Starting phenix.real_space_refine on Mon Jan 20 02:03:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c4e_45183/01_2025/9c4e_45183.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c4e_45183/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9c4e_45183/01_2025/9c4e_45183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c4e_45183/01_2025/9c4e_45183.map" model { file = "/net/cci-nas-00/data/ceres_data/9c4e_45183/01_2025/9c4e_45183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c4e_45183/01_2025/9c4e_45183.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 8.48, per 1000 atoms: 0.57 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: 3.19 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.88 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: 5.71 Time building geometry restraints manager: 3.77 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.310 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.080 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.140 ------------------------------------------------------------------------------- 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= 0.172 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 : 6.74 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP B 295 HIS 0.003 0.001 HIS B 138 PHE 0.006 0.001 PHE B 316 TYR 0.007 0.001 TYR A 182 ARG 0.004 0.000 ARG A 173 *********************** 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 : 1.693 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 162 average time/residue: 1.4787 time to fit residues: 261.2785 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 : 1.791 ------------------------------------------------------------------------------- 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 162 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 174 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.145048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118029 restraints weight = 17425.864| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.33 r_work: 0.3298 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15064 Z= 0.294 Angle : 0.545 7.203 20464 Z= 0.281 Chirality : 0.045 0.144 2324 Planarity : 0.003 0.037 2668 Dihedral : 5.210 54.535 2079 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.07 % Allowed : 19.44 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1924 helix: 1.43 (0.19), residues: 756 sheet: -1.20 (0.35), residues: 240 loop : -0.12 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 295 HIS 0.003 0.001 HIS B 198 PHE 0.009 0.001 PHE A 477 TYR 0.012 0.002 TYR D 479 ARG 0.004 0.000 ARG A 400 *********************** 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 205 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 1.804 Fit side-chains REVERT: A 78 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8269 (ttp) REVERT: A 167 TYR cc_start: 0.9026 (m-80) cc_final: 0.8756 (m-80) REVERT: A 335 THR cc_start: 0.9170 (p) cc_final: 0.8924 (p) REVERT: B 78 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8264 (ttp) REVERT: B 167 TYR cc_start: 0.9024 (m-80) cc_final: 0.8766 (m-80) REVERT: B 335 THR cc_start: 0.9175 (p) cc_final: 0.8932 (p) REVERT: C 78 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8288 (ttp) REVERT: C 125 GLU cc_start: 0.7519 (tt0) cc_final: 0.7109 (OUTLIER) REVERT: C 167 TYR cc_start: 0.9029 (m-80) cc_final: 0.8765 (m-80) REVERT: C 335 THR cc_start: 0.9175 (p) cc_final: 0.8929 (p) REVERT: D 78 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8260 (ttp) REVERT: D 335 THR cc_start: 0.9178 (p) cc_final: 0.8945 (p) outliers start: 17 outliers final: 3 residues processed: 201 average time/residue: 1.4017 time to fit residues: 308.8145 Evaluate side-chains 147 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain D residue 78 MET 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 7 optimal weight: 5.9990 chunk 149 optimal weight: 0.0980 chunk 80 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 152 optimal weight: 0.2980 chunk 139 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.148288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121569 restraints weight = 17399.415| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.33 r_work: 0.3365 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15064 Z= 0.162 Angle : 0.482 7.391 20464 Z= 0.247 Chirality : 0.043 0.138 2324 Planarity : 0.003 0.036 2668 Dihedral : 4.270 56.035 2059 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.26 % Allowed : 19.00 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.20), residues: 1924 helix: 1.46 (0.19), residues: 760 sheet: -1.76 (0.39), residues: 200 loop : -0.07 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 295 HIS 0.003 0.001 HIS A 138 PHE 0.008 0.001 PHE A 477 TYR 0.006 0.001 TYR A 182 ARG 0.005 0.000 ARG D 173 *********************** 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 204 