Starting phenix.real_space_refine on Thu Sep 18 06:09:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c4e_45183/09_2025/9c4e_45183.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c4e_45183/09_2025/9c4e_45183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c4e_45183/09_2025/9c4e_45183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c4e_45183/09_2025/9c4e_45183.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c4e_45183/09_2025/9c4e_45183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c4e_45183/09_2025/9c4e_45183.map" } resolution = 2.73 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= 0.001 sd= 0.044 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 68 5.16 5 C 9304 2.51 5 N 2536 2.21 5 O 2852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14760 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3690 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 460} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3690 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 460} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3690 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 460} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 3690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3690 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 460} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 3.47, per 1000 atoms: 0.24 Number of scatterers: 14760 At special positions: 0 Unit cell: (128.75, 91.67, 95.79, 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 68 16.00 O 2852 8.00 N 2536 7.00 C 9304 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: 1.15 Conformation dependent library (CDL) restraints added in 633.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3544 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 16 sheets defined 42.9% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 88 through 99 removed outlier: 3.575A pdb=" N THR A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 131 Processing helix chain 'A' and resid 145 through 159 removed outlier: 4.062A pdb=" N GLN A 149 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.869A pdb=" N VAL A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 247 removed outlier: 3.728A pdb=" N GLU A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 271 Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 286 through 292 removed outlier: 4.363A pdb=" N HIS A 289 " --> pdb=" O ASP A 286 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP A 291 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 360 through 370 Processing helix chain 'A' and resid 376 through 385 Processing helix chain 'A' and resid 385 through 392 Processing helix chain 'A' and resid 475 through 487 removed outlier: 5.649A pdb=" N ARG A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 99 removed outlier: 3.571A pdb=" N THR B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 131 Processing helix chain 'B' and resid 145 through 159 removed outlier: 4.064A pdb=" N GLN B 149 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 192 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.867A pdb=" N VAL B 224 " --> pdb=" O PRO B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 247 removed outlier: 3.727A pdb=" N GLU B 232 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 271 Processing helix chain 'B' and resid 279 through 285 Processing helix chain 'B' and resid 286 through 292 removed outlier: 4.363A pdb=" N HIS B 289 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP B 291 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 300 Processing helix chain 'B' and resid 312 through 323 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 360 through 370 Processing helix chain 'B' and resid 376 through 385 Processing helix chain 'B' and resid 385 through 392 Processing helix chain 'B' and resid 475 through 487 removed outlier: 5.666A pdb=" N ARG B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 99 removed outlier: 3.575A pdb=" N THR C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 131 Processing helix chain 'C' and resid 145 through 159 removed outlier: 4.065A pdb=" N GLN C 149 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 192 Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.863A pdb=" N VAL C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 247 removed outlier: 3.727A pdb=" N GLU C 232 " --> pdb=" O PRO C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 271 Processing helix chain 'C' and resid 279 through 285 Processing helix chain 'C' and resid 286 through 292 removed outlier: 4.364A pdb=" N HIS C 289 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP C 291 " --> pdb=" O SER C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'C' and resid 312 through 323 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 343 through 345 No H-bonds generated for 'chain 'C' and resid 343 through 345' Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 360 through 370 Processing helix chain 'C' and resid 376 through 385 Processing helix chain 'C' and resid 385 through 392 Processing helix chain 'C' and resid 475 through 487 removed outlier: 5.666A pdb=" N ARG C 481 " --> pdb=" O PHE C 477 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE C 482 " --> pdb=" O VAL C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 99 removed outlier: 3.576A pdb=" N THR D 93 " --> pdb=" O PHE D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 131 Processing helix chain 'D' and resid 145 through 159 removed outlier: 4.057A pdb=" N GLN D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU D 150 " --> pdb=" O LYS D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 