Starting phenix.real_space_refine on Fri Jul 3 22:24:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ozd_17305/07_2026/8ozd_17305.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozd_17305/07_2026/8ozd_17305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ozd_17305/07_2026/8ozd_17305.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ozd_17305/07_2026/8ozd_17305.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ozd_17305/07_2026/8ozd_17305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozd_17305/07_2026/8ozd_17305.map" model { file = "/net/cci-nas-00/data/ceres_data/8ozd_17305/07_2026/8ozd_17305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozd_17305/07_2026/8ozd_17305.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 609 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: 5 Type Number sf(0) Gaussians P 66 5.49 5 S 48 5.16 5 C 10118 2.51 5 N 2650 2.21 5 O 3119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16001 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain: "B" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "I" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "F" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 360 Classifications: {'RNA': 18} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "J" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain: "D" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Time building chain proxies: 3.12, per 1000 atoms: 0.19 Number of scatterers: 16001 At special positions: 0 Unit cell: (153.67, 128.26, 117.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 66 15.00 O 3119 8.00 N 2650 7.00 C 10118 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: 1.24 Conformation dependent library (CDL) restraints added in 634.4 milliseconds 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3396 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 20 sheets defined 40.1% alpha, 17.5% beta 11 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.774A pdb=" N GLU A 50 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 removed outlier: 3.505A pdb=" N LYS A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.252A pdb=" N ARG A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 219 through 224 removed outlier: 4.101A pdb=" N PHE A 223 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 224 " --> pdb=" O TYR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 3.700A pdb=" N GLU A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.530A pdb=" N ILE A 246 " --> pdb=" O PRO A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.689A pdb=" N ILE A 265 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 367 removed outlier: 4.348A pdb=" N ASN A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 384 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 46 through 61 removed outlier: 3.953A pdb=" N LYS B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 106 removed outlier: 3.669A pdb=" N ILE B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 132 removed outlier: 3.949A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.670A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.603A pdb=" N LEU B 214 " --> pdb=" O PHE B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.884A pdb=" N ASP B 233 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.858A pdb=" N GLN B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.795A pdb=" N TRP B 370 " --> pdb=" O ASN B 366 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 451 through 463 removed outlier: 4.044A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 491 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'C' and resid 14 through 29 Processing helix chain 'C' and resid 44 through 56 removed outlier: 3.774A pdb=" N GLU C 50 " --> pdb=" O TRP C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 89 removed outlier: 3.505A pdb=" N LYS C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 114 removed outlier: 4.251A pdb=" N ARG C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 138 Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 219 through 224 removed outlier: 4.100A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR C 224 " --> pdb=" O TYR C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 233 removed outlier: 3.700A pdb=" N GLU C 231 " --> pdb=" O PRO C 228 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR C 232 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR C 233 " --> pdb=" O THR C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 242 through 249 removed outlier: 3.531A pdb=" N ILE C 246 " --> pdb=" O PRO C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 280 removed outlier: 3.690A pdb=" N ILE C 265 " --> pdb=" O CYS C 261 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 302 No H-bonds generated for 'chain 'C' and resid 300 through 302' Processing helix chain 'C' and resid 353 through 367 removed outlier: 4.348A pdb=" N ASN C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 384 Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 22 through 31 Processing helix chain 'D' and resid 46 through 61 removed outlier: 3.953A pdb=" N LYS D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 83 Processing helix chain 'D' and resid 97 through 106 removed outlier: 3.668A pdb=" N ILE D 101 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 132 removed outlier: 3.950A pdb=" N LYS D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 150 removed