Starting phenix.real_space_refine on Tue Dec 31 02:30:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c4e_45183/12_2024/9c4e_45183.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c4e_45183/12_2024/9c4e_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_45183/12_2024/9c4e_45183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c4e_45183/12_2024/9c4e_45183.map" model { file = "/net/cci-nas-00/data/ceres_data/9c4e_45183/12_2024/9c4e_45183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c4e_45183/12_2024/9c4e_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-5532/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: 7.83, per 1000 atoms: 0.53 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: 3.36 Conformation dependent library (CDL) restraints added in 2.2 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: 1.87 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: 5.79 Time building geometry restraints manager: 3.86 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.960 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.080 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.030 ------------------------------------------------------------------------------- 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 : 1.675 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 162 average time/residue: 1.5052 time to fit residues: 266.0961 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 : 1.754 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 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 : 1.797 Fit side-chains REVERT: A 167 TYR cc_start: 0.8766 (m-80) cc_final: 0.8455 (m-80) REVERT: A 335 THR cc_start: 0.9007 (p) cc_final: 0.8704 (p) REVERT: A 444 LEU cc_start: 0.7817 (mt) cc_final: 0.7560 (mt) REVERT: B 167 TYR cc_start: 0.8776 (m-80) cc_final: 0.8474 (m-80) REVERT: B 335 THR cc_start: 0.9009 (p) cc_final: 0.8709 (p) REVERT: B 444 LEU cc_start: 0.7806 (mt) cc_final: 0.7555 (mt) REVERT: C 125 GLU cc_start: 0.6930 (tt0) cc_final: 0.6609 (OUTLIER) REVERT: C 167 TYR cc_start: 0.8760 (m-80) cc_final: 0.8460 (m-80) REVERT: C 335 THR cc_start: 0.9007 (p) cc_final: 0.8703 (p) REVERT: C 444 LEU cc_start: 0.7814 (mt) cc_final: 0.7562 (mt) REVERT: D 335 THR cc_start: 0.9011 (p) cc_final: 0.8721 (p) REVERT: D 444 LEU cc_start: 0.7821 (mt) cc_final: 0.7562 (mt) outliers start: 17 outliers final: 3 residues processed: 201 average time/residue: 1.3955 time to fit residues: 308.1359 Evaluate side-chains 147 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN 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 96 optimal weight: 10.0000 chunk 54 optimal weight: 0.0870 chunk 145 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 174 optimal weight: 0.7980 chunk 188 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15064 Z= 0.213 Angle : 0.503 7.465 20464 Z= 0.258 Chirality : 0.044 0.141 2324 Planarity : 0.003 0.039 2668 Dihedral : 4.159 21.508 2056 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.45 % Allowed : 18.88 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.45 (0.20), residues: 1924 helix: 1.43 (0.19), residues: 756 sheet: -1.17 (0.36), residues: 240 loop : -0.15 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 295 HIS 0.002 0.001 HIS C 138 PHE 0.008 0.001 PHE C 477 TYR 0.009 0.001 TYR C 479 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 