192 Processing helix chain 'D' and resid 201 through 216 Processing helix chain 'D' and resid 220 through 226 removed outlier: 3.864A pdb=" N VAL D 224 " --> pdb=" O PRO D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 247 removed outlier: 3.727A pdb=" N GLU D 232 " --> pdb=" O PRO D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 271 Processing helix chain 'D' and resid 279 through 285 Processing helix chain 'D' and resid 286 through 292 removed outlier: 4.368A pdb=" N HIS D 289 " --> pdb=" O ASP D 286 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP D 291 " --> pdb=" O SER D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 Processing helix chain 'D' and resid 312 through 323 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 360 through 370 Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 385 through 392 Processing helix chain 'D' and resid 475 through 487 removed outlier: 5.665A pdb=" N ARG D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE D 482 " --> pdb=" O VAL D 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 46 removed outlier: 5.320A pdb=" N ILE A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU A 38 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N PHE A 31 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS A 23 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALA A 33 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY A 21 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU A 18 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 46 removed outlier: 5.320A pdb=" N ILE A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU A 38 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N PHE A 31 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS A 23 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALA A 33 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY A 21 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL A 65 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS A 23 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N VAL A 25 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET A 64 " --> pdb=" O TRP A 412 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 445 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP A 413 " --> pdb=" O PRO A 443 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP A 415 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLY A 441 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL A 417 " --> pdb=" O CYS A 439 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N CYS A 439 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N LEU A 444 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU A 455 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL A 446 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 74 removed outlier: 6.178A pdb=" N GLY A 69 " --> pdb=" O MET A 103 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE A 105 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP A 71 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N HIS A 107 " --> pdb=" O ASP A 71 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N HIS A 73 " --> pdb=" O HIS A 107 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR A 102 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N SER A 136 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 104 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N HIS A 138 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP A 106 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASP A 140 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 108 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N SER A 163 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR A 167 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N PHE A 164 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N HIS A 198 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL A 166 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR A 275 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N THR A 253 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLU A 277 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 46 removed outlier: 5.303A pdb=" N ILE B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU B 38 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE B 31 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS B 23 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA B 33 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY B 21 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU B 18 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 41 through 46 removed outlier: 5.303A pdb=" N ILE B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU B 38 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE B 31 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS B 23 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA B 33 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY B 21 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL B 65 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS B 23 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N VAL B 25 " --> pdb=" O PRO B 67 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET B 64 " --> pdb=" O TRP B 412 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 445 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP B 413 " --> pdb=" O PRO B 443 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP B 415 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLY B 441 " --> pdb=" O ASP B 415 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL B 417 " --> pdb=" O CYS B 439 