outlier: 3.671A pdb=" N TYR D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 205 through 214 removed outlier: 3.604A pdb=" N LEU D 214 " --> pdb=" O PHE D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 234 removed outlier: 3.884A pdb=" N ASP D 233 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 248 through 264 Processing helix chain 'D' and resid 331 through 351 removed outlier: 3.858A pdb=" N GLN D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 377 removed outlier: 3.795A pdb=" N TRP D 370 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 451 through 463 removed outlier: 4.045A pdb=" N LEU D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 491 Processing helix chain 'D' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 removed outlier: 5.421A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LYS A 4 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N SER A 8 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE A 118 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 278 through 279 removed outlier: 7.342A pdb=" N CYS B 279 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N HIS B 360 " --> pdb=" O CYS B 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 278 through 279 removed outlier: 7.342A pdb=" N CYS B 279 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N HIS B 360 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL B 412 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLU B 3 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LYS A 411 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N TYR B 6 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASN A 413 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 414 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LYS A 167 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 180 removed outlier: 4.817A pdb=" N SER A 177 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE A 402 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A 401 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 283 through 286 Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.610A pdb=" N GLY A 312 " --> pdb=" O TRP A 319 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP A 319 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 19 through 20 removed outlier: 3.836A pdb=" N ILE B 12 " --> pdb=" O CYS B 20 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 92 through 95 removed outlier: 3.541A pdb=" N GLY B 45 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 32 through 33 removed outlier: 5.421A pdb=" N ILE C 5 " --> pdb=" O TRP C 33 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LYS C 4 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LEU C 61 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE C 6 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL C 63 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER C 8 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE C 118 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 278 through 279 removed outlier: 7.342A pdb=" N CYS D 279 " --> pdb=" O PHE D 358 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS D 360 " --> pdb=" O CYS D 279 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 278 through 279 removed outlier: 7.342A pdb=" N CYS D 279 " --> pdb=" O PHE D 358 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS D 360 " --> pdb=" O CYS D 279 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY D 385 " --> pdb=" O ASN D 446 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL D 412 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLU D 3 " --> pdb=" O VAL D 412 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN C 413 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N TYR D 6 " --> pdb=" O ASN C 413 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N SER C 415 " --> pdb=" O TYR D 6 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 414 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LYS C 167 " --> pdb=" O VAL C 414 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 180 removed outlier: 4.817A pdb=" N SER C 177 " --> pdb=" O SER C 404 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE C 402 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL C 401 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 186 through 189 Processing sheet with id=AB7, first strand: chain 'C' and resid 283 through 286 Processing sheet with id=AB8, first strand: chain 'C' and resid 304 through 305 Processing sheet with id=AB9, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.609A pdb=" N GLY C 312 " --> pdb=" O TRP C 319 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP C 319 " --> pdb=" O GLY C 312 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.836A pdb=" N ILE D 12 " --> pdb=" O CYS D 20 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 92 through 95 removed outlier: 3.541A pdb=" N GLY D 45 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY D 42 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE D 142 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE D 44 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TRP D 139 " --> pdb=" O GLN D 222 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE D 224 " --> pdb=" O TRP D 139 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL D 141 " --> pdb=" O PHE D 224 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3882 1.33 - 1.45: 3661 1.45 - 1.57: 8786 1.57 - 1.69: 130 1.69 - 1.81: 74 Bond restraints: 16533 Sorted by residual: bond pdb=" C3' DA E 28 " pdb=" C2' DA E 28 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.62e+00 bond pdb=" C3' DA E 26 " pdb=" C2' DA E 26 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.59e+00 bond pdb=" C3' DA J 10 " pdb=" C2' DA J 10 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.89e+00 bond pdb=" C3' DA J 12 " pdb=" C2' DA J 12 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.95e+00 bond pdb=" C3' DA E 29 " pdb=" C2' DA E 29 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.83e+00 ... (remaining 16528 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 22205 1.89 - 3.78: 367 3.78 - 5.68: 49 5.68 - 7.57: 4 7.57 - 9.46: 6 Bond angle restraints: 22631 Sorted by residual: angle pdb=" C LEU C 39 " pdb=" N ASP C 40 " pdb=" CA ASP C 40 " ideal model delta sigma weight residual 121.54 130.59 -9.05 1.91e+00 2.74e-01 2.24e+01 angle pdb=" C LEU A 39 " pdb=" N ASP A 40 " pdb=" CA ASP A 40 " ideal model delta sigma weight residual 121.54 130.51 -8.97 1.91e+00 2.74e-01 2.20e+01 angle pdb=" C TRP A 369 " pdb=" N ASN A 370 " pdb=" CA ASN A 370 " ideal model delta sigma weight residual 120.65 124.79 -4.14 1.32e+00 5.74e-01 9.85e+00 angle pdb=" O4' DA E 23 " pdb=" C4' DA E 23 " pdb=" C3' DA E 23 " ideal model delta sigma weight residual 106.00 104.12 1.88 6.00e-01 2.78e+00 9.85e+00 angle pdb=" C TRP C 369 " pdb=" N ASN C 370 " pdb=" CA ASN C 370 " ideal model delta sigma weight residual 120.65 124.75 -4.10 1.32e+00 5.74e-01 9.63e+00 ... (remaining 22626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.21: 9466 33.21 - 66.42: 341 66.42 - 99.62: 14 99.62 - 132.83: 1 132.83 - 166.04: 6 Dihedral angle restraints: 9828 sinusoidal: 4572 harmonic: 5256 Sorted by residual: dihedral pdb=" O4' U F 31 " pdb=" C1' U F 31 " pdb=" N1 U F 31 " pdb=" C2 U F 31 " ideal model delta sinusoidal sigma weight residual 200.00 33.96 166.04 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" O4' U I 13 " pdb=" C1' U I 13 " pdb=" N1 U I 13 " pdb=" C2 U I 13 " ideal model delta sinusoidal sigma weight residual 200.00 39.42 160.58 1 1.50e+01 4.44e-03 8.29e+01 dihedral pdb=" O4' U F 27 " pdb=" C1' U F 27 " pdb=" N1 U F 27 " pdb=" C2 U F 27 " ideal model delta sinusoidal sigma weight residual -160.00 -24.95 -135.05 1 1.50e+01 4.44e-03 7.29e+01 ... (remaining 9825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1779 0.039 - 0.078: 467 0.078 - 0.117: 211 0.117 - 0.156: 25 0.156 - 0.195: 2 Chirality restraints: 2484 Sorted by residual: chirality pdb=" CB ILE B 223 " pdb=" CA ILE B 223 " pdb=" CG1 ILE B 223 " pdb=" CG2 ILE B 223 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CB ILE D 223 " pdb=" CA ILE D 223 " pdb=" CG1 ILE D 223 " pdb=" CG2 ILE D 223 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CA GLN C 156 " pdb=" N GLN C 156 " pdb=" C GLN C 156 " pdb=" CB GLN C 156 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 2481 not shown) Planarity restraints: 2620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 437 " 0.050 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO B 438 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 438 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 438 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 437 " -0.050 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO D 438 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 438 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 438 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 132 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C LEU C 132 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU C 132 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU C 133 " -0.010 2.00e-02 2.50e+03 ... (remaining 2617 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 850 2.72 - 3.27: 16505 3.27 - 3.81: 27878 3.81 - 4.36: 33721 4.36 - 4.90: 54779 Nonbonded interactions: 133733 Sorted by model distance: nonbonded pdb=" NZ LYS A 162 " pdb=" O PRO B 427 " model vdw 2.178 3.120 nonbonded pdb=" OG SER D 493 " pdb=" OD1 ASP D 495 " model vdw 2.196 3.040 nonbonded pdb=" OG SER B 493 " pdb=" OD1 ASP B 495 " model vdw 2.197 3.040 nonbonded pdb=" NZ LYS C 24 " pdb=" O LEU D 29 " model vdw 2.224 3.120 nonbonded pdb=" O LEU C 227 " pdb=" OG1 THR C 230 " model vdw 2.229 3.040 ... (remaining 133728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'J' } ncs_group { reference = chain 'F' selection = (chain 'I' and (name P or name OP1 or name OP2 or name O5' or name C5' or name C \ 4' or name O4' or name C3' or name O3' or name C2' or name O2' or name C1' or na \ me N1 or name C2 or name O2 or name N3 or name C4 or name O4 or name C5 or name \ C6 )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.720 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16533 Z= 0.178 Angle : 0.602 9.461 22631 Z= 0.336 Chirality : 0.042 0.195 2484 Planarity : 0.004 0.077 2620 Dihedral : 16.005 166.041 6432 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.75 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1770 helix: 0.76 (0.22), residues: 582 sheet: -0.35 (0.31), residues: 292 loop : -0.72 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 374 TYR 0.007 0.001 TYR A 251 PHE 0.018 0.001 PHE C 273 TRP 0.013 0.001 TRP D 231 HIS 0.004 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.18 (16533) covalent geometry : angle 0.60161 / 0.34 (22631) hydrogen bonds : bond 0.19776 / 13.32 ( 599) hydrogen bonds : angle 8.04104 / 5.71 ( 1625) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.4934 (ttm110) cc_final: 0.4671 (ttm170) REVERT: A 277 MET cc_start: 0.6731 (mtp) cc_final: 0.5977 (mmp) REVERT: A 279 ASP cc_start: 0.7655 (t70) cc_final: 0.7181 (m-30) REVERT: A 364 GLN cc_start: 0.6917 (tp40) cc_final: 0.6700 (tp40) REVERT: A 395 MET cc_start: 0.7309 (ppp) cc_final: 0.6913 (ppp) REVERT: B 58 ASP cc_start: 0.8369 (p0) cc_final: 0.8093 (m-30) REVERT: B 474 ASP cc_start: 0.8353 (t70) cc_final: 0.7955 (t70) REVERT: C 193 MET cc_start: 0.6223 (ttt) cc_final: 0.5262 (tmm) REVERT: D 12 ILE cc_start: 0.9037 (pt) cc_final: 0.8646 (mm) REVERT: D 64 ILE cc_start: 0.8955 (mm) cc_final: 0.8543 (mm) REVERT: D 247 LYS cc_start: 0.8805 (mppt) cc_final: 0.8515 (mtmt) REVERT: D 309 ASP cc_start: 0.7700 (p0) cc_final: 0.7376 (p0) REVERT: D 362 LYS cc_start: 0.8377 (pptt) cc_final: 0.7899 (ptpt) REVERT: D 466 ASN cc_start: 0.8318 (t0) cc_final: 0.7674 (t0) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1154 time to fit residues: 43.3623 Evaluate side-chains 160 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN B 222 GLN B 329 HIS B 360 HIS B 446 ASN B 454 GLN C 70 GLN C 226 HIS D 59 HIS D 154 ASN D 222 GLN D 329 HIS D 360 HIS D 446 ASN D 468 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.101076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.078721 restraints weight = 67667.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.080670 restraints weight = 42946.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.081866 restraints weight = 31463.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.082623 restraints weight = 25916.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.083198 restraints weight = 23108.895| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.144 16533 Z= 0.385 Angle : 0.886 9.303 22631 Z= 0.461 Chirality : 0.049 0.206 2484 Planarity : 0.007 0.098 2620 Dihedral : 15.807 179.425 2788 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.54 % Favored : 93.90 % Rotamer: Outliers : 1.88 % Allowed : 11.14 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.19), residues: 1770 helix: 0.32 (0.21), residues: 586 sheet: -0.94 (0.29), residues: 302 loop : -0.93 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG C 374 TYR 0.041 0.003 TYR C 293 PHE 0.028 0.003 PHE A 45 TRP 0.054 0.004 TRP D 421 HIS 0.019 0.002 HIS A 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00848 / 0.39 (16533) covalent geometry : angle 0.88592 / 0.46 (22631) hydrogen bonds : bond 0.05982 / 4.13 ( 599) hydrogen bonds : angle 6.30427 / 4.46 ( 1625) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASP cc_start: 0.7755 (t70) cc_final: 0.7245 (m-30) REVERT: A 287 MET cc_start: -0.0660 (tpt) cc_final: -0.1008 (tpt) REVERT: A 291 THR cc_start: 0.3944 (m) cc_final: 0.3735 (m) REVERT: A 314 GLN cc_start: 0.5813 (mm-40) cc_final: 0.5368 (mm-40) REVERT: A 364 GLN cc_start: 0.7560 (tp40) cc_final: 0.6488 (tp40) REVERT: A 395 MET cc_start: 0.7641 (ppp) cc_final: 0.6650 (ppp) REVERT: B 92 THR cc_start: 0.8727 (m) cc_final: 0.8300 (p) REVERT: B 474 ASP cc_start: 0.8521 (t70) cc_final: 0.8166 (t70) REVERT: C 287 MET cc_start: 0.7387 (tpt) cc_final: 0.7093 (tpt) REVERT: C 395 MET cc_start: 0.8683 (ppp) cc_final: 0.8384 (ppp) REVERT: D 56 TYR cc_start: 0.8859 (t80) cc_final: 0.8604 (t80) REVERT: D 123 ASP cc_start: 0.8493 (p0) cc_final: 0.8288 (p0) REVERT: D 309 ASP cc_start: 0.8008 (p0) cc_final: 0.7706 (p0) REVERT: D 362 LYS cc_start: 0.8383 (pptt) cc_final: 0.8137 (ttpt) REVERT: D 421 TRP cc_start: 0.8590 (m-90) cc_final: 0.8350 (m-90) REVERT: D 456 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9004 (mm) REVERT: D 466 ASN cc_start: 0.8514 (t0) cc_final: 0.8173 (t0) outliers start: 30 outliers final: 18 residues processed: 175 average time/residue: 0.1083 time to fit residues: 29.3142 Evaluate side-chains 145 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 456 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 8 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS B 360 HIS C 226 HIS D 59 HIS D 154 ASN D 201 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.104339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.081481 restraints weight = 67520.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.083748 restraints weight = 41847.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.084966 restraints weight = 30094.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.085940 restraints weight = 24778.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.086347 restraints weight = 21810.271| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16533 Z= 0.146 Angle : 0.652 9.312 22631 Z= 0.341 Chirality : 0.045 0.261 2484 Planarity : 0.005 0.057 2620 Dihedral : 15.592 178.120 2788 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.80 % Favored : 94.75 % Rotamer: Outliers : 1.56 % Allowed : 14.27 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.20), residues: 1770 helix: 0.61 (0.21), residues: 590 sheet: -0.70 (0.30), residues: 302 loop : -0.96 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 263 TYR 0.020 0.001 TYR B 397 PHE 0.026 0.002 PHE D 78 TRP 0.047 0.002 TRP A 368 HIS 0.011 0.001 HIS D 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (16533) covalent geometry : angle 0.65240 / 0.34 (22631) hydrogen bonds : bond 0.05025 / 3.40 ( 599) hydrogen bonds : angle 5.83748 / 4.17 ( 