Starting phenix.real_space_refine on Sun Aug 24 03:19:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ozd_17305/08_2025/8ozd_17305.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozd_17305/08_2025/8ozd_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ozd_17305/08_2025/8ozd_17305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozd_17305/08_2025/8ozd_17305.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ozd_17305/08_2025/8ozd_17305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozd_17305/08_2025/8ozd_17305.map" } 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-2.0-5787/lib/python3.9/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: 4.03, per 1000 atoms: 0.25 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: 1.12 Conformation dependent library (CDL) restraints added in 645.0 milliseconds Enol-peptide restraints added in 1.7 microseconds 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: 1.85 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: 2.92 Time building geometry restraints manager: 1.51 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=" CG ARG C 374 " pdb=" CD ARG C 374 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" CG ARG A 374 " pdb=" CD ARG A 374 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" CB ASP C 40 " pdb=" CG ASP C 40 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.42e-01 bond pdb=" CB ASP A 40 " pdb=" CG ASP A 40 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.22e-01 bond pdb=" CA ASP A 146 " pdb=" C ASP A 146 " ideal model delta sigma weight residual 1.519 1.530 -0.010 1.14e-02 7.69e+03 8.38e-01 ... (remaining 16528 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 22229 1.89 - 3.78: 343 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=" 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 angle pdb=" C LYS A 86 " pdb=" N GLN A 87 " pdb=" CA GLN A 87 " ideal model delta sigma weight residual 121.14 116.10 5.04 1.75e+00 3.27e-01 8.29e+00 ... (remaining 22626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.21: 9523 33.21 - 66.42: 428 66.42 - 99.62: 14 99.62 - 132.83: 1 132.83 - 166.04: 6 Dihedral angle restraints: 9972 sinusoidal: 4716 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 9969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1819 0.039 - 0.078: 449 0.078 - 0.117: 189 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.400 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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: 19.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 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= 0.120 Angle : 0.589 9.461 22631 Z= 0.313 Chirality : 0.041 0.195 2484 Planarity : 0.004 0.077 2620 Dihedral : 16.885 166.041 6576 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 aren 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 covalent geometry : bond 0.00254 (16533) covalent geometry : angle 0.58896 (22631) hydrogen bonds : bond 0.19776 ( 599) hydrogen bonds : angle 8.04104 ( 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 : 0.557 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: 0.8092 (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: 0.8542 (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: 0.7675 (t0) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1337 time to fit residues: 49.3491 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 : 0.548 ------------------------------------------------------------------------------- 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: 0.5980 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: 5.9990 chunk 149 optimal weight: 20.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 358 HIS B 329 HIS B 360 HIS B 446 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 358 HIS D 59 HIS D 154 ASN D 201 ASN D 296 ASN 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 = 0.3860 r_free = 0.3860 target = 0.100499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.078243 restraints weight = 66865.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.080339 restraints weight = 41730.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.081476 restraints weight = 30268.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.082388 restraints weight = 24824.