Starting phenix.real_space_refine on Mon Oct 26 09:04:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wrl_66189/10_2026/9wrl_66189.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wrl_66189/10_2026/9wrl_66189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wrl_66189/10_2026/9wrl_66189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wrl_66189/10_2026/9wrl_66189.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wrl_66189/10_2026/9wrl_66189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wrl_66189/10_2026/9wrl_66189.map" } resolution = 3.2 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 12378 2.51 5 N 3498 2.21 5 O 3762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19716 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3287 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 426} Chain: "B" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3287 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 426} Chain: "C" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3287 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 426} Chain: "D" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3287 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 426} Chain: "E" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3284 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 426} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3284 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 426} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.53, per 1000 atoms: 0.23 Number of scatterers: 19716 At special positions: 0 Unit cell: (72, 156, 146.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 3762 8.00 N 3498 7.00 C 12378 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: 1.82 Conformation dependent library (CDL) restraints added in 898.0 milliseconds 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4836 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 25 sheets defined 45.6% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 Processing helix chain 'A' and resid 42 through 48 Processing helix chain 'A' and resid 54 through 60 removed outlier: 3.835A pdb=" N PHE A 60 " --> pdb=" O TRP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 88 Processing helix chain 'A' and resid 113 through 128 Processing helix chain 'A' and resid 159 through 166 removed outlier: 3.901A pdb=" N VAL A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 180 Processing helix chain 'A' and resid 204 through 226 Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 269 through 291 Proline residue: A 284 - end of helix removed outlier: 5.002A pdb=" N GLY A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ILE A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 4.074A pdb=" N ARG A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 364 Processing helix chain 'A' and resid 380 through 388 Processing helix chain 'A' and resid 395 through 405 Processing helix chain 'A' and resid 406 through 414 Processing helix chain 'A' and resid 414 through 433 removed outlier: 3.591A pdb=" N VAL A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 444 Processing helix chain 'B' and resid 4 through 17 Processing helix chain 'B' and resid 42 through 48 Processing helix chain 'B' and resid 54 through 60 removed outlier: 4.045A pdb=" N PHE B 60 " --> pdb=" O TRP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 88 Processing helix chain 'B' and resid 113 through 128 Processing helix chain 'B' and resid 159 through 166 removed outlier: 3.820A pdb=" N VAL B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 Processing helix chain 'B' and resid 204 through 226 Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 269 through 291 Proline residue: B 284 - end of helix removed outlier: 4.891A pdb=" N GLY B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ILE B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 removed outlier: 3.841A pdb=" N ARG B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 364 Processing helix chain 'B' and resid 380 through 387 Processing helix chain 'B' and resid 395 through 406 Processing helix chain 'B' and resid 406 through 414 Processing helix chain 'B' and resid 414 through 433 removed outlier: 3.509A pdb=" N VAL B 418 " --> pdb=" O GLY B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 444 Processing helix chain 'C' and resid 4 through 17 Processing helix chain 'C' and resid 42 through 48 Processing helix chain 'C' and resid 54 through 60 removed outlier: 4.013A pdb=" N PHE C 60 " --> pdb=" O TRP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 88 Processing helix chain 'C' and resid 113 through 128 Processing helix chain 'C' and resid 159 through 166 removed outlier: 3.843A pdb=" N VAL C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 180 Processing helix chain 'C' and resid 204 through 226 Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 269 through 291 Proline residue: C 284 - end of helix removed outlier: 5.255A pdb=" N GLY C 288 " --> pdb=" O PRO C 284 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 removed outlier: 3.818A pdb=" N ARG C 299 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 364 Processing helix chain 'C' and resid 380 through 387 Processing helix chain 'C' and resid 395 through 405 Processing helix chain 'C' and resid 406 through 414 Processing helix chain 'C' and resid 414 through 433 removed outlier: 3.535A pdb=" N VAL C 418 " --> pdb=" O GLY C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 444 Processing helix chain 'D' and resid 4 through 17 removed outlier: 4.216A pdb=" N GLU D 17 " --> pdb=" O GLN D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 48 Processing helix chain 'D' and resid 54 through 60 removed outlier: 4.107A pdb=" N PHE D 60 " --> pdb=" O TRP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 88 Processing helix chain 'D' and resid 113 through 128 Processing helix chain 'D' and resid 159 through 166 removed outlier: 3.815A pdb=" N VAL D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 180 Processing helix chain 'D' and resid 204 through 226 Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 269 through 291 Proline residue: D 284 - end of helix removed outlier: 4.937A pdb=" N GLY D 288 " --> pdb=" O PRO D 284 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ILE D 289 " --> pdb=" O ASP D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 300 removed outlier: 3.843A pdb=" N