206 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 1.533 Fit side-chains REVERT: A 135 TYR cc_start: 0.8091 (p90) cc_final: 0.7884 (p90) REVERT: A 167 TYR cc_start: 0.8731 (m-80) cc_final: 0.8467 (m-80) REVERT: A 440 ARG cc_start: 0.7468 (mmm-85) cc_final: 0.7213 (mmm-85) REVERT: A 444 LEU cc_start: 0.7820 (mt) cc_final: 0.7547 (mt) REVERT: B 135 TYR cc_start: 0.8080 (p90) cc_final: 0.7871 (p90) REVERT: B 167 TYR cc_start: 0.8741 (m-80) cc_final: 0.8484 (m-80) REVERT: B 444 LEU cc_start: 0.7818 (mt) cc_final: 0.7552 (mt) REVERT: C 135 TYR cc_start: 0.8041 (p90) cc_final: 0.7820 (p90) REVERT: C 167 TYR cc_start: 0.8725 (m-80) cc_final: 0.8476 (m-80) REVERT: C 440 ARG cc_start: 0.7466 (mmm-85) cc_final: 0.7201 (mmm-85) REVERT: C 444 LEU cc_start: 0.7816 (mt) cc_final: 0.7548 (mt) REVERT: D 335 THR cc_start: 0.9045 (p) cc_final: 0.8766 (p) REVERT: D 444 LEU cc_start: 0.7836 (mt) cc_final: 0.7564 (mt) REVERT: D 449 GLN cc_start: 0.7907 (mt0) cc_final: 0.7706 (mt0) outliers start: 23 outliers final: 10 residues processed: 206 average time/residue: 1.3667 time to fit residues: 309.0428 Evaluate side-chains 163 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 130 LYS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 210 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 chunk 185 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15064 Z= 0.148 Angle : 0.473 7.512 20464 Z= 0.241 Chirality : 0.042 0.137 2324 Planarity : 0.003 0.032 2668 Dihedral : 3.979 20.394 2056 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.33 % Allowed : 18.62 % Favored : 80.05 % 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: 1.55 (0.19), residues: 752 sheet: -1.67 (0.40), residues: 196 loop : -0.15 (0.20), residues: 976 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 0.008 0.001 PHE C 477 TYR 0.007 0.001 TYR B 182 ARG 0.003 0.000 ARG D 173 *********************** 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: 21 poor density : 190 time to evaluate : 1.614 Fit side-chains REVERT: A 135 TYR cc_start: 0.7928 (p90) cc_final: 0.7619 (p90) REVERT: A 167 TYR cc_start: 0.8670 (m-80) cc_final: 0.8419 (m-80) REVERT: A 327 GLN cc_start: 0.8281 (mp10) cc_final: 0.7926 (mp10) REVERT: A 440 ARG cc_start: 0.7469 (mmm-85) cc_final: 0.7227 (mmm-85) REVERT: B 135 TYR cc_start: 0.7926 (p90) cc_final: 0.7624 (p90) REVERT: B 167 TYR cc_start: 0.8681 (m-80) cc_final: 0.8436 (m-80) REVERT: B 327 GLN cc_start: 0.8254 (mp10) cc_final: 0.7902 (mp10) REVERT: C 135 TYR cc_start: 0.7932 (p90) cc_final: 0.7624 (p90) REVERT: C 167 TYR cc_start: 0.8665 (m-80) cc_final: 0.8433 (m-80) REVERT: C 270 LYS cc_start: 0.7536 (mppt) cc_final: 0.7233 (mppt) REVERT: C 327 GLN cc_start: 0.8256 (mp10) cc_final: 0.7907 (mp10) REVERT: C 335 THR cc_start: 0.9140 (p) cc_final: 0.8893 (p) REVERT: C 440 ARG cc_start: 0.7468 (mmm-85) cc_final: 0.7218 (mmm-85) REVERT: D 135 TYR cc_start: 0.7960 (p90) cc_final: 0.7636 (p90) REVERT: D 423 LYS cc_start: 0.9030 (ptmt) cc_final: 0.8508 (mtmm) outliers start: 21 outliers final: 18 residues processed: 209 average time/residue: 1.4638 time to fit residues: 334.9742 Evaluate side-chains 162 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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 72 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 210 