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.082752 restraints weight = 21910.753| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 16533 Z= 0.303 Angle : 0.770 8.716 22631 Z= 0.408 Chirality : 0.047 0.195 2484 Planarity : 0.006 0.057 2620 Dihedral : 17.739 179.213 2932 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.76 % Favored : 93.79 % Rotamer: Outliers : 2.07 % Allowed : 10.95 % 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 aren not related in a simple way. whole: -0.60 (0.19), residues: 1770 helix: 0.57 (0.21), residues: 588 sheet: -0.57 (0.29), residues: 318 loop : -0.95 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG C 374 TYR 0.036 0.002 TYR C 293 PHE 0.018 0.002 PHE D 121 TRP 0.032 0.003 TRP D 421 HIS 0.015 0.002 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00668 (16533) covalent geometry : angle 0.76975 (22631) hydrogen bonds : bond 0.05820 ( 599) hydrogen bonds : angle 6.06643 ( 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 189 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASP cc_start: 0.7789 (t70) cc_final: 0.7321 (m-30) REVERT: A 287 MET cc_start: -0.0078 (tpt) cc_final: -0.0597 (tpt) REVERT: A 291 THR cc_start: 0.3779 (m) cc_final: 0.3560 (m) REVERT: A 314 GLN cc_start: 0.5886 (mm-40) cc_final: 0.5543 (mm-40) REVERT: A 364 GLN cc_start: 0.7421 (tp40) cc_final: 0.6349 (tp40) REVERT: A 395 MET cc_start: 0.7797 (ppp) cc_final: 0.7189 (ppp) REVERT: B 92 THR cc_start: 0.8763 (m) cc_final: 0.8340 (p) REVERT: B 254 TRP cc_start: 0.9488 (m100) cc_final: 0.9010 (m100) REVERT: B 303 MET cc_start: 0.8240 (tmm) cc_final: 0.7777 (tmm) REVERT: B 435 MET cc_start: 0.3873 (mmt) cc_final: 0.3025 (mmp) REVERT: B 474 ASP cc_start: 0.8443 (t70) cc_final: 0.8139 (t70) REVERT: D 78 PHE cc_start: 0.8480 (t80) cc_final: 0.8041 (t80) REVERT: D 123 ASP cc_start: 0.8564 (p0) cc_final: 0.8344 (p0) REVERT: D 309 ASP cc_start: 0.8134 (p0) cc_final: 0.7854 (p0) REVERT: D 421 TRP cc_start: 0.8714 (m-90) cc_final: 0.8403 (m-90) REVERT: D 456 LEU cc_start: 0.9403 (mm) cc_final: 0.9141 (mm) REVERT: D 466 ASN cc_start: 0.8602 (t0) cc_final: 0.8276 (t0) outliers start: 33 outliers final: 18 residues processed: 177 average time/residue: 0.1101 time to fit residues: 30.8136 Evaluate side-chains 143 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE 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 223 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 1 MET 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 299 CYS Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 374 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 8 optimal weight: 1.9990 chunk 134 optimal weight: 0.0980 chunk 170 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 175 optimal weight: 0.0980 chunk 136 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.103776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.081288 restraints weight = 65832.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.083511 restraints weight = 39576.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.084752 restraints weight = 28038.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.085727 restraints weight = 22793.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.086190 restraints weight = 19992.566| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3185 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= 0.132 Angle : 0.624 9.784 22631 Z= 0.325 Chirality : 0.043 0.159 2484 Planarity : 0.005 0.057 2620 Dihedral : 17.480 175.793 2932 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.63 % Favored : 94.92 % Rotamer: Outliers : 1.75 % Allowed : 13.27 % Favored : 84.98 % 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 aren not related in a simple way. whole: -0.38 (0.20), residues: 1770 helix: 0.79 (0.21), residues: 590 sheet: -0.45 (0.31), residues: 288 loop : -0.86 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 374 TYR 0.020 0.001 TYR C 293 PHE 0.026 0.001 PHE A 17 TRP 0.028 0.002 TRP C 20 HIS 0.009 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00293 (16533) covalent geometry : angle 0.62432 (22631) hydrogen bonds : bond 0.04428 ( 599) hydrogen bonds : angle 5.53225 ( 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 178 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 PHE cc_start: 0.6448 (m-80) cc_final: 0.6099 (m-10) REVERT: A 279 ASP cc_start: 0.7738 (t70) cc_final: 0.7251 (m-30) REVERT: A 291 THR cc_start: 0.3141 (m) cc_final: 0.2878 (m) REVERT: A 357 GLN cc_start: 0.8785 (tp-100) cc_final: 0.8576 (tp40) REVERT: A 364 GLN cc_start: 0.7850 (tp40) cc_final: 0.7355 (tp40) REVERT: A 395 MET cc_start: 0.7936 (ppp) cc_final: 0.7425 (ppp) REVERT: B 