ARG D 299 " --> pdb=" O VAL D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 364 Processing helix chain 'D' and resid 380 through 387 Processing helix chain 'D' and resid 395 through 405 removed outlier: 3.510A pdb=" N ALA D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 414 Processing helix chain 'D' and resid 414 through 433 removed outlier: 3.514A pdb=" N VAL D 418 " --> pdb=" O GLY D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 444 Processing helix chain 'E' and resid 4 through 17 Processing helix chain 'E' and resid 42 through 48 Processing helix chain 'E' and resid 54 through 60 removed outlier: 3.715A pdb=" N PHE E 60 " --> pdb=" O TRP E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 88 Processing helix chain 'E' and resid 113 through 128 Processing helix chain 'E' and resid 159 through 166 removed outlier: 3.735A pdb=" N VAL E 163 " --> pdb=" O GLY E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 181 Processing helix chain 'E' and resid 204 through 226 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 269 through 291 Proline residue: E 284 - end of helix removed outlier: 5.126A pdb=" N GLY E 288 " --> pdb=" O PRO E 284 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ILE E 289 " --> pdb=" O ASP E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 300 removed outlier: 4.040A pdb=" N ARG E 299 " --> pdb=" O VAL E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 364 Processing helix chain 'E' and resid 380 through 387 Processing helix chain 'E' and resid 395 through 405 removed outlier: 3.763A pdb=" N ALA E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 414 Processing helix chain 'E' and resid 414 through 433 removed outlier: 3.690A pdb=" N VAL E 418 " --> pdb=" O GLY E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 444 Processing helix chain 'F' and resid 4 through 18 Processing helix chain 'F' and resid 42 through 48 Processing helix chain 'F' and resid 54 through 60 removed outlier: 3.970A pdb=" N PHE F 60 " --> pdb=" O TRP F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 88 Processing helix chain 'F' and resid 113 through 129 Processing helix chain 'F' and resid 159 through 166 removed outlier: 3.905A pdb=" N VAL F 163 " --> pdb=" O GLY F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 180 Processing helix chain 'F' and resid 204 through 226 Processing helix chain 'F' and resid 264 through 268 Processing helix chain 'F' and resid 269 through 291 Proline residue: F 284 - end of helix removed outlier: 4.929A pdb=" N GLY F 288 " --> pdb=" O PRO F 284 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE F 289 " --> pdb=" O ASP F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 300 removed outlier: 4.057A pdb=" N ARG F 299 " --> pdb=" O VAL F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 365 Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 395 through 405 removed outlier: 3.772A pdb=" N ALA F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 414 Processing helix chain 'F' and resid 414 through 433 removed outlier: 3.551A pdb=" N VAL F 418 " --> pdb=" O GLY F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 445 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 39 removed outlier: 5.716A pdb=" N VAL A 27 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N PHE A 102 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 39 removed outlier: 5.716A pdb=" N VAL A 27 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N PHE A 102 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 189 removed outlier: 4.389A pdb=" N HIS A 136 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 229 through 231 removed outlier: 6.405A pdb=" N TYR A 309 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL A 321 " --> pdb=" O TYR A 309 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS A 311 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N PHE A 323 " --> pdb=" O CYS A 311 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY A 313 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU A 390 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 39 removed outlier: 6.378A pdb=" N THR B 21 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA B 98 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE B 23 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA B 100 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N THR B 25 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE B 102 " --> pdb=" O THR B 25 " (cutoff:3.500A) removed outlier: 11.163A pdb=" N VAL B 27 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 33 through 39 removed outlier: 6.378A pdb=" N THR B 21 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA B 98 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE B 23 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA B 100 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N THR B 25 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE B 102 " --> pdb=" O THR B 25 " (cutoff:3.500A) removed outlier: 11.163A pdb=" N VAL B 27 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU B 95 " --> pdb=" O ILE B 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 184 through 189 removed outlier: 4.400A pdb=" N HIS B 136 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 184 through 189 removed outlier: 4.400A pdb=" N HIS B 136 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR B 309 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL B 321 " --> pdb=" O TYR B 309 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS B 311 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE B 323 " --> pdb=" O CYS B 311 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY B 313 " --> pdb=" O PHE B 323 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU B 390 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 33 through 39 removed outlier: 6.447A pdb=" N THR C 21 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA C 98 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE C 23 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA C 100 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N THR C 25 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE C 102 " --> pdb=" O THR C 25 " (cutoff:3.500A) removed outlier: 10.955A pdb=" N VAL C 27 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 33 through 39 removed outlier: 6.447A pdb=" N THR C 21 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA C 98 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE C 23 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA C 100 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N THR C 25 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE C 102 " --> pdb=" O THR C 25 " (cutoff:3.500A) removed outlier: 10.955A pdb=" N VAL C 27 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU C 95 " --> pdb=" O ILE C 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 184 through 189 removed outlier: 6.434A pdb=" N SER C 199 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE C 187 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU C 197 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN C 195 " --> pdb=" O PRO C 189 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS C 136 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 229 through 231 removed outlier: 6.610A pdb=" N GLY C 313 " --> pdb=" O PHE C 323 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 309 through 310 removed outlier: 3.825A pdb=" N LEU C 390 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 33 through 39 removed outlier: 6.359A pdb=" N THR D 21 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA D 98 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE D 23 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA D 100 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR D 25 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N PHE D 102 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 11.000A pdb=" N VAL D 27 " --> pdb=" O PHE D 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 33 through 39 removed outlier: 6.359A pdb=" N THR D 21 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA D 98 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE D 23 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA D 100 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR D 25 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N PHE D 102 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 11.000A pdb=" N VAL D 27 " --> pdb=" O PHE D 102 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 184 through 189 removed outlier: 6.437A pdb=" N SER D 199 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE D 187 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU D 197 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN D 195 " --> pdb=" O PRO D 189 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N HIS D 136 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 229 through 231 removed outlier: 6.585A pdb=" N TYR D 309 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL D 321 " --> pdb=" O TYR D 309 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS D 311 " --> pdb=" O VAL D 321 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N PHE D 323 " --> pdb=" O CYS D 311 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY D 313 " --> pdb=" O PHE D 323 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 390 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 33 through 39 removed outlier: 6.461A pdb=" N THR E 21 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA E 98 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE E 23 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA E 100 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N THR E 25 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE E 102 " --> pdb=" O THR E 25 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N VAL E 27 " --> pdb=" O PHE E 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 33 through 39 removed outlier: 6.461A pdb=" N THR E 21 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA E 98 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE E 23 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA E 100 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N THR E 25 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE E 102 " --> pdb=" O THR E 25 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N VAL E 27 " --> pdb=" O PHE E 102 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU E 95 " --> pdb=" O ILE E 91 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 184 through 189 removed outlier: 4.443A pdb=" N HIS E 136 " --> pdb=" O LEU E 200 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 184 through 189 removed outlier: 4.443A pdb=" N HIS E 136 " --> pdb=" O LEU E 200 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TYR E 309 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL E 321 " --> pdb=" O TYR E 309 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS E 311 " --> pdb=" O VAL E 321 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE E 323 " --> pdb=" O CYS E 311 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLY E 313 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU E 390 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 33 through 39 removed outlier: 6.304A pdb=" N THR F 21 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ALA F 98 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE F 23 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA F 100 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N THR F 25 " --> pdb=" O ALA F 100 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N PHE F 102 " --> pdb=" O THR F 25 " (cutoff:3.500A) removed outlier: 10.888A pdb=" N VAL F 27 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 33 through 39 removed outlier: 6.304A pdb=" N THR F 21 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ALA F 98 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE F 23 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA F 100 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N THR F 25 " --> pdb=" O ALA F 100 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N PHE F 102 " --> pdb=" O THR F 25 " (cutoff:3.500A) removed outlier: 10.888A pdb=" N VAL F 27 " --> pdb=" O PHE F 102 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU F 95 " --> pdb=" O ILE F 91 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 184 through 189 removed outlier: 6.424A pdb=" N SER F 199 " --> pdb=" O GLU F 185 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE F 187 " --> pdb=" O GLU F 197 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU F 197 " --> pdb=" O PHE F 187 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLN F 195 " --> pdb=" O PRO F 189 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N HIS F 136 " --> pdb=" O LEU F 200 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 229 through 231 removed outlier: 6.777A pdb=" N TYR F 309 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL F 321 " --> pdb=" O TYR F 309 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N CYS F 311 " --> pdb=" O VAL F 321 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE F 323 " --> pdb=" O CYS F 311 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY F 313 " --> pdb=" O PHE F 323 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU F 390 " --> pdb=" O ALA F 310 " (cutoff:3.500A) 1141 hydrogen bonds defined for protein. 