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 15064 Z= 0.377 Angle : 0.557 8.243 20464 Z= 0.285 Chirality : 0.047 0.148 2324 Planarity : 0.003 0.039 2668 Dihedral : 4.406 23.259 2056 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.52 % Allowed : 17.68 % Favored : 80.81 % 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: 0.44 (0.20), residues: 1924 helix: 1.34 (0.19), residues: 756 sheet: -0.59 (0.33), residues: 276 loop : -0.23 (0.21), residues: 892 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 0.009 0.002 PHE C 477 TYR 0.011 0.002 TYR C 479 ARG 0.005 0.001 ARG C 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 171 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 1.710 Fit side-chains REVERT: A 125 GLU cc_start: 0.6906 (tt0) cc_final: 0.6495 (tp30) REVERT: A 327 GLN cc_start: 0.8330 (mp10) cc_final: 0.7807 (mp10) REVERT: A 440 ARG cc_start: 0.7619 (mmm-85) cc_final: 0.7225 (mmm-85) REVERT: A 444 LEU cc_start: 0.8292 (mt) cc_final: 0.7956 (mt) REVERT: B 83 MET cc_start: 0.7168 (ptt) cc_final: 0.6860 (ptt) REVERT: B 125 GLU cc_start: 0.6912 (tt0) cc_final: 0.6503 (tp30) REVERT: B 327 GLN cc_start: 0.8311 (mp10) cc_final: 0.7794 (mp10) REVERT: B 444 LEU cc_start: 0.8307 (mt) cc_final: 0.7955 (mt) REVERT: C 125 GLU cc_start: 0.6823 (tt0) cc_final: 0.6479 (tp30) REVERT: C 327 GLN cc_start: 0.8314 (mp10) cc_final: 0.7797 (mp10) REVERT: C 440 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.7317 (mmm-85) REVERT: C 444 LEU cc_start: 0.8305 (mt) cc_final: 0.7976 (mt) REVERT: D 83 MET cc_start: 0.7179 (ptt) cc_final: 0.6863 (ptt) REVERT: D 125 GLU cc_start: 0.6889 (tt0) cc_final: 0.6484 (tp30) REVERT: D 327 GLN cc_start: 0.8296 (mp10) cc_final: 0.7856 (mp10) REVERT: D 444 LEU cc_start: 0.8303 (mt) cc_final: 0.7963 (mt) outliers start: 24 outliers final: 16 residues processed: 171 average time/residue: 1.5670 time to fit residues: 292.0323 Evaluate side-chains 159 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 210 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 15064 Z= 0.197 Angle : 0.496 8.334 20464 Z= 0.252 Chirality : 0.043 0.143 2324 Planarity : 0.003 0.036 2668 Dihedral : 4.162 21.852 2056 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.26 % Allowed : 17.30 % Favored : 81.44 % 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: 1.39 (0.19), residues: 760 sheet: -0.67 (0.33), residues: 280 loop : -0.23 (0.21), residues: 884 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 0.008 0.001 PHE C 477 TYR 0.008 0.001 TYR A 479 ARG 0.005 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 197 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 1.794 Fit side-chains REVERT: A 167 TYR cc_start: 0.8724 (m-80) cc_final: 0.8444 (m-80) REVERT: A 327 GLN cc_start: 0.8314 (mp10) cc_final: 0.7792 (mp10) REVERT: A 440 ARG cc_start: 0.7566 (mmm-85) cc_final: 0.7150 (mmm-85) REVERT: A 444 LEU cc_start: 0.8158 (mt) cc_final: 0.7827 (mt) REVERT: B 167 TYR cc_start: 0.8731 (m-80) cc_final: 0.8455 (m-80) REVERT: B 327 GLN cc_start: 0.8291 (mp10) cc_final: 0.7772 (mp10) REVERT: B 444 LEU cc_start: 0.8203 (mt) cc_final: 0.7874 (mt) REVERT: C 167 TYR cc_start: 0.8713 (m-80) cc_final: 0.8449 (m-80) REVERT: C 327 GLN cc_start: 0.8295 (mp10) cc_final: 0.7779 (mp10) REVERT: C 440 ARG cc_start: 0.7568 (mmm-85) cc_final: 0.7145 (mmm-85) REVERT: C 444 LEU cc_start: 0.8157 (mt) cc_final: 0.7829 (mt) REVERT: D 327 GLN cc_start: 0.8357 (mp10) cc_final: 0.7887 (mp10) REVERT: D 423 LYS cc_start: 0.9052 (ptmt) cc_final: 0.8649 (mtmm) REVERT: D 444 LEU cc_start: 0.8167 (mt) cc_final: 0.7831 (mt) outliers start: 20 outliers final: 18 residues processed: 197 average time/residue: 1.5087 time to fit residues: 326.7347 Evaluate side-chains 164 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 210 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 156 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 15064 Z= 0.371 Angle : 0.561 8.516 20464 Z= 0.286 Chirality : 0.046 0.147 2324 Planarity : 0.004 0.040 2668 Dihedral : 4.445 23.710 2056 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.45 % Allowed : 17.42 % Favored : 81.12 % 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: 0.36 (0.19), residues: 1924 helix: 1.26 (0.19), residues: 756 sheet: -0.59 (0.34), residues: 276 loop : -0.28 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 295 HIS 0.003 0.001 HIS A 138 PHE 0.009 0.002 PHE C 477 TYR 0.021 0.002 TYR C 251 ARG 0.006 0.001 ARG A 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 168 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 1.690 Fit side-chains REVERT: A 125 GLU cc_start: 0.6759 (tt0) cc_final: 0.6474 (tp30) REVERT: B 83 MET cc_start: 0.7164 (ptt) cc_final: 0.6803 (ptt) REVERT: B 125 GLU cc_start: 0.6766 (tt0) cc_final: 0.6495 (tp30) REVERT: C 125 GLU cc_start: 0.6799 (tt0) cc_final: 0.6477 (tp30) REVERT: D 125 GLU cc_start: 0.6887 (tt0) cc_final: 0.6483 (tp30) REVERT: D 325 ASP cc_start: 0.8165 (m-30) cc_final: 0.7957 (m-30) REVERT: D 327 GLN cc_start: 0.8332 (mp10) cc_final: 0.7770 (mp10) REVERT: D 423 LYS cc_start: 0.9073 (ptmt) cc_final: 0.8668 (mtmm) outliers start: 23 outliers final: 16 residues processed: 167 average time/residue: 1.5285 time to fit residues: 279.0075 Evaluate side-chains 158 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 210 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 145 optimal weight: 0.2980 chunk 168 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 15064 Z= 0.180 Angle : 0.496 8.755 20464 Z= 0.251 Chirality : 0.043 0.142 2324 Planarity : 0.003 0.035 2668 Dihedral : 4.128 21.701 2056 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.33 % Allowed : 17.74 % Favored : 80.93 % 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: 1.39 (0.19), residues: 760 sheet: -0.63 (0.33), residues: 280 loop : -0.22 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 295 HIS 0.003 0.001 HIS A 138 PHE 0.008 0.001 PHE C 477 TYR 0.019 0.001 TYR C 251 ARG 0.007 0.000 ARG C 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 204 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 1.766 Fit side-chains REVERT: A 167 TYR cc_start: 0.8695 (m-80) cc_final: 0.8421 (m-80) REVERT: A 325 ASP cc_start: 0.7712 (m-30) cc_final: 0.7043 (m-30) REVERT: A 423 LYS cc_start: 0.9119 (mtmm) cc_final: 0.8913 (mtmm) REVERT: A 440 ARG cc_start: 0.7546 (mmm-85) cc_final: 0.7133 (mmm-85) REVERT: A 444 LEU cc_start: 0.8243 (mt) cc_final: 0.7908 (mt) REVERT: B 167 TYR cc_start: 0.8707 (m-80) cc_final: 0.8436 (m-80) REVERT: B 325 ASP cc_start: 0.7692 (m-30) cc_final: 0.7060 (m-30) REVERT: B 423 LYS cc_start: 0.8977 (ptmt) cc_final: 0.8598 (mtmm) REVERT: B 444 LEU cc_start: 0.8242 (mt) cc_final: 0.7903 (mt) REVERT: C 167 TYR