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS B 439 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N LEU B 444 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU B 455 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B 446 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 69 through 74 removed outlier: 6.191A pdb=" N GLY B 69 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE B 105 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP B 71 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N HIS B 107 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 9.889A pdb=" N HIS B 73 " --> pdb=" O HIS B 107 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR B 102 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N SER B 136 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE B 104 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N HIS B 138 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASP B 106 " --> pdb=" O HIS B 138 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP B 140 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 108 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N SER B 163 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR B 167 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N PHE B 164 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N HIS B 198 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL B 166 " --> pdb=" O HIS B 198 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR B 275 " --> pdb=" O TYR B 251 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N THR B 253 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLU B 277 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AA9, first strand: chain 'C' and resid 41 through 46 removed outlier: 5.313A pdb=" N ILE C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU C 38 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE C 31 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS C 23 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALA C 33 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY C 21 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU C 18 " --> pdb=" O ILE C 58 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 46 removed outlier: 5.313A pdb=" N ILE C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU C 38 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE C 31 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS C 23 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALA C 33 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY C 21 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL C 65 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LYS C 23 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL C 25 " --> pdb=" O PRO C 67 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET C 64 " --> pdb=" O TRP C 412 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL C 445 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP C 413 " --> pdb=" O PRO C 443 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP C 415 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY C 441 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL C 417 " --> pdb=" O CYS C 439 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS C 439 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N LEU C 444 " --> pdb=" O GLU C 455 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU C 455 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL C 446 " --> pdb=" O VAL C 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 69 through 74 removed outlier: 6.180A pdb=" N GLY C 69 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE C 105 " --> pdb=" O GLY C 69 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP C 71 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N HIS C 107 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N HIS C 73 " --> pdb=" O HIS C 107 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR C 102 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N SER C 136 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 104 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N HIS C 138 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP C 106 " --> pdb=" O HIS C 138 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASP C 140 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL C 108 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N SER C 163 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR C 167 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N PHE C 164 " --> pdb=" O GLN C 196 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N HIS C 198 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL C 166 " --> pdb=" O HIS C 198 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR C 275 " --> pdb=" O TYR C 251 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N THR C 253 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU C 277 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AB4, first strand: chain 'D' and resid 41 through 46 removed outlier: 5.313A pdb=" N ILE D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU D 38 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N PHE D 31 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS D 23 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA D 33 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY D 21 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU D 18 " --> pdb=" O ILE D 58 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 41 through 46 removed outlier: 5.313A pdb=" N ILE D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU D 38 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N