3165 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6836 1.34 - 1.46: 4051 1.46 - 1.58: 9081 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 20088 Sorted by residual: bond pdb=" CG PRO E 369 " pdb=" CD PRO E 369 " ideal model delta sigma weight residual 1.503 1.444 0.059 3.40e-02 8.65e+02 2.96e+00 bond pdb=" CB PRO F 343 " pdb=" CG PRO F 343 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" N LEU E 14 " pdb=" CA LEU E 14 " ideal model delta sigma weight residual 1.459 1.476 -0.017 1.20e-02 6.94e+03 2.06e+00 bond pdb=" CB PRO E 369 " pdb=" CG PRO E 369 " ideal model delta sigma weight residual 1.492 1.556 -0.064 5.00e-02 4.00e+02 1.62e+00 bond pdb=" CB LYS F 407 " pdb=" CG LYS F 407 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.31e+00 ... (remaining 20083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 27027 2.25 - 4.51: 322 4.51 - 6.76: 35 6.76 - 9.02: 6 9.02 - 11.27: 4 Bond angle restraints: 27394 Sorted by residual: angle pdb=" CA GLU E 315 " pdb=" CB GLU E 315 " pdb=" CG GLU E 315 " ideal model delta sigma weight residual 114.10 123.94 -9.84 2.00e+00 2.50e-01 2.42e+01 angle pdb=" N PRO E 369 " pdb=" CD PRO E 369 " pdb=" CG PRO E 369 " ideal model delta sigma weight residual 103.20 95.90 7.30 1.50e+00 4.44e-01 2.37e+01 angle pdb=" CA PRO F 343 " pdb=" N PRO F 343 " pdb=" CD PRO F 343 " ideal model delta sigma weight residual 112.00 106.38 5.62 1.40e+00 5.10e-01 1.61e+01 angle pdb=" CB MET F 446 " pdb=" CG MET F 446 " pdb=" SD MET F 446 " ideal model delta sigma weight residual 112.70 123.97 -11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CA LYS F 365 " pdb=" CB LYS F 365 " pdb=" CG LYS F 365 " ideal model delta sigma weight residual 114.10 121.47 -7.37 2.00e+00 2.50e-01 1.36e+01 ... (remaining 27389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10772 17.95 - 35.89: 916 35.89 - 53.84: 181 53.84 - 71.79: 37 71.79 - 89.73: 18 Dihedral angle restraints: 11924 sinusoidal: 4358 harmonic: 7566 Sorted by residual: dihedral pdb=" CA MET F 268 " pdb=" C MET F 268 " pdb=" N THR F 269 " pdb=" CA THR F 269 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA CYS A 411 " pdb=" C CYS A 411 " pdb=" N ILE A 412 " pdb=" CA ILE A 412 " ideal model delta harmonic sigma weight residual -180.00 -162.20 -17.80 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA HIS A 136 " pdb=" C HIS A 136 " pdb=" N GLU A 137 " pdb=" CA GLU A 137 " ideal model delta harmonic sigma weight residual 180.00 162.43 17.57 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 11921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2861 0.074 - 0.148: 324 0.148 - 0.222: 4 0.222 - 0.296: 0 0.296 - 0.370: 1 Chirality restraints: 3190 Sorted by residual: chirality pdb=" CG LEU C 14 " pdb=" CB LEU C 14 " pdb=" CD1 LEU C 14 " pdb=" CD2 LEU C 14 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA GLU E 315 " pdb=" N GLU E 315 " pdb=" C GLU E 315 " pdb=" CB GLU E 315 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CA LEU E 14 " pdb=" N LEU E 14 " pdb=" C LEU E 14 " pdb=" CB LEU E 14 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 3187 not shown) Planarity restraints: 3636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 342 " -0.045 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO F 343 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO F 343 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 343 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 342 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO D 343 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 343 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 343 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 368 " -0.038 5.00e-02 4.00e+02 5.60e-02 5.01e+00 pdb=" N PRO E 369 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO E 369 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 369 " -0.031 5.00e-02 4.00e+02 ... (remaining 3633 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1860 2.74 - 3.28: 20105 3.28 - 3.82: 34935 3.82 - 4.36: 39254 4.36 - 4.90: 68572 Nonbonded interactions: 164726 Sorted by model distance: nonbonded pdb=" OD1 ASP D 210 " pdb=" OH TYR D 348 " model vdw 2.203 3.040 nonbonded pdb=" O PRO A 376 " pdb=" NH1 ARG A 384 " model vdw 2.240 3.120 nonbonded pdb=" O PRO C 376 " pdb=" NH1 ARG C 384 " model vdw 2.249 3.120 nonbonded pdb=" O GLN D 211 " pdb=" OG1 THR D 215 " model vdw 2.263 3.040 nonbonded pdb=" OE2 GLU E 137 " pdb=" NE2 HIS E 248 " model vdw 2.265 3.120 ... (remaining 164721 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 450)) selection = (chain 'B' and (resid 1 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 450)) selection = (chain 'C' and (resid 1 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 450)) selection = (chain 'D' and (resid 1 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 450)) selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 18.030 Find NCS groups from input model: 0.600 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 0.086 20088 Z= 0.125 Angle : 0.610 11.272 27394 Z= 0.324 Chirality : 0.043 0.370 3190 Planarity : 0.005 0.066 3636 Dihedral : 14.440 89.735 7088 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.40 % Allowed : 19.86 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.16), residues: 2688 helix: 2.34 (0.16), residues: 1056 sheet: 0.92 (0.24), residues: 456 loop : 0.70 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 391 TYR 0.012 0.001 TYR B 309 PHE 0.032 0.002 PHE A 46 TRP 0.012 0.001 TRP D 312 HIS 0.005 0.001 HIS F 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (20088) covalent geometry : angle 0.60971 / 0.32 (27394) hydrogen bonds : bond 0.12106 / 8.49 ( 1058) hydrogen bonds : angle 6.02456 / 4.44 ( 3165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 227 