1625) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASP cc_start: 0.7703 (t70) cc_final: 0.7221 (m-30) REVERT: A 291 THR cc_start: 0.3438 (m) cc_final: 0.3181 (m) REVERT: A 357 GLN cc_start: 0.8774 (tp-100) cc_final: 0.8557 (tp40) REVERT: A 364 GLN cc_start: 0.7903 (tp40) cc_final: 0.7207 (tp40) REVERT: A 368 TRP cc_start: 0.7112 (m-10) cc_final: 0.6420 (m-90) REVERT: A 395 MET cc_start: 0.7807 (ppp) cc_final: 0.7076 (ppp) REVERT: B 92 THR cc_start: 0.8674 (m) cc_final: 0.8273 (p) REVERT: B 303 MET cc_start: 0.8541 (tmm) cc_final: 0.8250 (tmm) REVERT: B 474 ASP cc_start: 0.8484 (t70) cc_final: 0.8160 (t70) REVERT: D 44 ILE cc_start: 0.9594 (OUTLIER) cc_final: 0.9199 (tp) REVERT: D 123 ASP cc_start: 0.8585 (p0) cc_final: 0.8333 (p0) REVERT: D 309 ASP cc_start: 0.8060 (p0) cc_final: 0.7758 (p0) REVERT: D 421 TRP cc_start: 0.8431 (m-90) cc_final: 0.8194 (m-90) REVERT: D 456 LEU cc_start: 0.9342 (mm) cc_final: 0.9068 (mm) REVERT: D 466 ASN cc_start: 0.8413 (t0) cc_final: 0.7932 (t0) REVERT: D 468 ASN cc_start: 0.8362 (t0) cc_final: 0.7979 (t0) outliers start: 25 outliers final: 15 residues processed: 165 average time/residue: 0.0971 time to fit residues: 25.7661 Evaluate side-chains 146 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 29 optimal weight: 0.0870 chunk 133 optimal weight: 0.0470 chunk 119 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN C 226 HIS D 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.104870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.082608 restraints weight = 65224.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.084812 restraints weight = 39168.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.086095 restraints weight = 27888.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.087121 restraints weight = 22547.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.087402 restraints weight = 19546.074| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16533 Z= 0.131 Angle : 0.621 9.582 22631 Z= 0.322 Chirality : 0.044 0.266 2484 Planarity : 0.004 0.050 2620 Dihedral : 15.489 175.828 2788 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.14 % Favored : 94.41 % Rotamer: Outliers : 1.88 % Allowed : 14.89 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.20), residues: 1770 helix: 0.83 (0.22), residues: 590 sheet: -0.63 (0.30), residues: 288 loop : -0.92 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 71 TYR 0.013 0.001 TYR D 397 PHE 0.023 0.001 PHE D 78 TRP 0.025 0.001 TRP A 46 HIS 0.012 0.001 HIS D 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (16533) covalent geometry : angle 0.62098 / 0.32 (22631) hydrogen bonds : bond 0.04576 / 3.10 ( 599) hydrogen bonds : angle 5.56883 / 3.98 ( 1625) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8359 (tptt) REVERT: A 155 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8637 (pp30) REVERT: A 279 ASP cc_start: 0.7751 (t70) cc_final: 0.7226 (m-30) REVERT: A 291 THR cc_start: 0.3206 (m) cc_final: 0.2948 (m) REVERT: A 352 ASP cc_start: 0.5820 (p0) cc_final: 0.4269 (t0) REVERT: A 364 GLN cc_start: 0.7769 (tp40) cc_final: 0.7173 (tp40) REVERT: A 395 MET cc_start: 0.7820 (ppp) cc_final: 0.7347 (ppp) REVERT: B 92 THR cc_start: 0.8598 (m) cc_final: 0.8161 (p) REVERT: B 303 MET cc_start: 0.8577 (tmm) cc_final: 0.8221 (tmm) REVERT: B 474 ASP cc_start: 0.8342 (t70) cc_final: 0.8040 (t70) REVERT: C 156 GLN cc_start: 0.6115 (OUTLIER) cc_final: 0.5706 (pt0) REVERT: D 44 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9101 (tp) REVERT: D 123 ASP cc_start: 0.8678 (p0) cc_final: 0.8381 (p0) REVERT: D 309 ASP cc_start: 0.8105 (p0) cc_final: 0.7855 (p0) REVERT: D 456 LEU cc_start: 0.9378 (mm) cc_final: 0.9052 (mm) REVERT: D 466 ASN cc_start: 0.8542 (t0) cc_final: 0.8066 (t0) outliers start: 30 outliers final: 16 residues processed: 164 average time/residue: 0.1096 time to fit residues: 28.3646 Evaluate side-chains 142 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 192 TRP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 72 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 176 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 ASN D 296 ASN D 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.103834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.081254 restraints weight = 66819.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.083350 restraints weight = 40712.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.084542 restraints weight = 29084.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.085494 restraints weight = 23934.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.085978 restraints weight = 20930.545| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16533 Z= 0.156 Angle : 0.623 9.552 22631 Z= 0.326 Chirality : 0.043 0.286 2484 Planarity : 0.005 0.054 2620 Dihedral : 15.448 175.066 2788 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.69 % Favored : 94.86 % Rotamer: Outliers : 2.50 % Allowed : 15.52 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.20), residues: 1770 helix: 0.89 (0.22), residues: 590 sheet: -0.67 (0.31), residues: 288 loop : -0.93 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 71 TYR 0.012 0.001 TYR A 251 PHE 0.023 0.001 PHE D 78 TRP 0.055 0.002 TRP A 368 HIS 0.007 0.001 HIS A 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (16533) covalent geometry : angle 0.62314 / 0.33 (22631) hydrogen bonds : bond 0.04443 / 3.00 ( 599) hydrogen bonds : angle 5.44596 / 3.88 ( 