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 1.881 Fit side-chains REVERT: A 135 TYR cc_start: 0.8518 (p90) cc_final: 0.8249 (p90) REVERT: A 167 TYR cc_start: 0.8983 (m-80) cc_final: 0.8749 (m-80) REVERT: A 335 THR cc_start: 0.9173 (p) cc_final: 0.8929 (p) REVERT: B 78 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8303 (ttp) REVERT: B 167 TYR cc_start: 0.8987 (m-80) cc_final: 0.8750 (m-80) REVERT: C 78 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8287 (ttp) REVERT: C 167 TYR cc_start: 0.8999 (m-80) cc_final: 0.8768 (m-80) REVERT: D 78 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8303 (ttp) REVERT: D 135 TYR cc_start: 0.8547 (p90) cc_final: 0.8294 (p90) outliers start: 20 outliers final: 10 residues processed: 200 average time/residue: 1.4728 time to fit residues: 322.4294 Evaluate side-chains 158 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 1.737 ------------------------------------------------------------------------------- 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 210 GLN Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 130 LYS 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 167 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 0.0060 chunk 40 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 134 optimal weight: 0.3980 overall best weight: 1.2800 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.146918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120069 restraints weight = 17346.343| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.32 r_work: 0.3339 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15064 Z= 0.205 Angle : 0.492 7.653 20464 Z= 0.252 Chirality : 0.043 0.141 2324 Planarity : 0.003 0.035 2668 Dihedral : 4.091 21.296 2056 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.08 % Allowed : 17.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.20), residues: 1924 helix: 1.49 (0.19), residues: 756 sheet: -1.16 (0.36), residues: 240 loop : -0.12 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 295 HIS 0.003 0.001 HIS B 138 PHE 0.008 0.001 PHE C 477 TYR 0.008 0.001 TYR C 479 ARG 0.004 0.000 ARG C 63 *********************** 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 211 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 1.711 Fit side-chains REVERT: A 167 TYR cc_start: 0.8987 (m-80) cc_final: 0.8776 (m-80) REVERT: B 78 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8321 (ttp) REVERT: B 167 TYR cc_start: 0.8992 (m-80) cc_final: 0.8782 (m-80) REVERT: C 78 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8308 (ttp) REVERT: C 167 TYR cc_start: 0.9000 (m-80) cc_final: 0.8793 (m-80) REVERT: C 335 THR cc_start: 0.9192 (p) cc_final: 0.8952 (p) REVERT: D 78 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8313 (ttp) REVERT: D 335 THR cc_start: 0.9209 (p) cc_final: 0.8989 (p) outliers start: 33 outliers final: 22 residues processed: 208 average time/residue: 1.3472 time to fit residues: 308.1131 Evaluate side-chains 166 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.918 ------------------------------------------------------------------------------- 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 136 SER 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 78 MET Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 136 SER 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 78 MET Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 136 SER 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 78 MET Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 136 SER 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 137 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 129 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.138850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.114382 restraints weight = 17340.279| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.36 r_work: 0.3283 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15064 Z= 0.290 Angle : 0.524 8.161 20464 Z= 0.269 Chirality : 0.045 0.146 2324 Planarity : 0.003 0.038 2668 Dihedral : 4.275 22.467 2056 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.77 % Allowed : 18.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1924 helix: 1.41 (0.19), residues: 756 sheet: -0.66 (0.33), residues: 280 loop : -0.19 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 295 HIS 0.003 0.001 HIS B 138 PHE 0.009 0.001 PHE C 477 TYR 0.010 0.002 TYR D 479 ARG 0.003 0.000 ARG B 63 *********************** 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: 28 poor density : 173 time to evaluate : 1.697 Fit side-chains REVERT: A 125 GLU cc_start: 0.7504 (tt0) cc_final: 0.7025 (tp30) REVERT: A 167 TYR cc_start: 0.9031 (m-80) cc_final: 0.8777 (m-80) REVERT: A 472 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8403 (mmpt) REVERT: B 78 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8303 (ttp) REVERT: B 125 GLU cc_start: 0.7513 (tt0) cc_final: 0.7047 (tp30) REVERT: B 167 TYR cc_start: 0.9035 (m-80) cc_final: 0.8777 (m-80) REVERT: B 327 GLN cc_start: 0.8457 (mp10) cc_final: 0.8163 (mp10) REVERT: B 335 THR cc_start: 0.9201 (p) cc_final: 0.8975 (p) REVERT: C 78 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8301 (ttp) REVERT: C 125 GLU cc_start: 0.7514 (tt0) cc_final: 0.7125 (tp30) REVERT: C 167 TYR cc_start: 0.9039 (m-80) cc_final: 0.8786 (m-80) REVERT: C 335 THR cc_start: 0.9182 (p) cc_final: 0.8952 (p) REVERT: C 472 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8404 (mmpt) REVERT: D 78 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8296 (ttp) REVERT: D 125 GLU cc_start: 0.7513 (tt0) cc_final: 0.7026 (tp30) REVERT: D 327 GLN cc_start: 0.8461 (mp10) cc_final: 0.8158 (mp10) REVERT: D 335 THR cc_start: 0.9194 (p) cc_final: 0.8971 (p) REVERT: D 423 LYS cc_start: 0.9137 (ptmt) cc_final: 0.8689 (mtmm) REVERT: D 472 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8420 (mmpt) outliers start: 28 outliers final: 20 residues processed: 198 average time/residue: 1.4197 time to fit residues: 308.2032 Evaluate side-chains 194 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 1.734 ------------------------------------------------------------------------------- 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 A residue 472 LYS Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 78 MET 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 78 MET 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 472 LYS Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 78 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 0.0970 chunk 157 optimal weight: 0.9990 chunk 164 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.144278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117954 restraints weight = 17541.126| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.37 r_work: 0.3330 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15064 Z= 0.192 Angle : 0.489 8.333 20464 Z= 0.249 Chirality : 0.043 0.142 2324 Planarity : 0.003 0.036 2668 Dihedral : 4.138 21.647 2056 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.77 % Allowed : 17.74 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1924 helix: 1.42 (0.19), residues: 760 sheet: -1.16 (0.36), residues: 240 loop : -0.20 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 295 HIS 0.003 0.001 HIS D 138 PHE 0.008 0.001 PHE C 477 TYR 0.010 0.001 TYR B 251 ARG 0.002 0.000 ARG C 63 *********************** 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 199 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 1.680 Fit side-chains REVERT: A 167 TYR cc_start: 0.8987 (m-80) cc_final: 0.8753 (m-80) REVERT: B 78 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8303 (ttp) REVERT: B 167 TYR cc_start: 0.8984 (m-80) cc_final: 0.8744 (m-80) REVERT: B 335 THR cc_start: 0.9207 (p) cc_final: 0.8983 (p) REVERT: C 78 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8321 (ttp) REVERT: C 167 TYR cc_start: 0.8995 (m-80) cc_final: 0.8760 (m-80) REVERT: C 335 THR cc_start: 0.9198 (p) cc_final: 0.8960 (p) REVERT: D 78 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8299 (ttp) REVERT: D 335 THR cc_start: 0.9207 (p) cc_final: 0.8990 (p) REVERT: D 423 LYS cc_start: 0.9103 (ptmt) cc_final: 0.8739 (mtmm) REVERT: D 472 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8421 (mmpt) outliers start: 28 outliers final: 23 residues processed: 195 average time/residue: 1.3454 time to fit residues: 289.2737 Evaluate side-chains 170 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.834 ------------------------------------------------------------------------------- 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 78 MET Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 136 SER 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 78 MET Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 136 SER 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 78 MET Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 136 SER 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 141 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 159 optimal weight: 0.8980 chunk 180 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.144309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.117313 restraints weight = 17744.372| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.35 r_work: 0.3296 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 15064 Z= 0.266 Angle : 0.516 8.417 20464 Z= 0.264 Chirality : 0.045 0.145 2324 Planarity : 0.003 0.038 2668 Dihedral : 4.260 22.472 2056 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.64 % Allowed : 17.87 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1924 helix: 1.38 (0.19), residues: 756 sheet: -1.13 (0.38), residues: 220 loop : -0.17 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 295 HIS 0.003 0.001 HIS C 138 PHE 0.008 0.001 PHE C 477 TYR 