cc_start: 0.8692 (m-80) cc_final: 0.8434 (m-80) REVERT: C 325 ASP cc_start: 0.7977 (m-30) cc_final: 0.7554 (m-30) REVERT: C 423 LYS cc_start: 0.9119 (mtmm) cc_final: 0.8911 (mtmm) REVERT: C 440 ARG cc_start: 0.7546 (mmm-85) cc_final: 0.7120 (mmm-85) REVERT: C 444 LEU cc_start: 0.8183 (mt) cc_final: 0.7856 (mt) REVERT: D 327 GLN cc_start: 0.8334 (mp10) cc_final: 0.7807 (mp10) REVERT: D 423 LYS cc_start: 0.9047 (ptmt) cc_final: 0.8644 (mtmm) REVERT: D 444 LEU cc_start: 0.8252 (mt) cc_final: 0.7920 (mt) outliers start: 21 outliers final: 17 residues processed: 204 average time/residue: 1.3900 time to fit residues: 312.4235 Evaluate side-chains 168 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 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 130 LYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 210 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 52 optimal weight: 0.4980 chunk 155 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15064 Z= 0.188 Angle : 0.503 8.745 20464 Z= 0.253 Chirality : 0.043 0.140 2324 Planarity : 0.003 0.035 2668 Dihedral : 4.097 21.612 2056 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.14 % Allowed : 17.99 % Favored : 80.87 % 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: 0.45 (0.20), residues: 1924 helix: 1.40 (0.19), residues: 760 sheet: -1.12 (0.38), residues: 220 loop : -0.17 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 295 HIS 0.003 0.001 HIS C 138 PHE 0.008 0.001 PHE C 477 TYR 0.019 0.002 TYR D 251 ARG 0.007 0.000 ARG D 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 196 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 1.601 Fit side-chains REVERT: A 167 TYR cc_start: 0.8691 (m-80) cc_final: 0.8464 (m-80) REVERT: A 325 ASP cc_start: 0.7721 (m-30) cc_final: 0.7085 (m-30) REVERT: A 423 LYS cc_start: 0.9116 (mtmm) cc_final: 0.8905 (mtmm) REVERT: A 440 ARG cc_start: 0.7553 (mmm-85) cc_final: 0.7149 (mmm-85) REVERT: A 444 LEU cc_start: 0.8151 (mt) cc_final: 0.7824 (mt) REVERT: B 167 TYR cc_start: 0.8702 (m-80) cc_final: 0.8477 (m-80) REVERT: B 325 ASP cc_start: 0.7709 (m-30) cc_final: 0.7065 (m-30) REVERT: B 423 LYS cc_start: 0.8977 (ptmt) cc_final: 0.8597 (mtmm) REVERT: B 444 LEU cc_start: 0.8173 (mt) cc_final: 0.7846 (mt) REVERT: C 167 TYR cc_start: 0.8686 (m-80) cc_final: 0.8473 (m-80) REVERT: C 325 ASP cc_start: 0.8043 (m-30) cc_final: 0.7631 (m-30) REVERT: C 423 LYS cc_start: 0.9116 (mtmm) cc_final: 0.8904 (mtmm) REVERT: C 440 ARG cc_start: 0.7553 (mmm-85) cc_final: 0.7136 (mmm-85) REVERT: C 444 LEU cc_start: 0.8168 (mt) cc_final: 0.7843 (mt) REVERT: D 327 GLN cc_start: 0.8369 (mp10) cc_final: 0.7839 (mp10) REVERT: D 423 LYS cc_start: 0.9047 (ptmt) cc_final: 0.8641 (mtmm) REVERT: D 444 LEU cc_start: 0.8142 (mt) cc_final: 0.7808 (mt) outliers start: 18 outliers final: 18 residues processed: 196 average time/residue: 1.4166 time to fit residues: 304.4878 Evaluate side-chains 170 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 1.724 ------------------------------------------------------------------------------- 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 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 130 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 191 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15064 Z= 0.175 Angle : 0.495 8.804 20464 Z= 0.252 Chirality : 0.043 0.141 