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 398 ASP cc_start: 0.8758 (m-30) cc_final: 0.8488 (m-30) outliers start: 8 outliers final: 3 residues processed: 231 average time/residue: 0.1371 time to fit residues: 49.6186 Evaluate side-chains 217 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 214 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain F residue 442 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 GLN B 304 ASN ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 ASN E 195 GLN ** E 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.124241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.088336 restraints weight = 36537.982| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.65 r_work: 0.3046 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20088 Z= 0.152 Angle : 0.547 9.134 27394 Z= 0.281 Chirality : 0.042 0.307 3190 Planarity : 0.005 0.047 3636 Dihedral : 3.918 21.651 2898 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.52 % Allowed : 16.78 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.16), residues: 2688 helix: 2.36 (0.15), residues: 1104 sheet: 0.71 (0.23), residues: 492 loop : 1.01 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 391 TYR 0.014 0.002 TYR D 348 PHE 0.020 0.001 PHE A 46 TRP 0.009 0.001 TRP D 312 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (20088) covalent geometry : angle 0.54730 / 0.28 (27394) hydrogen bonds : bond 0.03648 / 2.52 ( 1058) hydrogen bonds : angle 4.69242 / 3.42 ( 3165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 MET cc_start: 0.8008 (tpp) cc_final: 0.7749 (tpp) REVERT: A 300 MET cc_start: 0.5756 (mtm) cc_final: 0.4996 (mtm) REVERT: B 13 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7722 (tm-30) REVERT: B 141 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8786 (tt) REVERT: B 300 MET cc_start: 0.5863 (tmm) cc_final: 0.5242 (mtm) REVERT: D 44 ASN cc_start: 0.8820 (p0) cc_final: 0.8601 (p0) REVERT: E 131 ASP cc_start: 0.8443 (m-30) cc_final: 0.8225 (m-30) REVERT: F 84 ASP cc_start: 0.8007 (t0) cc_final: 0.7520 (t0) REVERT: F 108 THR cc_start: 0.8332 (m) cc_final: 0.7767 (p) outliers start: 50 outliers final: 27 residues processed: 260 average time/residue: 0.1381 time to fit residues: 56.8418 Evaluate side-chains 233 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 249 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [26, 177, 118, 146, 195, 3, 237, 162, 65, 49, 13] chunk 26 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 118 optimal weight: 0.0870 chunk 146 optimal weight: 0.8980 chunk 195 optimal weight: 0.0060 chunk 3 optimal weight: 0.0040 chunk 237 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 335 ASN E 44 ASN F 79 GLN F 248 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.126216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.089943 restraints weight = 36701.791| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.72 r_work: 0.3056 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 20088 Z= 0.103 Angle : 0.505 8.900 27394 Z= 0.255 Chirality : 0.041 0.233 3190 Planarity : 0.004 0.049 3636 Dihedral : 3.658 21.613 2892 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.52 % Allowed : 17.04 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.16), residues: 2688 helix: 2.51 (0.15), residues: 1104 sheet: 0.74 (0.24), residues: 468 loop : 0.99 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 391 TYR 0.012 0.001 TYR D 348 PHE 0.015 0.001 PHE A 249 TRP 0.010 0.001 TRP D 312 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (20088) covalent geometry : angle 0.50458 / 0.26 (27394) hydrogen bonds : bond 0.03235 / 2.22 ( 1058) hydrogen bonds : angle 4.33858 / 3.17 ( 3165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 214 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6885 (mt-10) REVERT: A 84 ASP cc_start: 0.8487 (t0) cc_final: 0.7972 (t0) REVERT: A 257 MET cc_start: 0.7816 (mtt) cc_final: 0.7599 (mtt) REVERT: A 300 MET cc_start: 0.5990 (mtm) cc_final: 0.5372 (mtp) REVERT: B 13 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: B 268 MET cc_start: 0.8182 (tpp) cc_final: 0.7968 (tpp) REVERT: B 300 MET cc_start: 0.5706 (tmm) cc_final: 0.5075 (mtm) REVERT: E 246 HIS cc_start: 0.8914 (m-70) cc_final: 0.8703 (m-70) REVERT: F 79 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7241 (mp10) REVERT: F 84 ASP cc_start: 0.8169 (t0) cc_final: 0.7579 (t0) REVERT: F 108 THR cc_start: 0.8367 (m) cc_final: 0.7814 (p) outliers start: 50 outliers final: 30 residues processed: 242 average time/residue: 0.1378 time to fit residues: 52.8418 Evaluate side-chains 231 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 211 GLN Chi-restraints excluded: chain F residue 249 PHE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 442 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [7, 263, 252, 62, 21, 41, 0, 169, 34, 68, 112] chunk 7 optimal weight: 4.9990 chunk 263 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 169 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 248 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.124671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.088563 restraints weight = 36777.884| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.74 r_work: 0.3028 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 20088 Z= 0.109 Angle : 0.488 7.703 27394 Z= 0.248 Chirality : 0.041 0.143 3190 Planarity : 0.004 0.043 3636 Dihedral : 3.567 24.376 2892 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 3.33 % Allowed : 16.78 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.16), residues: 2688 helix: 2.56 (0.15), residues: 1104 sheet: 0.80 (0.24), residues: 468 loop : 0.97 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 42 TYR 0.011 0.001 TYR D 348 PHE 0.015 0.001 PHE A 249 TRP 0.007 0.001 TRP D 155 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (20088) covalent geometry : angle 0.48822 / 0.25 (27394) hydrogen bonds : bond 0.03038 / 2.09 ( 1058) hydrogen bonds : angle 4.19501 / 3.06 ( 3165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 214 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6874 (mt-10) REVERT: A 84 ASP cc_start: 0.8531 (t0) cc_final: 0.8106 (t0) REVERT: A 300 MET cc_start: 0.6090 (mtm) cc_final: 0.5448 (mtp) REVERT: B 13 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: B 141 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8843 (tt) REVERT: B 300 MET cc_start: 0.5792 (tmm) cc_final: 0.5152 (mtm) REVERT: D 81 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7929 (mp) REVERT: E 186 GLN cc_start: 0.7708 (mt0) cc_final: 0.7394 (mt0) REVERT: F 108 THR cc_start: 0.8623 (m) cc_final: 0.8101 (p) outliers start: 66 outliers final: 39 residues processed: 255 average time/residue: 0.1313 time to fit residues: 53.4369 Evaluate side-chains 237 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 211 GLN Chi-restraints excluded: chain F residue 249 PHE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 442 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [243, 267, 84, 14, 11, 12, 150, 200, 265, 163, 90] chunk 243 optimal weight: 0.6980 chunk 267 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 265 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 90 optimal weight: 30.