1625) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8235 (tptt) REVERT: A 155 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8649 (pp30) REVERT: A 279 ASP cc_start: 0.7729 (t70) cc_final: 0.7224 (m-30) REVERT: A 287 MET cc_start: -0.0116 (tpt) cc_final: -0.0581 (tpt) REVERT: A 291 THR cc_start: 0.3427 (m) cc_final: 0.3147 (m) REVERT: A 352 ASP cc_start: 0.6018 (p0) cc_final: 0.4557 (t0) REVERT: A 395 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7042 (ppp) REVERT: B 92 THR cc_start: 0.8560 (m) cc_final: 0.8171 (p) REVERT: B 279 CYS cc_start: 0.8569 (t) cc_final: 0.8324 (t) REVERT: B 303 MET cc_start: 0.8515 (tmm) cc_final: 0.8258 (tmm) REVERT: B 474 ASP cc_start: 0.8374 (t70) cc_final: 0.7966 (t0) REVERT: C 156 GLN cc_start: 0.6197 (OUTLIER) cc_final: 0.5740 (pt0) REVERT: D 123 ASP cc_start: 0.8638 (p0) cc_final: 0.8372 (p0) REVERT: D 309 ASP cc_start: 0.8131 (p0) cc_final: 0.7906 (p0) REVERT: D 466 ASN cc_start: 0.8620 (t0) cc_final: 0.8191 (t0) REVERT: D 476 GLU cc_start: 0.8111 (pm20) cc_final: 0.5903 (pm20) REVERT: D 481 ARG cc_start: 0.8056 (ttm-80) cc_final: 0.7124 (ttm-80) outliers start: 40 outliers final: 25 residues processed: 165 average time/residue: 0.0984 time to fit residues: 26.3624 Evaluate side-chains 155 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 192 TRP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 179 optimal weight: 0.2980 chunk 135 optimal weight: 2.9990 chunk 162 optimal weight: 0.5980 chunk 28 optimal weight: 20.0000 chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN D 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.103073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.080830 restraints weight = 66299.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.082894 restraints weight = 40564.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.084245 restraints weight = 29118.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.085114 restraints weight = 23448.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.085342 restraints weight = 20716.817| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16533 Z= 0.142 Angle : 0.632 10.116 22631 Z= 0.325 Chirality : 0.044 0.286 2484 Planarity : 0.004 0.051 2620 Dihedral : 15.420 174.514 2788 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.92 % Favored : 94.63 % Rotamer: Outliers : 2.50 % Allowed : 16.77 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.20), residues: 1770 helix: 0.94 (0.22), residues: 588 sheet: -0.67 (0.31), residues: 288 loop : -0.92 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 374 TYR 0.012 0.001 TYR B 397 PHE 0.018 0.001 PHE C 273 TRP 0.036 0.002 TRP A 368 HIS 0.006 0.001 HIS A 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (16533) covalent geometry : angle 0.63160 / 0.33 (22631) hydrogen bonds : bond 0.04250 / 2.87 ( 599) hydrogen bonds : angle 5.33646 / 3.79 ( 1625) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8251 (tptt) REVERT: A 155 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8599 (pp30) REVERT: A 279 ASP cc_start: 0.7708 (t70) cc_final: 0.7211 (m-30) REVERT: A 352 ASP cc_start: 0.6018 (p0) cc_final: 0.4584 (t0) REVERT: A 364 GLN cc_start: 0.7434 (tp40) cc_final: 0.7087 (tp-100) REVERT: A 395 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7369 (ppp) REVERT: B 92 THR cc_start: 0.8616 (m) cc_final: 0.8226 (p) REVERT: B 279 CYS cc_start: 0.8577 (t) cc_final: 0.8357 (t) REVERT: B 303 MET cc_start: 0.8492 (tmm) cc_final: 0.8144 (tmm) REVERT: B 474 ASP cc_start: 0.8340 (t70) cc_final: 0.7985 (t0) REVERT: C 156 GLN cc_start: 0.6239 (OUTLIER) cc_final: 0.5779 (pt0) REVERT: D 44 ILE cc_start: 0.9483 (OUTLIER) cc_final: 0.9023 (tp) REVERT: D 123 ASP cc_start: 0.8602 (p0) cc_final: 0.8336 (p0) REVERT: D 309 ASP cc_start: 0.8035 (p0) cc_final: 0.7806 (p0) REVERT: D 466 ASN cc_start: 0.8635 (t0) cc_final: 0.8257 (t0) REVERT: D 468 ASN cc_start: 0.8353 (t0) cc_final: 0.7993 (t0) REVERT: D 476 GLU cc_start: 0.8112 (pm20) cc_final: 0.6302 (pm20) REVERT: D 481 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7263 (ttm-80) outliers start: 40 outliers final: 25 residues processed: 168 average time/residue: 0.1059 time to fit residues: 28.7466 Evaluate side-chains 155 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 192 TRP Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 48 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN D 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.103077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.080788 restraints weight = 66861.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.082876 restraints weight = 41646.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.084062 restraints weight = 29809.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.085061 restraints weight = 24389.