PHE D 31 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS D 23 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA D 33 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY D 21 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL D 65 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS D 23 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N VAL D 25 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET D 64 " --> pdb=" O TRP D 412 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 445 " --> pdb=" O ILE D 411 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP D 413 " --> pdb=" O PRO D 443 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ASP D 415 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLY D 441 " --> pdb=" O ASP D 415 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL D 417 " --> pdb=" O CYS D 439 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS D 439 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N LEU D 444 " --> pdb=" O GLU D 455 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU D 455 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL D 446 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 69 through 74 removed outlier: 6.191A pdb=" N GLY D 69 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE D 105 " --> pdb=" O GLY D 69 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASP D 71 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N HIS D 107 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N HIS D 73 " --> pdb=" O HIS D 107 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR D 102 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N SER D 136 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE D 104 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N HIS D 138 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP D 106 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASP D 140 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL D 108 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N SER D 163 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR D 167 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N PHE D 164 " --> pdb=" O GLN D 196 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N HIS D 198 " --> pdb=" O PHE D 164 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL D 166 " --> pdb=" O HIS D 198 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TYR D 275 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N THR D 253 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU D 277 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 79 through 80 644 hydrogen bonds defined for protein. 1812 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: 2.69 Time building geometry restraints manager: 1.57 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: 4951 1.34 - 1.46: 2651 1.46 - 1.57: 7350 1.57 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 15064 Sorted by residual: bond pdb=" CA VAL D 494 " pdb=" CB VAL D 494 " ideal model delta sigma weight residual 1.537 1.525 0.012 1.29e-02 6.01e+03 9.24e-01 bond pdb=" CB GLN D 327 " pdb=" CG GLN D 327 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.12e-01 bond pdb=" CA SER A 304 " pdb=" C SER A 304 " ideal model delta sigma weight residual 1.520 1.529 -0.009 1.23e-02 6.61e+03 5.56e-01 bond pdb=" CA SER D 304 " pdb=" C SER D 304 " ideal model delta sigma weight residual 1.520 1.529 -0.009 1.23e-02 6.61e+03 5.17e-01 bond pdb=" CA ILE A 104 " pdb=" CB ILE A 104 " ideal model delta sigma weight residual 1.544 1.553 -0.009 1.32e-02 5.74e+03 4.95e-01 ... (remaining 15059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 20272 2.12 - 4.24: 159 4.24 - 6.37: 25 6.37 - 8.49: 0 8.49 - 10.61: 8 Bond angle restraints: 20464 Sorted by residual: angle pdb=" C GLN A 77 " pdb=" N MET A 78 " pdb=" CA MET A 78 " ideal model delta sigma weight residual 120.69 110.08 10.61 2.95e+00 1.15e-01 1.29e+01 angle pdb=" C GLN D 77 " pdb=" N MET D 78 " pdb=" CA MET D 78 " ideal model delta sigma weight residual 120.69 110.10 10.59 2.95e+00 1.15e-01 1.29e+01 angle pdb=" C GLN B 77 " pdb=" N MET B 78 " pdb=" CA MET B 78 " ideal model delta sigma weight residual 120.69 110.13 10.56 2.95e+00 1.15e-01 1.28e+01 angle pdb=" C GLN C 77 " pdb=" N MET C 78 " pdb=" CA MET C 78 " ideal model delta sigma weight residual 120.69 110.15 10.54 2.95e+00 1.15e-01 1.28e+01 angle pdb=" CA ILE A 104 " pdb=" CB ILE A 104 " pdb=" CG1 ILE A 104 " ideal model delta sigma weight residual 110.40 115.01 -4.61 1.70e+00 3.46e-01 7.36e+00 ... (remaining 20459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7982 17.75 - 35.49: 711 35.49 - 53.24: 261 53.24 - 70.99: 38 70.99 - 88.73: 12 Dihedral angle restraints: 9004 sinusoidal: 3484 harmonic: 5520 Sorted by residual: dihedral pdb=" CA SER A 304 " pdb=" C SER A 304 " pdb=" N PRO A 305 " pdb=" CA PRO A 305 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA SER C 304 " pdb=" C SER C 304 " pdb=" N PRO C 305 " pdb=" CA PRO C 305 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA SER B 304 " pdb=" C SER B 304 " pdb=" N PRO B 305 " pdb=" CA PRO B 305 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 9001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1453 0.028 - 0.057: 503 0.057 - 0.085: 175 0.085 - 0.113: 162 0.113 - 0.142: 31 Chirality restraints: 2324 Sorted by residual: chirality pdb=" CA LYS A 130 " pdb=" N LYS A 130 " pdb=" C LYS A 130 " pdb=" CB LYS A 130 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA LYS B 130 " pdb=" N LYS B 130 " pdb=" C LYS B 130 " pdb=" CB LYS B 130 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA LYS D 130 " pdb=" N LYS D 130 " pdb=" C