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 HIS F 79 GLN F 136 HIS F 396 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.121940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.086375 restraints weight = 36246.052| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.59 r_work: 0.3011 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20088 Z= 0.114 Angle : 0.502 12.084 27394 Z= 0.253 Chirality : 0.041 0.275 3190 Planarity : 0.004 0.043 3636 Dihedral : 3.550 28.530 2892 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.43 % Allowed : 16.99 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.16), residues: 2688 helix: 2.62 (0.15), residues: 1104 sheet: 0.76 (0.24), residues: 492 loop : 1.03 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 431 TYR 0.010 0.001 TYR D 348 PHE 0.016 0.001 PHE A 249 TRP 0.028 0.001 TRP D 312 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (20088) covalent geometry : angle 0.50247 / 0.25 (27394) hydrogen bonds : bond 0.03006 / 2.07 ( 1058) hydrogen bonds : angle 4.11053 / 2.99 ( 3165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 209 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 84 ASP cc_start: 0.8587 (t0) cc_final: 0.8164 (t0) REVERT: A 300 MET cc_start: 0.5962 (mtm) cc_final: 0.5350 (mtp) REVERT: A 325 LYS cc_start: 0.8369 (mmtp) cc_final: 0.8163 (mptt) REVERT: B 13 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7959 (tm-30) REVERT: B 141 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8782 (tt) REVERT: B 300 MET cc_start: 0.5603 (tmm) cc_final: 0.4942 (mtm) REVERT: B 372 THR cc_start: 0.8087 (m) cc_final: 0.7875 (t) REVERT: D 81 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7770 (mp) REVERT: E 186 GLN cc_start: 0.7759 (mt0) cc_final: 0.7416 (mt0) REVERT: E 203 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8433 (mm-40) REVERT: F 79 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: F 108 THR cc_start: 0.8631 (m) cc_final: 0.8074 (p) REVERT: F 426 GLN cc_start: 0.8659 (mt0) cc_final: 0.8458 (mt0) outliers start: 68 outliers final: 40 residues processed: 253 average time/residue: 0.1355 time to fit residues: 54.2725 Evaluate side-chains 241 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 249 PHE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 442 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [85, 139, 88, 223, 81, 238, 159, 4, 209, 2, 168] chunk 85 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 223 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 238 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 209 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 168 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 246 HIS F 58 HIS F 79 GLN F 248 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.122093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.086167 restraints weight = 36674.029| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.66 r_work: 0.2990 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20088 Z= 0.118 Angle : 0.494 7.451 27394 Z= 0.249 Chirality : 0.041 0.287 3190 Planarity : 0.004 0.045 3636 Dihedral : 3.502 20.605 2892 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.23 % Allowed : 17.39 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.16), residues: 2688 helix: 2.64 (0.15), residues: 1104 sheet: 0.78 (0.24), residues: 492 loop : 1.01 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 391 TYR 0.009 0.001 TYR D 348 PHE 0.015 0.001 PHE A 249 TRP 0.029 0.001 TRP F 312 HIS 0.004 0.001 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (20088) covalent geometry : angle 0.49421 / 0.25 (27394) hydrogen bonds : bond 0.03000 / 2.07 ( 1058) hydrogen bonds : angle 4.10578 / 2.98 ( 3165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 206 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 84 ASP cc_start: 0.8591 (t0) cc_final: 0.8173 (t0) REVERT: A 268 MET cc_start: 0.7880 (tpp) cc_final: 0.7590 (tpp) REVERT: A 300 MET cc_start: 0.6004 (mtm) cc_final: 0.5384 (mtp) REVERT: B 13 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: B 141 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8786 (tt) REVERT: B 300 MET cc_start: 0.5595 (tmm) cc_final: 0.4934 (mtm) REVERT: C 360 ASP cc_start: 0.8660 (t0) cc_final: 0.8333 (t0) REVERT: D 17 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: D 81 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7771 (mp) REVERT: D 325 LYS cc_start: 0.7939 (mmmm) cc_final: 0.7591 (mmmm) REVERT: E 203 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8465 (mm-40) REVERT: E 309 TYR cc_start: 0.6743 (OUTLIER) cc_final: 0.5492 (t80) REVERT: E 339 LYS cc_start: 0.8750 (mmtp) cc_final: 0.8480 (mmtt) REVERT: F 79 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7134 (mp10) REVERT: F 108 THR cc_start: 0.8661 (m) cc_final: 0.8111 (p) REVERT: F 426 GLN cc_start: 0.8710 (mt0) cc_final: 0.8484 (mt0) outliers start: 64 outliers final: 43 residues processed: 249 average time/residue: 0.1306 time to fit residues: 51.4440 Evaluate side-chains 244 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 309 TYR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 249 PHE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 355 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [214, 230, 240, 149, 224, 55, 199, 164, 118, 104, 200] chunk 214 optimal weight: 0.0970 chunk 230 optimal weight: 0.9990 chunk 240 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 224 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 199 optimal weight: 6.9990 chunk 164 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 246 HIS