92 THR cc_start: 0.8729 (m) cc_final: 0.8295 (p) REVERT: B 279 CYS cc_start: 0.8555 (t) cc_final: 0.8347 (t) REVERT: B 303 MET cc_start: 0.8244 (tmm) cc_final: 0.7855 (tmm) REVERT: B 360 HIS cc_start: 0.8711 (m-70) cc_final: 0.8499 (m170) REVERT: B 474 ASP cc_start: 0.8313 (t70) cc_final: 0.8080 (t70) REVERT: D 123 ASP cc_start: 0.8687 (p0) cc_final: 0.8424 (p0) REVERT: D 309 ASP cc_start: 0.8128 (p0) cc_final: 0.7899 (p0) REVERT: D 456 LEU cc_start: 0.9404 (mm) cc_final: 0.9099 (mm) REVERT: D 466 ASN cc_start: 0.8711 (t0) cc_final: 0.8342 (t0) REVERT: D 481 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7255 (ttm-80) outliers start: 28 outliers final: 15 residues processed: 173 average time/residue: 0.1174 time to fit residues: 32.2666 Evaluate side-chains 141 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 147 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 406 LEU 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 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 374 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 56 optimal weight: 0.0370 chunk 76 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 55 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS D 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.104262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.081379 restraints weight = 66618.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.083559 restraints weight = 40761.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.085021 restraints weight = 29046.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.085702 restraints weight = 23531.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.086312 restraints weight = 20971.848| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3486 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= 0.123 Angle : 0.612 10.225 22631 Z= 0.315 Chirality : 0.042 0.220 2484 Planarity : 0.004 0.055 2620 Dihedral : 17.386 176.101 2932 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.86 % Favored : 94.69 % Rotamer: Outliers : 2.13 % Allowed : 14.52 % Favored : 83.35 % 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 aren not related in a simple way. whole: -0.28 (0.20), residues: 1770 helix: 1.03 (0.22), residues: 586 sheet: -0.51 (0.30), residues: 310 loop : -0.86 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 152 TYR 0.012 0.001 TYR D 397 PHE 0.017 0.001 PHE A 17 TRP 0.030 0.002 TRP D 421 HIS 0.009 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00275 (16533) covalent geometry : angle 0.61162 (22631) hydrogen bonds : bond 0.04091 ( 599) hydrogen bonds : angle 5.28723 ( 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 181 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.8024 (m100) cc_final: 0.7805 (m100) REVERT: A 217 PHE cc_start: 0.6012 (m-80) cc_final: 0.5691 (m-10) REVERT: A 279 ASP cc_start: 0.7609 (t70) cc_final: 0.7158 (m-30) REVERT: A 291 THR cc_start: 0.3260 (m) cc_final: 0.2987 (m) REVERT: A 352 ASP cc_start: 0.6112 (p0) cc_final: 0.4557 (t0) REVERT: A 395 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7344 (ppp) REVERT: B 92 THR cc_start: 0.8618 (m) cc_final: 0.8258 (p) REVERT: B 279 CYS cc_start: 0.8506 (t) cc_final: 0.8262 (t) REVERT: B 303 MET cc_start: 0.8273 (tmm) cc_final: 0.7914 (tmm) REVERT: B 360 HIS cc_start: 0.8533 (m-70) cc_final: 0.8321 (m170) REVERT: B 435 MET cc_start: 0.4162 (mmt) cc_final: 0.3194 (mmp) REVERT: B 474 ASP cc_start: 0.8307 (t70) cc_final: 0.7999 (t0) REVERT: C 156 GLN cc_start: 0.6032 (OUTLIER) cc_final: 0.5488 (pt0) REVERT: C 309 MET cc_start: 0.8533 (tpp) cc_final: 0.8301 (tpp) REVERT: D 78 PHE cc_start: 0.8129 (t80) cc_final: 0.7779 (t80) REVERT: D 123 ASP cc_start: 0.8588 (p0) cc_final: 0.8340 (p0) REVERT: D 303 MET cc_start: 0.8729 (tmm) cc_final: 0.8467 (tmm) REVERT: D 309 ASP cc_start: 0.8074 (p0) cc_final: 0.7865 (p0) REVERT: D 456 LEU cc_start: 0.9346 (mm) cc_final: 0.9044 (mm) REVERT: D 466 ASN cc_start: 0.8635 (t0) cc_final: 0.8237 (t0) REVERT: D 476 GLU cc_start: 0.7992 (pm20) cc_final: 0.6257 (pm20) REVERT: D 481 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7210 (ttm-80) outliers start: 34 outliers final: 25 residues processed: 173 average time/residue: 0.1173 time to fit residues: 32.3879 Evaluate side-chains 157 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 141 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 87 GLN 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 329 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 85 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 72 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN B 329 HIS D 59 HIS D 129 ASN D 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.099308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.076878 restraints weight = 67174.