LYS D 130 " pdb=" CB LYS D 130 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 2321 not shown) Planarity restraints: 2668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 304 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO D 305 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 305 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 305 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 304 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO C 305 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 305 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 305 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 304 " 0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO A 305 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 305 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 305 " 0.018 5.00e-02 4.00e+02 ... (remaining 2665 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2092 2.75 - 3.29: 14184 3.29 - 3.83: 27111 3.83 - 4.36: 32959 4.36 - 4.90: 57309 Nonbonded interactions: 133655 Sorted by model distance: nonbonded pdb=" OD1 ASP C 128 " pdb=" OH TYR C 135 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASP A 128 " pdb=" OH TYR A 135 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASP B 128 " pdb=" OH TYR B 135 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP D 128 " pdb=" OH TYR D 135 " model vdw 2.223 3.040 nonbonded pdb=" N GLN D 327 " pdb=" OE1 GLN D 327 " model vdw 2.233 3.120 ... (remaining 133650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.480 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.420 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 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 0.025 15064 Z= 0.116 Angle : 0.532 10.609 20464 Z= 0.273 Chirality : 0.042 0.142 2324 Planarity : 0.003 0.033 2668 Dihedral : 16.117 88.733 5460 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.82 % Allowed : 19.57 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.56 (0.19), residues: 1924 helix: 1.50 (0.19), residues: 748 sheet: -1.08 (0.33), residues: 236 loop : -0.06 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.007 0.001 TYR A 182 PHE 0.006 0.001 PHE B 316 TRP 0.007 0.001 TRP B 295 HIS 0.003 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00261 (15064) covalent geometry : angle 0.53194 (20464) hydrogen bonds : bond 0.14266 ( 612) hydrogen bonds : angle 6.66935 ( 1812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.576 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 162 average time/residue: 0.6925 time to fit residues: 122.1568 Evaluate side-chains 159 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 385 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.6980 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.140997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.113837 restraints weight = 17664.143| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.33 r_work: 0.3239 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 15064 Z= 0.301 Angle : 0.626 7.617 20464 Z= 0.324 Chirality : 0.049 0.150 2324 Planarity : 0.004 0.045 2668 Dihedral : 5.570 56.528 2079 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.58 % Allowed : 18.75 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.30 (0.19), residues: 1924 helix: 1.17 (0.19), residues: 756 sheet: -0.64 (0.32), residues: 276 loop : -0.26 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 400 TYR 0.016 0.003 TYR D 479 PHE 0.012 0.002 PHE D 477 TRP 0.011 0.002 TRP C 295 HIS 0.004 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00732 (15064) covalent geometry : angle 0.62597 (20464) hydrogen bonds : bond 0.04554 ( 612) hydrogen bonds : angle 4.98473 ( 1812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.582 Fit side-chains REVERT: A 125 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6984 (tp30) REVERT: A 325 ASP cc_start: 0.8386 (m-30) cc_final: 0.8092 (m-30) REVERT: A 335 THR cc_start: 0.9180 (p) cc_final: 0.8951 (p) REVERT: A 444 LEU cc_start: 0.8404 (mt) cc_final: 0.8113 (mt) REVERT: B 125 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7005 (tp30) REVERT: B 325 ASP cc_start: 0.8438 (m-30) cc_final: 0.8162 (m-30) REVERT: B 335 THR cc_start: 0.9183 (p) cc_final: 0.8955 (p) REVERT: B 444 LEU cc_start: 0.8402 (mt) cc_final: 0.8110 (mt) REVERT: C 125 GLU cc_start: 0.7475 (tt0) cc_final: 0.7069 (tp30) REVERT: C 325 ASP cc_start: 0.8429 (m-30) cc_final: 0.8141 (m-30) REVERT: C 335 THR cc_start: 0.9190 (p) cc_final: 0.8964 (p) REVERT: C 444 LEU cc_start: 0.8400 (mt) cc_final: 0.8113 (mt) REVERT: D 125 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7008 (tp30) REVERT: D 325 ASP cc_start: 0.8447 (m-30) cc_final: 0.8164 (m-30) REVERT: D 327 GLN cc_start: 0.8463 (mp10) cc_final: 0.8228 (mp10) REVERT: D 335 THR cc_start: 0.9186 (p) cc_final: 0.8960 (p) REVERT: D 444 LEU cc_start: 0.8413 (mt) cc_final: 0.8114 (mt) outliers start: 25 outliers final: 6 residues processed: 173 average time/residue: 0.7125 time to fit residues: 133.9800 Evaluate side-chains 149 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 210 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 145 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120411 restraints weight = 17576.307| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.35 r_work: 0.3331 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15064 Z= 0.109 Angle : 0.491 7.575 20464 Z= 0.252 Chirality : 0.043 0.141 2324 Planarity : 0.003 0.039 2668 Dihedral : 4.157 21.266 2056 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.95 % Allowed : 18.75 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.38 (0.20), residues: 