F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.122432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.086696 restraints weight = 36829.264| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.66 r_work: 0.2992 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20088 Z= 0.101 Angle : 0.496 10.369 27394 Z= 0.250 Chirality : 0.041 0.370 3190 Planarity : 0.004 0.045 3636 Dihedral : 3.456 23.444 2892 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.97 % Allowed : 17.84 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.16), residues: 2688 helix: 2.64 (0.15), residues: 1104 sheet: 0.81 (0.24), residues: 492 loop : 1.01 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 386 TYR 0.009 0.001 TYR D 348 PHE 0.015 0.001 PHE A 249 TRP 0.013 0.001 TRP F 312 HIS 0.005 0.001 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (20088) covalent geometry : angle 0.49594 / 0.25 (27394) hydrogen bonds : bond 0.02906 / 2.01 ( 1058) hydrogen bonds : angle 4.04419 / 2.94 ( 3165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 205 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 84 ASP cc_start: 0.8642 (t0) cc_final: 0.8258 (t0) REVERT: A 246 HIS cc_start: 0.8824 (m-70) cc_final: 0.8493 (m-70) REVERT: A 268 MET cc_start: 0.7912 (tpp) cc_final: 0.7597 (tpp) REVERT: A 300 MET cc_start: 0.6070 (mtm) cc_final: 0.5465 (mtp) REVERT: B 13 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: B 141 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8890 (tt) REVERT: B 300 MET cc_start: 0.5747 (tmm) cc_final: 0.5101 (mtm) REVERT: D 17 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: D 81 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7864 (mp) REVERT: D 137 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8135 (mt-10) REVERT: D 325 LYS cc_start: 0.7976 (mmmm) cc_final: 0.7741 (mmmm) REVERT: E 203 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8481 (mm-40) REVERT: E 309 TYR cc_start: 0.6746 (OUTLIER) cc_final: 0.5198 (t80) REVERT: E 339 LYS cc_start: 0.8850 (mmtp) cc_final: 0.8559 (mmtt) REVERT: E 391 ARG cc_start: 0.7181 (tpm170) cc_final: 0.6950 (tpm170) REVERT: F 79 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: F 108 THR cc_start: 0.8763 (m) cc_final: 0.8247 (p) REVERT: F 398 ASP cc_start: 0.9106 (m-30) cc_final: 0.8753 (m-30) REVERT: F 426 GLN cc_start: 0.8665 (mt0) cc_final: 0.8417 (mt0) outliers start: 59 outliers final: 43 residues processed: 242 average time/residue: 0.1370 time to fit residues: 51.9930 Evaluate side-chains 244 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 391 ARG Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 309 TYR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 249 PHE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 379 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [38, 0, 23, 68, 173, 266, 31, 36, 106, 208, 90] chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 0.0570 chunk 173 optimal weight: 7.9990 chunk 266 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 90 optimal weight: 30.0000 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN E 246 HIS ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.115334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.079956 restraints weight = 36588.730| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.56 r_work: 0.2894 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20088 Z= 0.205 Angle : 0.568 9.077 27394 Z= 0.289 Chirality : 0.043 0.327 3190 Planarity : 0.004 0.052 3636 Dihedral : 3.771 26.165 2892 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.02 % Allowed : 18.25 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.16), residues: 2688 helix: 2.50 (0.15), residues: 1104 sheet: 0.59 (0.24), residues: 492 loop : 0.89 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 80 TYR 0.015 0.002 TYR F 191 PHE 0.017 0.002 PHE C 249 TRP 0.017 0.001 TRP B 155 HIS 0.004 0.001 HIS B 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (20088) covalent geometry : angle 0.56819 / 0.29 (27394) hydrogen bonds : bond 0.03489 / 2.40 ( 1058) hydrogen bonds : angle 4.31105 / 3.12 ( 3165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 190 time to evaluate : 0.775 Fit side-chains REVERT: A 41 ARG cc_start: 0.9378 (mmm160) cc_final: 0.9177 (mmm-85) REVERT: A 84 ASP cc_start: 0.8738 (t0) cc_final: 0.8277 (t0) REVERT: A 300 MET cc_start: 0.6137 (mtm) cc_final: 0.5571 (mtp) REVERT: A 339 LYS cc_start: 0.8787 (mtpp) cc_final: 0.8527 (mtpp) REVERT: B 13 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: B 141 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8726 (tt) REVERT: B 300 MET cc_start: 0.6134 (tmm) cc_final: 0.5476 (mtm) REVERT: C 360 ASP cc_start: 0.8720 (t0) cc_final: 0.8495 (t0) REVERT: D 17 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: D 81 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7854 (mp) REVERT: D 137 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8241 (mt-10) REVERT: D 325 LYS cc_start: 0.8351 (mmmm) cc_final: 0.8080 (mmmm) REVERT: E 309 TYR cc_start: 0.6759 (OUTLIER) cc_final: 0.5293 (t80) REVERT: F 79 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: F 108 THR cc_start: 0.8813 (m) cc_final: 0.8309 (p) REVERT: F 398 ASP cc_start: 0.9169 (m-30) cc_final: 0.8810 (m-30) REVERT: F 426 GLN cc_start: 0.8784 (mt0) cc_final: 0.8512 (mt0) outliers start: 60 outliers final: 44 residues processed: 230 average time/residue: 0.1468 time to fit residues: 52.1284 Evaluate side-chains 228 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 309 TYR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain F residue 379 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [116, 88, 244, 75, 165, 59, 230, 130, 13, 68, 147] chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 75 optimal weight: 0.0770 chunk 165 optimal weight: 0.0770 chunk 59 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 186 GLN E 246 HIS F 248 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.118157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.083165 restraints weight = 36072.101| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.54 r_work: 0.2947 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20088 Z= 0.101 Angle : 0.513 10.029 27394 Z= 0.259 Chirality : 0.042 0.378 3190 Planarity : 0.004 0.046 3636 Dihedral : 3.566 24.476 2892 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.37 % Allowed : 19.20 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.17), residues: 