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.085310 restraints weight = 21229.959| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16533 Z= 0.138 Angle : 0.641 10.174 22631 Z= 0.326 Chirality : 0.044 0.283 2484 Planarity : 0.004 0.053 2620 Dihedral : 15.396 174.251 2788 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.75 % Favored : 94.80 % Rotamer: Outliers : 2.32 % Allowed : 17.52 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.20), residues: 1770 helix: 0.99 (0.22), residues: 586 sheet: -0.67 (0.31), residues: 288 loop : -0.88 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 71 TYR 0.013 0.001 TYR D 56 PHE 0.020 0.001 PHE C 273 TRP 0.037 0.002 TRP A 46 HIS 0.006 0.001 HIS A 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (16533) covalent geometry : angle 0.64051 / 0.33 (22631) hydrogen bonds : bond 0.04180 / 2.84 ( 599) hydrogen bonds : angle 5.25509 / 3.73 ( 1625) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASP cc_start: 0.7672 (t70) cc_final: 0.7194 (m-30) REVERT: A 352 ASP cc_start: 0.6052 (p0) cc_final: 0.4618 (t0) REVERT: A 395 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7270 (ppp) REVERT: B 92 THR cc_start: 0.8633 (m) cc_final: 0.8254 (p) REVERT: B 279 CYS cc_start: 0.8562 (t) cc_final: 0.8345 (t) REVERT: B 303 MET cc_start: 0.8477 (tmm) cc_final: 0.8132 (tmm) REVERT: B 435 MET cc_start: 0.3903 (mmt) cc_final: 0.3337 (mmp) REVERT: B 474 ASP cc_start: 0.8373 (t70) cc_final: 0.8028 (t0) REVERT: C 156 GLN cc_start: 0.6127 (OUTLIER) cc_final: 0.5569 (pt0) REVERT: D 123 ASP cc_start: 0.8569 (p0) cc_final: 0.8339 (p0) REVERT: D 309 ASP cc_start: 0.8000 (p0) cc_final: 0.7798 (p0) REVERT: D 466 ASN cc_start: 0.8623 (t0) cc_final: 0.8238 (t0) REVERT: D 468 ASN cc_start: 0.8318 (t0) cc_final: 0.7961 (t0) REVERT: D 476 GLU cc_start: 0.7989 (pm20) cc_final: 0.6266 (pm20) REVERT: D 481 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7270 (ttm-80) outliers start: 37 outliers final: 31 residues processed: 165 average time/residue: 0.1066 time to fit residues: 28.7200 Evaluate side-chains 156 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 192 TRP Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 61 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 152 optimal weight: 0.4980 chunk 85 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN D 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.103440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.081269 restraints weight = 65869.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.083443 restraints weight = 39892.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.084701 restraints weight = 28278.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.085720 restraints weight = 22891.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.085991 restraints weight = 19800.125| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16533 Z= 0.126 Angle : 0.643 10.635 22631 Z= 0.326 Chirality : 0.044 0.302 2484 Planarity : 0.004 0.050 2620 Dihedral : 15.368 174.256 2788 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.86 % Favored : 94.69 % Rotamer: Outliers : 2.38 % Allowed : 18.02 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.20), residues: 1770 helix: 1.02 (0.22), residues: 586 sheet: -0.66 (0.31), residues: 288 loop : -0.90 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 71 TYR 0.014 0.001 TYR A 293 PHE 0.019 0.001 PHE C 273 TRP 0.031 0.001 TRP C 20 HIS 0.005 0.001 HIS A 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (16533) covalent geometry : angle 0.64313 / 0.33 (22631) hydrogen bonds : bond 0.04110 / 2.79 ( 599) hydrogen bonds : angle 5.22553 / 3.70 ( 1625) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.5616 (ttt) cc_final: 0.5072 (mmm) REVERT: A 279 ASP cc_start: 0.7571 (t70) cc_final: 0.7088 (m-30) REVERT: A 352 ASP cc_start: 0.6051 (p0) cc_final: 0.4634 (t0) REVERT: A 364 GLN cc_start: 0.7379 (tp40) cc_final: 0.7032 (tp-100) REVERT: A 395 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7261 (ppp) REVERT: B 92 THR cc_start: 0.8589 (m) cc_final: 0.8207 (p) REVERT: B 279 CYS cc_start: 0.8575 (t) cc_final: 0.8343 (t) REVERT: B 303 MET cc_start: 0.8491 (tmm) cc_final: 0.8108 (tmm) REVERT: B 435 MET cc_start: 0.4249 (OUTLIER) cc_final: 0.3656 (mmp) REVERT: B 474 ASP cc_start: 0.8295 (t70) cc_final: 0.7972 (t0) REVERT: C 156 GLN cc_start: 0.6084 (OUTLIER) cc_final: 0.5535 (pt0) REVERT: C 287 MET cc_start: 0.7282 (tpt) cc_final: 0.6694 (tpt) REVERT: D 123 ASP cc_start: 0.8614 (p0) cc_final: 0.8347 (p0) REVERT: D 309 ASP cc_start: 0.8131 (p0) cc_final: 0.7897 (p0) REVERT: D 466 ASN cc_start: 0.8638 (t0) cc_final: 0.8218 (t0) REVERT: D 468 ASN cc_start: 0.8310 (t0) cc_final: 0.7934 (t0) outliers start: 38 outliers final: 29 residues processed: 165 average time/residue: 0.1061 time to fit residues: 28.4926 Evaluate side-chains 157 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 192 TRP Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 73 optimal weight: 0.0970 chunk 68 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.101772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.079439 restraints weight = 66985.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.081548 restraints weight = 41381.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.082691 restraints weight = 29878.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.083693 restraints weight = 24515.