1924 helix: 1.38 (0.19), residues: 760 sheet: -1.27 (0.36), residues: 240 loop : -0.19 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 173 TYR 0.008 0.001 TYR D 251 PHE 0.009 0.001 PHE A 477 TRP 0.010 0.001 TRP C 295 HIS 0.003 0.001 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.00251 (15064) covalent geometry : angle 0.49113 (20464) hydrogen bonds : bond 0.03355 ( 612) hydrogen bonds : angle 4.58357 ( 1812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.568 Fit side-chains REVERT: A 167 TYR cc_start: 0.8988 (m-80) cc_final: 0.8780 (m-80) REVERT: A 335 THR cc_start: 0.9237 (p) cc_final: 0.9023 (p) REVERT: B 167 TYR cc_start: 0.8986 (m-80) cc_final: 0.8777 (m-80) REVERT: B 335 THR cc_start: 0.9221 (p) cc_final: 0.9007 (p) REVERT: B 444 LEU cc_start: 0.8152 (mt) cc_final: 0.7945 (mt) REVERT: B 460 HIS cc_start: 0.7872 (m-70) cc_final: 0.7648 (m-70) REVERT: C 167 TYR cc_start: 0.8998 (m-80) cc_final: 0.8789 (m-80) REVERT: C 335 THR cc_start: 0.9229 (p) cc_final: 0.9017 (p) REVERT: C 444 LEU cc_start: 0.8148 (mt) cc_final: 0.7943 (mt) REVERT: C 460 HIS cc_start: 0.7880 (m-70) cc_final: 0.7656 (m-70) REVERT: D 335 THR cc_start: 0.9231 (p) cc_final: 0.9021 (p) REVERT: D 423 LYS cc_start: 0.9102 (ptmt) cc_final: 0.8654 (mtmm) outliers start: 15 outliers final: 9 residues processed: 192 average time/residue: 0.6115 time to fit residues: 128.8403 Evaluate side-chains 150 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 210 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 60 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 101 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.134944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110440 restraints weight = 17438.121| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.37 r_work: 0.3236 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 15064 Z= 0.276 Angle : 0.590 7.829 20464 Z= 0.304 Chirality : 0.048 0.154 2324 Planarity : 0.004 0.045 2668 Dihedral : 4.567 24.216 2056 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.52 % Allowed : 18.06 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.24 (0.19), residues: 1924 helix: 1.18 (0.19), residues: 756 sheet: -0.86 (0.32), residues: 300 loop : -0.27 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 173 TYR 0.014 0.002 TYR C 479 PHE 0.011 0.002 PHE A 477 TRP 0.011 0.002 TRP B 295 HIS 0.003 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00672 (15064) covalent geometry : angle 0.58984 (20464) hydrogen bonds : bond 0.04312 ( 612) hydrogen bonds : angle 4.73362 ( 1812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.586 Fit side-chains REVERT: A 125 GLU cc_start: 0.7474 (tt0) cc_final: 0.7011 (tp30) REVERT: A 325 ASP cc_start: 0.8419 (m-30) cc_final: 0.8170 (m-30) REVERT: A 335 THR cc_start: 0.9237 (p) cc_final: 0.9034 (p) REVERT: B 125 GLU cc_start: 0.7479 (tt0) cc_final: 0.7022 (tp30) REVERT: B 325 ASP cc_start: 0.8446 (m-30) cc_final: 0.8112 (m-30) REVERT: B 335 THR cc_start: 0.9245 (p) cc_final: 0.9042 (p) REVERT: B 444 LEU cc_start: 0.8460 (mt) cc_final: 0.8154 (mt) REVERT: C 125 GLU cc_start: 0.7439 (tt0) cc_final: 0.7028 (tp30) REVERT: C 325 ASP cc_start: 0.8412 (m-30) cc_final: 0.8162 (m-30) REVERT: C 335 THR cc_start: 0.9242 (p) cc_final: 0.9040 (p) REVERT: C 444 LEU cc_start: 0.8451 (mt) cc_final: 0.8153 (mt) REVERT: D 125 GLU cc_start: 0.7402 (tt0) cc_final: 0.6990 (tp30) REVERT: D 327 GLN cc_start: 0.8438 (mp10) cc_final: 0.8050 (mp10) REVERT: D 335 THR cc_start: 0.9244 (p) cc_final: 0.9043 (p) REVERT: D 423 LYS cc_start: 0.9167 (ptmt) cc_final: 0.8712 (mtmm) outliers start: 24 outliers final: 16 residues processed: 176 average time/residue: 0.7175 time to fit residues: 137.4301 Evaluate side-chains 155 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 210 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 87 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 94 optimal weight: 0.0060 chunk 176 optimal weight: 0.7980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.141671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.117418 restraints weight = 17228.201| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.36 r_work: 0.3336 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15064 Z= 0.099 Angle : 0.485 8.089 20464 Z= 0.248 Chirality : 0.043 0.141 2324 Planarity : 0.003 0.036 2668 Dihedral : 4.129 21.460 2056 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.39 % Allowed : 18.43 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.42 (0.20), residues: 1924 helix: 1.38 (0.19), residues: 760 sheet: -0.76 (0.33), residues: 280 loop : -0.25 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 173 TYR 0.006 0.001 TYR B 182 PHE 0.008 0.001 PHE C 477 TRP 0.010 0.001 TRP B 295 HIS 0.003 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00223 (15064) covalent geometry : angle 0.48494 (20464) hydrogen bonds : bond 0.03176 ( 612) hydrogen bonds : angle 4.45079 ( 1812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.465 Fit side-chains REVERT: A 167 TYR cc_start: 0.8963 (m-80) cc_final: 0.8734 (m-80) REVERT: A 440 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7754 (mmm-85) REVERT: B 167 TYR cc_start: 0.8963 (m-80) cc_final: 0.8735 (m-80) REVERT: B 444 LEU cc_start: 0.8237 (mt) cc_final: 0.8021 (mt) REVERT: C 167 TYR cc_start: 0.8968 (m-80) cc_final: 0.8744 (m-80) REVERT: C 440 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7580 (mmm-85) REVERT: C 444 LEU cc_start: 0.8214 (mt) cc_final: 0.7999 (mt) REVERT: D 325 ASP cc_start: 0.8212 (m-30) cc_final: 0.7771 (m-30) REVERT: D 423 LYS cc_start: 0.9112 (ptmt) cc_final: 0.8744 (mtmm) outliers start: 22 outliers final: 19 residues