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.078931 restraints weight = 41658.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.080110 restraints weight = 29764.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.081042 restraints weight = 24340.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.081415 restraints weight = 21440.359| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16533 Z= 0.222 Angle : 0.671 9.844 22631 Z= 0.351 Chirality : 0.044 0.255 2484 Planarity : 0.005 0.063 2620 Dihedral : 17.591 173.314 2932 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.20 % Favored : 94.46 % Rotamer: Outliers : 3.07 % Allowed : 16.08 % Favored : 80.85 % 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 aren not related in a simple way. whole: -0.41 (0.20), residues: 1770 helix: 1.02 (0.21), residues: 586 sheet: -0.76 (0.29), residues: 318 loop : -0.94 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 263 TYR 0.016 0.002 TYR B 425 PHE 0.019 0.002 PHE A 17 TRP 0.028 0.002 TRP C 20 HIS 0.009 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00496 (16533) covalent geometry : angle 0.67051 (22631) hydrogen bonds : bond 0.04474 ( 599) hydrogen bonds : angle 5.40981 ( 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 188 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TRP cc_start: 0.8102 (m100) cc_final: 0.7892 (m100) REVERT: A 217 PHE cc_start: 0.6170 (m-80) cc_final: 0.5823 (m-10) REVERT: A 279 ASP cc_start: 0.7643 (t70) cc_final: 0.7153 (m-30) REVERT: A 332 PHE cc_start: 0.8558 (m-80) cc_final: 0.8117 (m-10) REVERT: A 352 ASP cc_start: 0.6346 (p0) cc_final: 0.4900 (t0) REVERT: A 395 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7232 (ppp) REVERT: B 92 THR cc_start: 0.8740 (m) cc_final: 0.8362 (p) REVERT: B 123 ASP cc_start: 0.8632 (p0) cc_final: 0.8374 (p0) REVERT: B 254 TRP cc_start: 0.9506 (m100) cc_final: 0.9048 (m100) REVERT: B 303 MET cc_start: 0.8359 (tmm) cc_final: 0.7889 (tmm) REVERT: B 435 MET cc_start: 0.4352 (mmt) cc_final: 0.3670 (mmm) REVERT: C 20 TRP cc_start: 0.8040 (t60) cc_final: 0.7827 (t60) REVERT: C 156 GLN cc_start: 0.6225 (OUTLIER) cc_final: 0.5834 (pt0) REVERT: C 309 MET cc_start: 0.8542 (tpp) cc_final: 0.8276 (tpp) REVERT: D 78 PHE cc_start: 0.8427 (t80) cc_final: 0.8093 (t80) REVERT: D 123 ASP cc_start: 0.8573 (p0) cc_final: 0.8336 (p0) REVERT: D 303 MET cc_start: 0.8871 (tmm) cc_final: 0.8645 (tmm) REVERT: D 309 ASP cc_start: 0.8292 (p0) cc_final: 0.8087 (p0) REVERT: D 481 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7190 (ttm-80) outliers start: 49 outliers final: 30 residues processed: 177 average time/residue: 0.1093 time to fit residues: 31.7563 Evaluate side-chains 158 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 403 VAL 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 147 ILE Chi-restraints excluded: chain B residue 205 GLN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 87 GLN 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 329 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 365 PHE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 463 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 63 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 179 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN D 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.101290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.079007 restraints weight = 65744.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.081149 restraints weight = 39979.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.082410 restraints weight = 28479.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.082924 restraints weight = 23045.