2324 Planarity : 0.003 0.035 2668 Dihedral : 4.040 21.146 2056 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.52 % Allowed : 17.87 % Favored : 80.62 % 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: 0.52 (0.20), residues: 1924 helix: 1.46 (0.19), residues: 756 sheet: -1.05 (0.38), residues: 216 loop : -0.14 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 295 HIS 0.003 0.001 HIS C 138 PHE 0.007 0.001 PHE C 477 TYR 0.011 0.001 TYR C 251 ARG 0.007 0.000 ARG D 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 193 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 1.664 Fit side-chains REVERT: A 78 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7895 (ptt) REVERT: A 325 ASP cc_start: 0.7710 (m-30) cc_final: 0.7148 (m-30) REVERT: A 423 LYS cc_start: 0.9134 (mtmm) cc_final: 0.8920 (mtmm) REVERT: A 440 ARG cc_start: 0.7563 (mmm-85) cc_final: 0.7147 (mmm-85) REVERT: A 444 LEU cc_start: 0.8135 (mt) cc_final: 0.7799 (mt) REVERT: A 467 ARG cc_start: 0.7751 (mtm180) cc_final: 0.7426 (mtm180) REVERT: B 78 MET cc_start: 0.8230 (ptm) cc_final: 0.7875 (ptt) REVERT: B 325 ASP cc_start: 0.7687 (m-30) cc_final: 0.7120 (m-30) REVERT: B 444 LEU cc_start: 0.8129 (mt) cc_final: 0.7802 (mt) REVERT: B 467 ARG cc_start: 0.7811 (mtm180) cc_final: 0.7494 (mtm180) REVERT: C 78 MET cc_start: 0.8224 (ptm) cc_final: 0.7875 (ptt) REVERT: C 325 ASP cc_start: 0.8008 (m-30) cc_final: 0.7624 (m-30) REVERT: C 423 LYS cc_start: 0.9114 (mtmm) cc_final: 0.8901 (mtmm) REVERT: C 440 ARG cc_start: 0.7602 (mmm-85) cc_final: 0.7183 (mmm-85) REVERT: C 444 LEU cc_start: 0.8134 (mt) cc_final: 0.7800 (mt) REVERT: C 467 ARG cc_start: 0.7808 (mtm180) cc_final: 0.7531 (mtm110) REVERT: D 78 MET cc_start: 0.8199 (ptm) cc_final: 0.7852 (ptt) REVERT: D 327 GLN cc_start: 0.8380 (mp10) cc_final: 0.7855 (mp10) REVERT: D 444 LEU cc_start: 0.8131 (mt) cc_final: 0.7800 (mt) outliers start: 24 outliers final: 18 residues processed: 192 average time/residue: 1.5077 time to fit residues: 315.6967 Evaluate side-chains 174 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 78 MET 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 130 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain C residue 72 VAL 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 136 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 210 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 140 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 133 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.142430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115946 restraints weight = 17504.613| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.35 r_work: 0.3310 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15064 Z= 0.284 Angle : 0.535 8.667 20464 Z= 0.274 Chirality : 0.045 0.152 2324 Planarity : 0.003 0.037 2668 Dihedral : 4.238 22.531 2056 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.20 % Allowed : 18.12 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.40 (0.19), residues: 752 sheet: -1.15 (0.38), residues: 220 loop : -0.14 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 295 HIS 0.003 0.001 HIS A 138 PHE 0.007 0.001 PHE B 392 TYR 0.021 0.002 TYR C 251 ARG 0.006 0.001 ARG D 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4938.27 seconds wall clock time: 90 minutes 28.87 seconds (5428.87 seconds total)