0.011 0.002 TYR D 479 ARG 0.006 0.000 ARG B 173 *********************** 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 200 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 1.790 Fit side-chains REVERT: A 167 TYR cc_start: 0.9039 (m-80) cc_final: 0.8795 (m-80) REVERT: A 423 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8855 (ptmt) REVERT: A 472 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8394 (mmpt) REVERT: B 78 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8317 (ttp) REVERT: B 125 GLU cc_start: 0.7516 (tt0) cc_final: 0.7153 (tp30) REVERT: B 167 TYR cc_start: 0.9040 (m-80) cc_final: 0.8795 (m-80) REVERT: B 327 GLN cc_start: 0.8471 (mp10) cc_final: 0.8126 (mp10) REVERT: B 335 THR cc_start: 0.9199 (p) cc_final: 0.8976 (p) REVERT: B 423 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8859 (ptmt) REVERT: C 78 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8318 (ttp) REVERT: C 167 TYR cc_start: 0.9028 (m-80) cc_final: 0.8786 (m-80) REVERT: C 327 GLN cc_start: 0.8509 (mp10) cc_final: 0.8229 (mp10) REVERT: C 335 THR cc_start: 0.9192 (p) cc_final: 0.8965 (p) REVERT: D 327 GLN cc_start: 0.8473 (mp10) cc_final: 0.8111 (mp10) REVERT: D 335 THR cc_start: 0.9199 (p) cc_final: 0.8982 (p) REVERT: D 423 LYS cc_start: 0.9122 (ptmt) cc_final: 0.8758 (mtmm) REVERT: D 472 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8453 (mmpt) outliers start: 26 outliers final: 18 residues processed: 197 average time/residue: 1.3744 time to fit residues: 297.0009 Evaluate side-chains 163 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.853 ------------------------------------------------------------------------------- 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 472 LYS Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 78 MET 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 78 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 129 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 0.0060 chunk 120 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.146492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.119741 restraints weight = 17527.820| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.33 r_work: 0.3351 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15064 Z= 0.187 Angle : 0.490 8.592 20464 Z= 0.250 Chirality : 0.043 0.142 2324 Planarity : 0.003 0.035 2668 Dihedral : 4.129 21.624 2056 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.64 % Allowed : 17.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.20), residues: 1924 helix: 1.42 (0.19), residues: 760 sheet: -1.01 (0.38), residues: 216 loop : -0.18 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 295 HIS 0.003 0.001 HIS A 138 PHE 0.008 0.001 PHE C 477 TYR 0.008 0.001 TYR C 479 ARG 0.007 0.000 ARG B 173 *********************** 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 199 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 1.630 Fit side-chains REVERT: A 423 LYS cc_start: 0.9084 (mtmm) cc_final: 0.8872 (ptmt) REVERT: B 78 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8324 (ttp) REVERT: B 327 GLN cc_start: 0.8500 (mp10) cc_final: 0.8168 (mp10) REVERT: B 335 THR cc_start: 0.9200 (p) cc_final: 0.8978 (p) REVERT: B 423 LYS cc_start: 0.9084 (mtmm) cc_final: 0.8876 (ptmt) REVERT: C 78 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8352 (ttp) REVERT: C 327 GLN cc_start: 0.8531 (mp10) cc_final: 0.8157 (mp10) REVERT: C 335 THR cc_start: 0.9200 (p) cc_final: 0.8979 (p) REVERT: D 423 LYS cc_start: 0.9096 (ptmt) cc_final: 0.8735 (mtmm) REVERT: D 472 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8444 (mmpt) outliers start: 26 outliers final: 18 residues processed: 197 average time/residue: 1.3296 time to fit residues: 288.5018 Evaluate side-chains 165 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.714 ------------------------------------------------------------------------------- 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 78 MET Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 136 SER 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 78 MET Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 136 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 171 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.146872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.120020 restraints weight = 17576.665| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.33 r_work: 0.3336 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1306 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= 0.194 Angle : 0.496 8.797 20464 Z= 0.252 Chirality : 0.043 0.141 2324 Planarity : 0.003 0.036 2668 Dihedral : 4.119 21.629 2056 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.39 % Allowed : 18.