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.083738 restraints weight = 20740.853| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4328 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= 0.127 Angle : 0.629 9.730 22631 Z= 0.319 Chirality : 0.043 0.253 2484 Planarity : 0.004 0.059 2620 Dihedral : 17.397 173.941 2932 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.63 % Favored : 95.03 % Rotamer: Outliers : 2.82 % Allowed : 17.27 % Favored : 79.91 % 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 aren not related in a simple way. whole: -0.28 (0.20), residues: 1770 helix: 1.14 (0.22), residues: 586 sheet: -0.63 (0.30), residues: 296 loop : -0.91 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 362 TYR 0.011 0.001 TYR D 56 PHE 0.019 0.001 PHE A 17 TRP 0.022 0.001 TRP C 20 HIS 0.027 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00286 (16533) covalent geometry : angle 0.62874 (22631) hydrogen bonds : bond 0.03900 ( 599) hydrogen bonds : angle 5.20285 ( 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 193 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.670 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: 0.7652 (t70) cc_final: 0.7163 (m-30) REVERT: A 352 ASP cc_start: 0.6297 (p0) cc_final: 0.4813 (t0) REVERT: A 395 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7322 (ppp) REVERT: B 92 THR cc_start: 0.8750 (m) cc_final: 0.8341 (p) REVERT: B 303 MET cc_start: 0.8395 (tmm) cc_final: 0.7929 (tmm) REVERT: B 360 HIS cc_start: 0.8629 (m-70) cc_final: 0.8407 (m170) REVERT: B 396 LEU cc_start: 0.8349 (pt) cc_final: 0.8011 (tt) REVERT: B 435 MET cc_start: 0.4551 (mmt) cc_final: 0.3920 (mmp) REVERT: C 156 GLN cc_start: 0.6320 (OUTLIER) cc_final: 0.5800 (pt0) REVERT: C 309 MET cc_start: 0.8646 (tpp) cc_final: 0.8361 (tpp) REVERT: D 9 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: D 78 PHE cc_start: 0.8345 (t80) cc_final: 0.8044 (t80) REVERT: D 123 ASP cc_start: 0.8598 (p0) cc_final: 0.8329 (p0) REVERT: D 303 MET cc_start: 0.8838 (tmm) cc_final: 0.8627 (tmm) REVERT: D 309 ASP cc_start: 0.8259 (p0) cc_final: 0.8050 (p0) REVERT: D 476 GLU cc_start: 0.7875 (pm20) cc_final: 0.6904 (pm20) REVERT: D 481 ARG cc_start: 0.7668 (ttm-80) cc_final: 0.7147 (ttm-80) outliers start: 45 outliers final: 29 residues processed: 181 average time/residue: 0.1126 time to fit residues: 33.1201 Evaluate side-chains 163 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 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 403 TYR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 87 GLN 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 329 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 85 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 48 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 4 optimal weight: 0.0020 chunk 175 optimal weight: 0.4980 chunk 120 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS D 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.102235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.080181 restraints weight = 65225.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.082344 restraints weight = 39347.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.083556 restraints weight = 27864.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.084575 restraints weight = 22528.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.085133 restraints weight = 19524.394| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4465 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= 0.121 Angle : 0.635 10.030 22631 Z= 0.319 Chirality : 0.042 0.268 2484 Planarity : 0.004 0.057 2620 Dihedral : 17.201 173.969 2932 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.75 % Favored : 94.92 % Rotamer: Outliers : 2.44 % Allowed : 17.90 % Favored : 79.66 % 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 aren not related in a simple way. whole: -0.31 (0.20), residues: 1770 helix: 1.09 (0.22), residues: 588 sheet: -0.65 (0.30), residues: 296 loop : -0.90 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 71 TYR 0.015 0.001 TYR A 293 PHE 0.015 0.001 PHE A 17 TRP 0.037 0.001 TRP A 46 HIS 0.027 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00271 (16533) covalent geometry : angle 0.63471 (22631) hydrogen bonds : bond 0.03843 ( 599) hydrogen bonds : angle 5.13471 ( 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 182 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLN cc_start: 0.8707 (pm20) cc_final: 0.8447 (pm20) REVERT: A 277 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6754 (ptp) REVERT: A 279 ASP cc_start: 0.7651 (t70) cc_final: 0.7198 (m-30) REVERT: A 352 ASP cc_start: 0.6360 (p0) cc_final: 0.4839 (t0) REVERT: A 395 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7422 (ppp) REVERT: B 92 THR cc_start: 0.8736 (m) cc_final: 0.8330 (p) REVERT: B 303 MET cc_start: 0.8320 (tmm) cc_final: 0.7861 (tmm) REVERT: B 396 LEU cc_start: 0.8352 (pt) cc_final: 0.8051 (tt) REVERT: B 435 MET cc_start: 0.4535 (mmt) cc_final: 0.4019 (mmp) REVERT: B 470 CYS cc_start: 0.8118 (t) cc_final: 0.7103 (p) REVERT: C 155 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7082 (pm20) REVERT: C 156 GLN cc_start: 0.6342 (OUTLIER) cc_final: 0.5644 (pt0) REVERT: C 309 MET cc_start: 0.8642 (tpp) cc_final: 0.8333 (tpp) REVERT: C 395 MET cc_start: 0.8703 (ppp) cc_final: 0.8454 (ppp) REVERT: D 9 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: D 78 PHE cc_start: 0.8290 (t80) cc_final: 0.7828 (t80) REVERT: D 86 TRP cc_start: 0.8291 (t60) cc_final: 0.7967 (t60) REVERT: D 123 ASP cc_start: 0.8639 (p0) cc_final: 0.8370 (p0) REVERT: D 303 MET cc_start: 0.8842 (tmm) cc_final: 0.8603 (tmm) REVERT: D 309 ASP cc_start: 0.8248 (p0) cc_final: 0.8048 (p0) REVERT: D 476 GLU cc_start: 0.7963 (pm20) cc_final: 0.7000 (pm20) REVERT: D 481 ARG cc_start: 0.7635 (ttm-80) cc_final: 0.7145 (ttm-80) outliers start: 39 outliers final: 28 residues processed: 170 average time/residue: 0.1072 time to fit residues: 30.1355 Evaluate side-chains 170 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 277 MET 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 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 403 TYR 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 B residue 507 ILE Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 87 GLN 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 329 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 85 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 61 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 85 optimal weight: 0.0870 chunk 73 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 overall best weight: 2.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN B 360 HIS D 59 HIS D 302 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.098299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.076125 restraints weight = 67947.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.078046 restraints weight = 42192.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.079354 restraints weight = 30480.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.080078 restraints weight = 24674.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.080635 restraints weight = 21909.455| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 16533 Z= 0.208 Angle : 0.693 12.444 22631 Z= 0.355 Chirality : 0.044 0.301 2484 Planarity : 0.005 0.061 2620 Dihedral : 17.295 172.857 2932 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.42 % Favored : 94.29 % Rotamer: Outliers : 2.57 % Allowed : 19.02 % Favored : 78.41 % 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 aren not related in a simple way. whole: -0.43 (0.20), residues: 1770 helix: 1.01 (0.21), residues: 592 sheet: -0.83 (0.29), residues: 318 loop : -0.95 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 263 TYR 0.018 0.001 TYR D 65 PHE 0.020 0.002 PHE A 45 TRP 0.046 0.002 TRP A 46 HIS 0.031 0.002 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00464 (16533) covalent geometry : angle 0.69350 (22631) hydrogen bonds : bond 0.04256 ( 599) hydrogen bonds : angle 5.25907 ( 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 181 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLN cc_start: 0.8772 (pm20) cc_final: 0.8510 (pm20) REVERT: A 279 ASP cc_start: 0.7660 (t70) cc_final: 0.7172 (m-30) REVERT: A 352 ASP cc_start: 0.6504 (p0) cc_final: 0.5156 (t0) REVERT: A 395 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7455 (ppp) REVERT: B 92 THR cc_start: 0.8802 (m) cc_final: 0.8420 (p) REVERT: B 123 ASP cc_start: 0.8597 (p0) cc_final: 0.8328 (p0) REVERT: B 254 TRP cc_start: 0.9510 (m100) cc_final: 0.8984 (m100) REVERT: B 303 MET cc_start: 0.8376 (tmm) cc_final: 0.7917 (tmm) REVERT: B 396 LEU cc_start: 0.8511 (pt) cc_final: 0.8196 (tt) REVERT: B 435 MET cc_start: 0.4740 (mmt) cc_final: 0.4283 (mmp) REVERT: B 470 CYS cc_start: 0.7844 (t) cc_final: 0.7033 (p) REVERT: C 156 GLN cc_start: 0.6309 (OUTLIER) cc_final: 0.5973 (pt0) REVERT: C 193 MET cc_start: 0.7139 (ttt) cc_final: 0.6548 (tmm) REVERT: C 309 MET cc_start: 0.8551 (tpp) cc_final: 0.8294 (tpp) REVERT: D 78 PHE cc_start: 0.8382 (t80) cc_final: 0.7891 (t80) REVERT: D 86 TRP cc_start: 0.8428 (t60) cc_final: 0.8135 (t60) REVERT: D 481 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7541 (ttm-80) outliers start: 41 outliers final: 29 residues processed: 168 average time/residue: 0.1121 time to fit residues: 30.5492 Evaluate side-chains 162 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 207 HIS 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 360 HIS 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 87 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 329 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 85 LYS 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: 2.9990 chunk 85 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 34 optimal weight: 0.0000 chunk 73 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 176 optimal weight: 0.0770 chunk 123 optimal weight: 0.2980 chunk 108 optimal weight: 9.