.3330 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27264 Z= 0.163 Angle : 0.519 8.917 37062 Z= 0.272 Chirality : 0.039 0.172 4134 Planarity : 0.005 0.050 4716 Dihedral : 3.751 18.873 3732 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.41 % Allowed : 13.99 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.43 (0.15), residues: 3318 helix: 2.36 (0.11), residues: 2142 sheet: 2.50 (0.47), residues: 162 loop : -0.18 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 38 TYR 0.012 0.001 TYR B 292 PHE 0.019 0.002 PHE A 106 TRP 0.014 0.001 TRP A 217 HIS 0.006 0.001 HIS E 117 Details of bonding type rmsd covalent geometry : bond 0.00381 (27264) covalent geometry : angle 0.51877 (37062) hydrogen bonds : bond 0.06400 ( 1584) hydrogen bonds : angle 3.90339 ( 4644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11776.87 seconds wall clock time: 199 minutes 42.36 seconds (11982.36 seconds total)