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.20), residues: 1924 helix: 1.47 (0.19), residues: 756 sheet: -1.03 (0.38), residues: 216 loop : -0.12 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 295 HIS 0.003 0.001 HIS D 138 PHE 0.008 0.001 PHE C 477 TYR 0.007 0.001 TYR B 182 ARG 0.007 0.000 ARG C 173 *********************** 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 199 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 1.623 Fit side-chains REVERT: A 423 LYS cc_start: 0.9082 (mtmm) cc_final: 0.8866 (ptmt) REVERT: A 467 ARG cc_start: 0.8389 (mtm180) cc_final: 0.8151 (mtm110) REVERT: B 78 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8320 (ttp) REVERT: B 327 GLN cc_start: 0.8514 (mp10) cc_final: 0.8077 (mp10) REVERT: B 335 THR cc_start: 0.9204 (p) cc_final: 0.8982 (p) REVERT: B 423 LYS cc_start: 0.9087 (mtmm) cc_final: 0.8873 (ptmt) REVERT: C 78 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8350 (ttp) REVERT: C 327 GLN cc_start: 0.8484 (mp10) cc_final: 0.8092 (mp10) REVERT: C 335 THR cc_start: 0.9193 (p) cc_final: 0.8969 (p) REVERT: D 472 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8440 (mmpt) outliers start: 22 outliers final: 17 residues processed: 197 average time/residue: 1.3941 time to fit residues: 300.8614 Evaluate side-chains 164 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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 78 MET Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 136 SER 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 78 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 140 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 2 optimal weight: 0.0870 chunk 159 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 0.0570 chunk 168 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.148393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121791 restraints weight = 17586.862| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.33 r_work: 0.3414 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15064 Z= 0.162 Angle : 0.485 8.892 20464 Z= 0.246 Chirality : 0.043 0.139 2324 Planarity : 0.003 0.034 2668 Dihedral : 4.021 20.812 2056 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.45 % Allowed : 18.31 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.20), residues: 1924 helix: 1.48 (0.19), residues: 760 sheet: -1.73 (0.41), residues: 176 loop : -0.01 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 295 HIS 0.003 0.001 HIS B 138 PHE 0.006 0.001 PHE D 348 TYR 0.007 0.001 TYR B 182 ARG 0.007 0.000 ARG A 173 ********************** 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 203 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 1.704 Fit side-chains REVERT: A 423 LYS cc_start: 0.9066 (mtmm) cc_final: 0.8848 (ptmt) REVERT: A 467 ARG cc_start: 0.8304 (mtm180) cc_final: 0.8081 (mtm110) REVERT: B 78 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8271 (ttp) REVERT: B 335 THR cc_start: 0.9193 (p) cc_final: 0.8962 (p) REVERT: B 423 LYS cc_start: 0.9072 (mtmm) cc_final: 0.8857 (ptmt) REVERT: B 467 ARG cc_start: 0.8407 (mtm110) cc_final: 0.8160 (mtm180) REVERT: C 78 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8282 (ttp) REVERT: C 335 THR cc_start: 0.9184 (p) cc_final: 0.8950 (p) REVERT: C 423 LYS cc_start: 0.9059 (mtmm) cc_final: 0.8849 (ptmt) REVERT: C 467 ARG cc_start: 0.8266 (mtm180) cc_final: 0.8038 (mtm110) REVERT: D 472 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8375 (mmpt) outliers start: 23 outliers final: 18 residues processed: 198 average time/residue: 1.4604 time to fit residues: 317.2952 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 : 1.783 ------------------------------------------------------------------------------- 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 78 MET Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 136 SER 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 78 MET Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 136 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 5 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 185 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 147 optimal weight: 0.0980 chunk 76 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.141585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.117429 restraints weight = 17240.285| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.35 r_work: 0.3347 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15064 Z= 0.181 Angle : 0.488 8.725 20464 Z= 0.249 Chirality : 0.043 0.140 2324 Planarity : 0.003 0.035 2668 Dihedral : 4.038 20.977 2056 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.39 % Allowed : 18.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1924 helix: 1.48 (0.19), residues: 760 sheet: -1.06 (0.38), residues: 216 loop : -0.07 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 295 HIS 0.003 0.001 HIS A 138 PHE 0.007 0.001 PHE C 477 TYR 0.019 0.002 TYR A 251 ARG 0.007 0.000 ARG D 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9092.83 seconds wall clock time: 163 minutes 33.92 seconds (9813.92 seconds total)