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS C 370 ASN D 59 HIS D 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.101837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.080409 restraints weight = 66203.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.082365 restraints weight = 40451.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.083709 restraints weight = 29102.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.084294 restraints weight = 23592.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.084873 restraints weight = 21130.236| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4924 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= 0.122 Angle : 0.661 10.468 22631 Z= 0.332 Chirality : 0.043 0.271 2484 Planarity : 0.004 0.057 2620 Dihedral : 17.132 172.373 2932 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.75 % Favored : 94.97 % Rotamer: Outliers : 2.57 % Allowed : 19.34 % Favored : 78.10 % 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 aren not related in a simple way. whole: -0.35 (0.20), residues: 1770 helix: 1.08 (0.22), residues: 590 sheet: -0.72 (0.31), residues: 288 loop : -0.94 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 114 TYR 0.011 0.001 TYR B 148 PHE 0.015 0.001 PHE A 273 TRP 0.045 0.002 TRP A 46 HIS 0.034 0.002 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00274 (16533) covalent geometry : angle 0.66119 (22631) hydrogen bonds : bond 0.03815 ( 599) hydrogen bonds : angle 5.12059 ( 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 191 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.5631 (tpt90) cc_final: 0.3490 (mpt180) REVERT: A 155 GLN cc_start: 0.8772 (pm20) cc_final: 0.8527 (pm20) REVERT: A 279 ASP cc_start: 0.7656 (t70) cc_final: 0.7172 (m-30) REVERT: A 352 ASP cc_start: 0.6550 (p0) cc_final: 0.5245 (t0) REVERT: B 92 THR cc_start: 0.8613 (m) cc_final: 0.8233 (p) REVERT: B 145 ASP cc_start: 0.8726 (m-30) cc_final: 0.8399 (p0) REVERT: B 303 MET cc_start: 0.8354 (tmm) cc_final: 0.7903 (tmm) REVERT: B 396 LEU cc_start: 0.8490 (pt) cc_final: 0.8204 (tt) REVERT: B 435 MET cc_start: 0.4724 (mmt) cc_final: 0.4359 (mmp) REVERT: B 470 CYS cc_start: 0.7622 (t) cc_final: 0.6797 (p) REVERT: C 156 GLN cc_start: 0.6010 (OUTLIER) cc_final: 0.5541 (pt0) REVERT: C 193 MET cc_start: 0.7066 (ttt) cc_final: 0.6339 (tmm) REVERT: C 287 MET cc_start: 0.7386 (tpt) cc_final: 0.6806 (tpt) REVERT: C 309 MET cc_start: 0.8503 (tpp) cc_final: 0.8242 (tpp) REVERT: C 395 MET cc_start: 0.8691 (ppp) cc_final: 0.8454 (ppp) REVERT: D 476 GLU cc_start: 0.8032 (pm20) cc_final: 0.7226 (pm20) REVERT: D 481 ARG cc_start: 0.7628 (ttm-80) cc_final: 0.7335 (ttm-80) outliers start: 41 outliers final: 31 residues processed: 178 average time/residue: 0.1177 time to fit residues: 33.4796 Evaluate side-chains 175 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 105 LEU 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 223 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 360 HIS Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 87 GLN 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 329 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 85 LYS 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: 0.7980 chunk 129 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 98 optimal weight: 0.0020 chunk 68 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN B 360 HIS D 59 HIS D 207 HIS D 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.099566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.077665 restraints weight = 66807.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.079670 restraints weight = 41447.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.080859 restraints weight = 29781.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.081736 restraints weight = 24319.