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.084187 restraints weight = 21323.580| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16533 Z= 0.170 Angle : 0.656 10.281 22631 Z= 0.336 Chirality : 0.044 0.291 2484 Planarity : 0.004 0.053 2620 Dihedral : 15.405 173.831 2788 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.03 % Favored : 94.58 % Rotamer: Outliers : 2.38 % Allowed : 18.21 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1770 helix: 1.06 (0.22), residues: 584 sheet: -0.72 (0.31), residues: 288 loop : -0.93 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 263 TYR 0.012 0.001 TYR B 425 PHE 0.017 0.001 PHE C 273 TRP 0.035 0.002 TRP C 20 HIS 0.005 0.001 HIS A 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (16533) covalent geometry : angle 0.65625 / 0.34 (22631) hydrogen bonds : bond 0.04215 / 2.85 ( 599) hydrogen bonds : angle 5.27539 / 3.73 ( 1625) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASP cc_start: 0.7560 (t70) cc_final: 0.7088 (m-30) REVERT: A 352 ASP cc_start: 0.6136 (p0) cc_final: 0.4672 (t0) REVERT: A 395 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7318 (ppp) REVERT: B 92 THR cc_start: 0.8695 (m) cc_final: 0.8315 (p) REVERT: B 303 MET cc_start: 0.8523 (tmm) cc_final: 0.8137 (tmm) REVERT: B 435 MET cc_start: 0.4443 (OUTLIER) cc_final: 0.3834 (mmp) REVERT: B 474 ASP cc_start: 0.8313 (t70) cc_final: 0.8022 (t0) REVERT: C 156 GLN cc_start: 0.6177 (OUTLIER) cc_final: 0.5623 (pt0) REVERT: D 123 ASP cc_start: 0.8594 (p0) cc_final: 0.8369 (p0) REVERT: D 309 ASP cc_start: 0.8165 (p0) cc_final: 0.7946 (p0) REVERT: D 466 ASN cc_start: 0.8599 (t0) cc_final: 0.8235 (t0) REVERT: D 468 ASN cc_start: 0.8280 (t0) cc_final: 0.7939 (t0) outliers start: 38 outliers final: 28 residues processed: 162 average time/residue: 0.1064 time to fit residues: 28.2401 Evaluate side-chains 158 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 192 TRP Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 59 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 chunk 100 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 329 HIS D 129 ASN D 302 GLN D 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.100561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.078280 restraints weight = 67766.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.080340 restraints weight = 42469.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.081566 restraints weight = 30440.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.082381 restraints weight = 24857.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.082649 restraints weight = 22060.698| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16533 Z= 0.205 Angle : 0.711 12.279 22631 Z= 0.367 Chirality : 0.045 0.342 2484 Planarity : 0.005 0.053 2620 Dihedral : 15.433 173.240 2788 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.97 % Favored : 94.69 % Rotamer: Outliers : 2.07 % Allowed : 18.77 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1770 helix: 0.90 (0.21), residues: 588 sheet: -0.82 (0.30), residues: 288 loop : -1.00 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 263 TYR 0.018 0.001 TYR A 293 PHE 0.019 0.002 PHE C 273 TRP 0.040 0.002 TRP A 46 HIS 0.028 0.002 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 (16533) covalent geometry : angle 0.71066 / 0.37 (22631) hydrogen bonds : bond 0.04360 / 2.94 ( 599) hydrogen bonds : angle 5.36037 / 3.78 ( 1625) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.4982 (tpp) cc_final: 0.4584 (tpp) REVERT: A 217 PHE cc_start: 0.6610 (m-80) cc_final: 0.6233 (m-10) REVERT: A 279 ASP cc_start: 0.7606 (t70) cc_final: 0.7103 (m-30) REVERT: A 332 PHE cc_start: 0.8411 (m-80) cc_final: 0.7997 (m-10) REVERT: A 352 ASP cc_start: 0.6265 (p0) cc_final: 0.4927 (t0) REVERT: A 395 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7329 (ppp) REVERT: B 92 THR cc_start: 0.8694 (m) cc_final: 0.8299 (p) REVERT: B 303 MET cc_start: 0.8569 (tmm) cc_final: 0.8133 (tmm) REVERT: B 435 MET cc_start: 0.4458 (OUTLIER) cc_final: 0.3884 (mmp) REVERT: C 156 GLN cc_start: 0.6205 (OUTLIER) cc_final: 0.5723 (pt0) REVERT: C 287 MET cc_start: 0.7293 (tpt) cc_final: 0.6872 (tpt) REVERT: D 123 ASP cc_start: 0.8582 (p0) cc_final: 0.8309 (p0) REVERT: D 309 ASP cc_start: 0.8244 (p0) cc_final: 0.8018 (p0) REVERT: D 466 ASN cc_start: 0.8672 (t0) cc_final: 0.8343 (t0) outliers start: 33 outliers final: 25 residues processed: 156 average time/residue: 0.1025 time to fit residues: 26.4764 Evaluate side-chains 159 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 192 TRP Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 114 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 1 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.101387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.079134 restraints weight = 66730.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.081223 restraints weight = 41499.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.082413 restraints weight = 29703.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.083385 restraints weight = 24200.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.083647 restraints weight = 21176.264| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16533 Z= 0.144 Angle : 0.684 11.024 22631 Z= 0.349 Chirality : 0.044 0.303 2484 Planarity : 0.004 0.051 2620 Dihedral : 15.388 173.386 2788 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.80 % Favored : 94.92 % Rotamer: Outliers : 1.75 % Allowed : 19.34 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.20), residues: 1770 helix: 0.94 (0.21), residues: 588 sheet: -0.78 (0.31), residues: 278 loop : -0.98 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 263 TYR 0.012 0.001 TYR A 251 PHE 0.039 0.001 PHE A 17 TRP 0.034 0.001 TRP A 46 HIS 0.004 0.001 HIS A 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (16533) covalent geometry : angle 0.68385 / 0.35 (22631) hydrogen bonds : bond 0.04175 / 2.80 ( 599) hydrogen bonds : angle 5.27575 / 3.72 ( 1625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2437.72 seconds wall clock time: 43 minutes 24.50 seconds (2604.50 seconds total)