processed: 201 average time/residue: 0.6418 time to fit residues: 141.5431 Evaluate side-chains 163 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 210 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 129 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 61 optimal weight: 0.0870 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.141925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115054 restraints weight = 17668.617| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.33 r_work: 0.3279 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 15064 Z= 0.207 Angle : 0.544 8.266 20464 Z= 0.279 Chirality : 0.046 0.148 2324 Planarity : 0.003 0.041 2668 Dihedral : 4.404 23.383 2056 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.45 % Allowed : 17.87 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.32 (0.19), residues: 1924 helix: 1.33 (0.19), residues: 756 sheet: -1.15 (0.38), residues: 216 loop : -0.29 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 173 TYR 0.021 0.002 TYR A 251 PHE 0.010 0.001 PHE C 477 TRP 0.010 0.001 TRP B 295 HIS 0.004 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00501 (15064) covalent geometry : angle 0.54414 (20464) hydrogen bonds : bond 0.03854 ( 612) hydrogen bonds : angle 4.54542 ( 1812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.573 Fit side-chains REVERT: A 125 GLU cc_start: 0.7432 (tt0) cc_final: 0.7064 (tp30) REVERT: B 125 GLU cc_start: 0.7444 (tt0) cc_final: 0.7082 (tp30) REVERT: B 325 ASP cc_start: 0.8437 (m-30) cc_final: 0.8176 (m-30) REVERT: B 444 LEU cc_start: 0.8499 (mt) cc_final: 0.8238 (mt) REVERT: B 472 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8430 (mmpt) REVERT: C 125 GLU cc_start: 0.7533 (tt0) cc_final: 0.7160 (tp30) REVERT: C 325 ASP cc_start: 0.8440 (m-30) cc_final: 0.8231 (m-30) REVERT: C 444 LEU cc_start: 0.8474 (mt) cc_final: 0.8218 (mt) REVERT: D 125 GLU cc_start: 0.7533 (tt0) cc_final: 0.7160 (tp30) REVERT: D 325 ASP cc_start: 0.8310 (m-30) cc_final: 0.7930 (m-30) REVERT: D 327 GLN cc_start: 0.8431 (mp10) cc_final: 0.8182 (mp10) REVERT: D 423 LYS cc_start: 0.9153 (ptmt) cc_final: 0.8791 (mtmm) REVERT: D 472 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8437 (mmpt) outliers start: 23 outliers final: 18 residues processed: 176 average time/residue: 0.6776 time to fit residues: 130.1052 Evaluate side-chains 160 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 472 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 55 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.145354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.118667 restraints weight = 17492.971| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.32 r_work: 0.3309 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15064 Z= 0.128 Angle : 0.504 8.589 20464 Z= 0.257 Chirality : 0.043 0.143 2324 Planarity : 0.003 0.038 2668 Dihedral : 4.211 22.202 2056 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.33 % Allowed : 18.24 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.34 (0.20), residues: 1924 helix: 1.34 (0.19), residues: 760 sheet: -1.20 (0.37), residues: 220 loop : -0.25 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 173 TYR 0.019 0.001 TYR A 251 PHE 0.008 0.001 PHE C 477 TRP 0.010 0.001 TRP B 295 HIS 0.003 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00305 (15064) covalent geometry : angle 0.50448 (20464) hydrogen bonds : bond 0.03358 ( 612) hydrogen bonds : angle 4.41685 ( 1812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.594 Fit side-chains REVERT: A 167 TYR cc_start: 0.9001 (m-80) cc_final: 0.8771 (m-80) REVERT: B 167 TYR cc_start: 0.8987 (m-80) cc_final: 0.8758 (m-80) REVERT: B 444 LEU cc_start: 0.8328 (mt) cc_final: 0.8077 (mt) REVERT: C 167 TYR cc_start: 0.8996 (m-80) cc_final: 0.8767 (m-80) REVERT: C 444 LEU cc_start: 0.8332 (mt) cc_final: 0.8091 (mt) REVERT: D 325 ASP cc_start: 0.8257 (m-30) cc_final: 0.7778 (m-30) REVERT: D 327 GLN cc_start: 0.8406 (mp10) cc_final: 0.8103 (mp10) REVERT: D 423 LYS cc_start: 0.9129 (ptmt) cc_final: 0.8761 (mtmm) outliers start: 21 outliers final: 17 residues processed: 195 average time/residue: 0.6062 time to fit residues: 129.9569 Evaluate side-chains 159 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 210 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 112 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 179 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.146397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119538 restraints weight = 17613.151| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.33 r_work: 0.3334 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15064 Z= 0.121 Angle : 0.508 8.679 20464 Z= 0.257 Chirality : 0.043 0.140 2324 Planarity : 0.003 0.037 2668 Dihedral : 4.125 21.820 2056 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.39 % Allowed : 18.43 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.40 (0.20), residues: 1924 helix: 1.38 (0.19), residues: 760 sheet: -1.18 (0.37), residues: 220 loop : -0.22 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 173 TYR 0.008 0.001 TYR D 479 PHE 0.008 0.001 PHE C 477 TRP 0.010 0.001 TRP A 295 HIS 0.003 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00288 (15064) covalent geometry : angle 0.50819 (20464) hydrogen bonds : bond 0.03250 ( 612) hydrogen bonds : angle 4.37881 ( 1812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.464 Fit side-chains REVERT: A 167 TYR cc_start: 0.8984 (m-80) cc_final: 0.8751 (m-80) REVERT: A 440 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7731 (mmm-85) REVERT: B 444 LEU cc_start: 0.8319 (mt) cc_final: 0.8067 (mt) REVERT: C 325 ASP cc_start: 0.8265 (m-30) cc_final: 0.7905 (m-30) REVERT: C 440 ARG cc_start: 0.8112 (mmm-85) cc_final: 0.7753 (mmm-85) REVERT: C 444 LEU cc_start: 0.8326 (mt) cc_final: 0.8086 (mt) REVERT: C 472 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8462 (mmpt) REVERT: D 325 ASP cc_start: 0.8348 (m-30) cc_final: 0.7962 (m-30) REVERT: D 327 GLN cc_start: 0.8427 (mp10) cc_final: 0.8148 (mp10) REVERT: D 423 LYS cc_start: 0.9111 (ptmt) cc_final: 0.8745 (mtmm) outliers start: 22 outliers final: 17 residues processed: 202 average time/residue: 0.6351 time to fit residues: 140.5504 Evaluate side-chains 175 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 385 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 135 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 147 optimal weight: 0.3980 chunk 142 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.142053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115154 restraints weight = 17764.598| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.33 r_work: 0.3265 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15064 Z= 0.208 Angle : 0.563 8.736 20464 Z= 0.286 Chirality : 0.046 0.146 2324 Planarity : 0.004 0.040 2668 Dihedral : 4.380 23.332 2056 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.39 % Allowed : 18.31 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.36 (0.19), residues: 1924 helix: 1.32 (0.19), residues: 752 sheet: -1.14 (0.38), residues: 216 loop : -0.22 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 173 TYR 0.021 0.002 TYR D 251 PHE 0.009 0.001 PHE C 477 TRP 0.010 0.001 TRP B 295 HIS 0.004 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00506 (15064) covalent geometry : angle 0.56332 (20464) hydrogen bonds : bond 0.03810 ( 612) hydrogen bonds : angle 4.50983 ( 1812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.602 Fit side-chains REVERT: A 125 GLU cc_start: 0.7434 (tt0) cc_final: 0.7052 (tp30) REVERT: B 125 GLU cc_start: 0.7440 (tt0) cc_final: 0.7063 (tp30) REVERT: B 444 LEU cc_start: 0.8541 (mt) cc_final: 0.8250 (mt) REVERT: C 125 GLU cc_start: 0.7528 (tt0) cc_final: 0.7153 (tp30) REVERT: C 444 LEU cc_start: 0.8537 (mt) cc_final: 0.8258 (mt) REVERT: C 472 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8427 (mmpt) REVERT: D 125 GLU cc_start: 0.7529 (tt0) cc_final: 0.7155 (tp30) REVERT: D 327 GLN cc_start: 0.8456 (mp10) cc_final: 0.8184 (mp10) REVERT: D 423 LYS cc_start: 0.9148 (ptmt) cc_final: 0.8781 (mtmm) outliers start: 22 outliers final: 20 residues processed: 174 average time/residue: 0.6326 time to fit residues: 120.2316 Evaluate side-chains 167 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 385 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.0020 chunk 186 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.142028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117815 restraints weight = 17267.644| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.36 r_work: 0.3350 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15064 Z= 0.099 Angle : 0.501 8.819 20464 Z= 0.253 Chirality : 0.043 0.139 2324 Planarity : 0.003 0.035 2668 Dihedral : 4.062 21.358 2056 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.20 % Allowed : 18.88 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.42 (0.20), residues: 1924 helix: 1.42 (0.19), residues: 760 sheet: -1.73 (0.41), residues: 176 loop : -0.15 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 173 TYR 0.019 0.001 TYR D 251 PHE 0.007 0.001 PHE C 477 TRP 0.010 0.001 TRP B 295 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00234 (15064) covalent geometry : angle 0.50082 (20464) hydrogen bonds : bond 0.03063 ( 612) hydrogen bonds : angle 4.32746 ( 1812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.573 Fit side-chains REVERT: A 325 ASP cc_start: 0.8234 (m-30) cc_final: 0.7615 (m-30) REVERT: A 440 ARG cc_start: 0.8061 (mmm-85) cc_final: 0.7700 (mmm-85) REVERT: A 467 ARG cc_start: 0.8324 (mtm180) cc_final: 0.8058 (mtm110) REVERT: B 325 ASP cc_start: 0.8292 (m-30) cc_final: 0.7779 (m-30) REVERT: B 444 LEU cc_start: 0.8341 (mt) cc_final: 0.8067 (mt) REVERT: C 325 ASP cc_start: 0.8263 (m-30) cc_final: 0.7705 (m-30) REVERT: C 440 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7684 (mmm-85) REVERT: C 444 LEU cc_start: 0.8345 (mt) cc_final: 0.8074 (mt) outliers start: 19 outliers final: 18 residues processed: 201 average time/residue: 0.6409 time to fit residues: 140.7400 Evaluate side-chains 164 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 385 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 0.0050 chunk 91 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.147545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121049 restraints weight = 17441.215| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.31 r_work: 0.3376 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15064 Z= 0.102 Angle : 0.494 8.653 20464 Z= 0.252 Chirality : 0.043 0.142 2324 Planarity : 0.003 0.036 2668 Dihedral : 3.991 20.854 2056 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.14 % Allowed : 18.50 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.50 (0.20), residues: 1924 helix: 1.48 (0.19), residues: 756 sheet: -1.76 (0.41), residues: 176 loop : -0.08 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 173 TYR 0.018 0.001 TYR B 251 PHE 0.007 0.001 PHE C 348 TRP 0.010 0.001 TRP B 295 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00241 (15064) covalent geometry : angle 0.49388 (20464) hydrogen bonds : bond 0.03053 ( 612) hydrogen bonds : angle 4.28475 ( 1812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4587.11 seconds wall clock time: 79 minutes 18.14 seconds (4758.14 seconds total)