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.082092 restraints weight = 21503.751| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16533 Z= 0.166 Angle : 0.670 9.911 22631 Z= 0.342 Chirality : 0.043 0.281 2484 Planarity : 0.004 0.059 2620 Dihedral : 17.068 172.052 2932 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.37 % Favored : 94.41 % Rotamer: Outliers : 2.13 % Allowed : 19.90 % Favored : 77.97 % 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 aren not related in a simple way. whole: -0.37 (0.20), residues: 1770 helix: 1.11 (0.22), residues: 590 sheet: -0.76 (0.30), residues: 288 loop : -0.98 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 263 TYR 0.013 0.001 TYR D 56 PHE 0.016 0.001 PHE B 365 TRP 0.047 0.002 TRP A 46 HIS 0.022 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00374 (16533) covalent geometry : angle 0.66985 (22631) hydrogen bonds : bond 0.03965 ( 599) hydrogen bonds : angle 5.15221 ( 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 171 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.5507 (tpt90) cc_final: 0.3184 (mpt180) REVERT: A 279 ASP cc_start: 0.7702 (t70) cc_final: 0.7227 (m-30) REVERT: A 352 ASP cc_start: 0.6626 (p0) cc_final: 0.5331 (t0) REVERT: B 92 THR cc_start: 0.8778 (m) cc_final: 0.8436 (p) REVERT: B 123 ASP cc_start: 0.8566 (p0) cc_final: 0.8299 (p0) REVERT: B 145 ASP cc_start: 0.8740 (m-30) cc_final: 0.8420 (p0) REVERT: B 254 TRP cc_start: 0.9453 (m100) cc_final: 0.8980 (m100) REVERT: B 303 MET cc_start: 0.8381 (tmm) cc_final: 0.7924 (tmm) REVERT: B 360 HIS cc_start: 0.8379 (OUTLIER) cc_final: 0.8055 (m90) REVERT: B 396 LEU cc_start: 0.8484 (pt) cc_final: 0.8196 (tt) REVERT: B 435 MET cc_start: 0.4601 (mmt) cc_final: 0.4238 (mmp) REVERT: B 470 CYS cc_start: 0.7569 (t) cc_final: 0.6862 (p) REVERT: C 156 GLN cc_start: 0.6016 (OUTLIER) cc_final: 0.5607 (pt0) REVERT: C 287 MET cc_start: 0.7636 (tpt) cc_final: 0.6945 (tpt) REVERT: C 309 MET cc_start: 0.8557 (tpp) cc_final: 0.8281 (tpp) REVERT: C 395 MET cc_start: 0.8693 (ppp) cc_final: 0.8488 (ppp) REVERT: D 303 MET cc_start: 0.8676 (tmm) cc_final: 0.8444 (tmm) REVERT: D 476 GLU cc_start: 0.8161 (pm20) cc_final: 0.7372 (pm20) REVERT: D 481 ARG cc_start: 0.7739 (ttm-80) cc_final: 0.7461 (ttm-80) outliers start: 34 outliers final: 30 residues processed: 162 average time/residue: 0.1137 time to fit residues: 29.7269 Evaluate side-chains 168 residues out of total 1598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 105 LEU 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 223 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 360 HIS 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 87 GLN 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 329 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 207 HIS 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: 1.9990 chunk 131 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 175 optimal weight: 0.0770 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS D 59 HIS D 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.099294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.077839 restraints weight = 65979.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.079802 restraints weight = 40591.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.080999 restraints weight = 29076.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.081934 restraints weight = 23584.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.082439 restraints weight = 20569.442| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16533 Z= 0.158 Angle : 0.673 11.483 22631 Z= 0.343 Chirality : 0.043 0.275 2484 Planarity : 0.004 0.059 2620 Dihedral : 17.037 171.362 2932 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.97 % Favored : 94.80 % Rotamer: Outliers : 2.25 % Allowed : 19.90 % Favored : 77.85 % 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 aren not related in a simple way. whole: -0.38 (0.20), residues: 1770 helix: 1.06 (0.21), residues: 592 sheet: -0.72 (0.30), residues: 288 loop : -0.96 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 71 TYR 0.021 0.001 TYR D 56 PHE 0.016 0.001 PHE B 365 TRP 0.048 0.002 TRP A 46 HIS 0.021 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00357 (16533) covalent geometry : angle 0.67251 (22631) hydrogen bonds : bond 0.03897 ( 599) hydrogen bonds : angle 5.21312 ( 1625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2700.74 seconds wall clock time: 48 minutes 6.21 seconds (2886.21 seconds total)