2688 helix: 2.63 (0.15), residues: 1104 sheet: 0.67 (0.24), residues: 492 loop : 0.95 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 386 TYR 0.014 0.001 TYR B 191 PHE 0.026 0.001 PHE F 249 TRP 0.013 0.001 TRP F 312 HIS 0.006 0.001 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (20088) covalent geometry : angle 0.51285 / 0.26 (27394) hydrogen bonds : bond 0.02974 / 2.04 ( 1058) hydrogen bonds : angle 4.08785 / 2.96 ( 3165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 0.703 Fit side-chains REVERT: A 84 ASP cc_start: 0.8690 (t0) cc_final: 0.8283 (t0) REVERT: A 246 HIS cc_start: 0.8975 (m-70) cc_final: 0.8625 (m-70) REVERT: A 300 MET cc_start: 0.6119 (mtm) cc_final: 0.5543 (mtp) REVERT: A 339 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8375 (mtpp) REVERT: B 13 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8051 (tm-30) REVERT: B 300 MET cc_start: 0.6286 (tmm) cc_final: 0.5588 (mtm) REVERT: C 360 ASP cc_start: 0.8668 (t0) cc_final: 0.8339 (t0) REVERT: D 17 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8127 (mp0) REVERT: D 81 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7851 (mp) REVERT: D 137 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8245 (mt-10) REVERT: E 203 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8528 (mm-40) REVERT: E 253 MET cc_start: 0.7335 (tpp) cc_final: 0.6953 (tpp) REVERT: E 309 TYR cc_start: 0.6675 (OUTLIER) cc_final: 0.5353 (t80) REVERT: E 339 LYS cc_start: 0.8868 (mmtt) cc_final: 0.8430 (mmtp) REVERT: F 108 THR cc_start: 0.8889 (m) cc_final: 0.8432 (p) REVERT: F 283 LEU cc_start: 0.8914 (tp) cc_final: 0.8643 (tt) REVERT: F 398 ASP cc_start: 0.9142 (m-30) cc_final: 0.8795 (m-30) REVERT: F 426 GLN cc_start: 0.8737 (mt0) cc_final: 0.8450 (mt0) outliers start: 47 outliers final: 36 residues processed: 225 average time/residue: 0.1469 time to fit residues: 50.6478 Evaluate side-chains 225 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 309 TYR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 379 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [134, 250, 124, 74, 56, 42, 82, 97, 263, 99, 181] chunk 134 optimal weight: 4.9990 chunk 250 optimal weight: 0.1980 chunk 124 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 263 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 211 GLN E 246 HIS F 136 HIS F 248 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.115567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.080184 restraints weight = 36807.438| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.56 r_work: 0.2905 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20088 Z= 0.171 Angle : 0.547 9.861 27394 Z= 0.276 Chirality : 0.043 0.395 3190 Planarity : 0.004 0.046 3636 Dihedral : 3.678 27.058 2892 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.27 % Allowed : 19.25 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.16), residues: 2688 helix: 2.60 (0.15), residues: 1104 sheet: 0.59 (0.24), residues: 492 loop : 0.89 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 386 TYR 0.013 0.001 TYR D 191 PHE 0.029 0.002 PHE F 249 TRP 0.012 0.001 TRP D 155 HIS 0.006 0.001 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (20088) covalent geometry : angle 0.54717 / 0.28 (27394) hydrogen bonds : bond 0.03205 / 2.20 ( 1058) hydrogen bonds : angle 4.17791 / 3.03 ( 3165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 0.494 Fit side-chains REVERT: A 84 ASP cc_start: 0.8679 (t0) cc_final: 0.8276 (t0) REVERT: A 300 MET cc_start: 0.6098 (mtm) cc_final: 0.5552 (mtp) REVERT: A 355 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9164 (mp) REVERT: A 407 LYS cc_start: 0.9352 (tppp) cc_final: 0.9048 (tppp) REVERT: A 411 CYS cc_start: 0.8794 (m) cc_final: 0.8437 (m) REVERT: B 13 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: B 300 MET cc_start: 0.6177 (tmm) cc_final: 0.5526 (mtm) REVERT: C 360 ASP cc_start: 0.8682 (t0) cc_final: 0.8236 (t70) REVERT: D 17 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8171 (mp0) REVERT: D 81 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7880 (mp) REVERT: D 137 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8284 (mt-10) REVERT: E 253 MET cc_start: 0.7283 (tpp) cc_final: 0.6963 (tpp) REVERT: E 309 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.5332 (t80) REVERT: F 108 THR cc_start: 0.8900 (m) cc_final: 0.8432 (p) REVERT: F 283 LEU cc_start: 0.8864 (tp) cc_final: 0.8577 (tt) REVERT: F 398 ASP cc_start: 0.9182 (m-30) cc_final: 0.8847 (m-30) REVERT: F 426 GLN cc_start: 0.8796 (mt0) cc_final: 0.8493 (mt0) outliers start: 45 outliers final: 40 residues processed: 216 average time/residue: 0.1454 time to fit residues: 47.8478 Evaluate side-chains 225 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 CYS Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 309 TYR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain F residue 379 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [241, 138, 221, 9, 129, 54, 229, 7, 235, 126, 225] chunk 241 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 129 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 chunk 229 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 126 optimal weight: 0.1980 chunk 225 optimal weight: 20.0000 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 211 GLN F 136 HIS F 248 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.117109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.081857 restraints weight = 36448.161| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.58 r_work: 0.2934 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20088 Z= 0.103 Angle : 0.520 10.241 27394 Z= 0.262 Chirality : 0.042 0.390 3190 Planarity : 0.004 0.047 3636 Dihedral : 3.597 26.144 2892 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.57 % Allowed : 19.41 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.16), residues: 2688 helix: 2.62 (0.15), residues: 1104 sheet: 0.63 (0.24), residues: 492 loop : 0.92 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 391 TYR 0.009 0.001 TYR F 191 PHE 0.026 0.001 PHE F 249 TRP 0.011 0.001 TRP F 312 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (20088) covalent geometry : angle 0.52036 / 0.26 (27394) hydrogen bonds : bond 0.02999 / 2.07 ( 1058) hydrogen bonds : angle 4.07114 / 2.96 ( 3165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4074.29 seconds wall clock time: 70 minutes 33.87 seconds (4233.87 seconds total)