Starting phenix.real_space_refine on Sat Feb 7 13:47:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k97_36977/02_2026/8k97_36977.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k97_36977/02_2026/8k97_36977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k97_36977/02_2026/8k97_36977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k97_36977/02_2026/8k97_36977.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k97_36977/02_2026/8k97_36977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k97_36977/02_2026/8k97_36977.map" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 168 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 42 5.16 5 B 6 2.79 5 C 21264 2.51 5 N 6024 2.21 5 O 6312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33654 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "F" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "E" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "D" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "C" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5576 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'BO2': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'BO2': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'BO2': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'BO2': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'BO2': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'BO2': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.44, per 1000 atoms: 0.22 Number of scatterers: 33654 At special positions: 0 Unit cell: (130.38, 145.14, 164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 6 15.00 O 6312 8.00 N 6024 7.00 C 21264 6.00 B 6 5.00 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.4 seconds 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 54 sheets defined 55.1% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 58 through 70 Processing helix chain 'A' and resid 96 through 119 removed outlier: 4.059A pdb=" N HIS A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 153 removed outlier: 4.171A pdb=" N ALA A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 224 through 242 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 314 through 319 Processing helix chain 'A' and resid 322 through 332 Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.690A pdb=" N GLY A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 Processing helix chain 'A' and resid 393 through 408 removed outlier: 3.517A pdb=" N GLY A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 427 Processing helix chain 'A' and resid 436 through 451 Processing helix chain 'A' and resid 456 through 471 removed outlier: 3.707A pdb=" N SER A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 531 through 535 Processing helix chain 'A' and resid 539 through 557 Processing helix chain 'A' and resid 583 through 597 Processing helix chain 'A' and resid 621 through 636 Processing helix chain 'A' and resid 649 through 654 removed outlier: 4.650A pdb=" N ALA A 652 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 694 through 719 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 58 through 70 Processing helix chain 'F' and resid 96 through 119 removed outlier: 4.066A pdb=" N HIS F 100 " --> pdb=" O GLY F 96 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASN F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG F 114 " --> pdb=" O LEU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 153 removed outlier: 4.171A pdb=" N ALA F 153 " --> pdb=" O GLU F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 221 Proline residue: F 216 - end of helix Processing helix chain 'F' and resid 224 through 242 Processing helix chain 'F' and resid 246 through 250 Processing helix chain 'F' and resid 273 through 278 Processing helix chain 'F' and resid 293 through 295 No H-bonds generated for 'chain 'F' and resid 293 through 295' Processing helix chain 'F' and resid 300 through 305 Processing helix chain 'F' and resid 314 through 321 removed outlier: 3.710A pdb=" N GLU F 320 " --> pdb=" O SER F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 363 through 369 removed outlier: 3.698A pdb=" N GLY F 369 " --> pdb=" O GLU F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 379 Processing helix chain 'F' and resid 393 through 408 removed outlier: 3.512A pdb=" N GLY F 408 " --> pdb=" O LEU F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 427 Processing helix chain 'F' and resid 436 through 451 Processing helix chain 'F' and resid 456 through 471 removed outlier: 3.706A pdb=" N SER F 471 " --> pdb=" O ARG F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 539 through 557 Processing helix chain 'F' and resid 583 through 597 Processing helix chain 'F' and resid 621 through 636 Processing helix chain 'F' and resid 649 through 654 removed outlier: 4.637A pdb=" N ALA F 652 " --> pdb=" O ALA F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 657 through 666 Processing helix chain 'F' and resid 676 through 686 removed outlier: 3.546A pdb=" N ALA F 680 " --> pdb=" O THR F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 694 through 719 Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 58 through 70 Processing helix chain 'E' and resid 96 through 119 removed outlier: 4.059A pdb=" N HIS E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASN E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 153 removed outlier: 4.175A pdb=" N ALA E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 221 Proline residue: E 216 - end of helix Processing helix chain 'E' and resid 224 through 242 Processing helix chain 'E' and resid 246 through 250 Processing helix chain 'E' and resid 273 through 278 Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 314 through 321 Processing helix chain 'E' and resid 322 through 332 Processing helix chain 'E' and resid 363 through 369 removed outlier: 3.651A pdb=" N GLY E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 379 Processing helix chain 'E' and resid 393 through 408 removed outlier: 3.508A pdb=" N GLY E 408 " --> pdb=" O LEU E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 427 Processing helix chain 'E' and resid 436 through 451 Processing helix chain 'E' and resid 456 through 471 removed outlier: 3.721A pdb=" N SER E 471 " --> pdb=" O ARG E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 539 through 557 Processing helix chain 'E' and resid 583 through 597 Processing helix chain 'E' and resid 621 through 636 Processing helix chain 'E' and resid 649 through 654 removed outlier: 4.622A pdb=" N ALA E 652 " --> pdb=" O ALA E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 666 Processing helix chain 'E' and resid 676 through 686 removed outlier: 3.527A pdb=" N ALA E 680 " --> pdb=" O THR E 676 " (cutoff:3.500A) Processing helix chain 'E' and resid 694 through 719 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 58 through 70 Processing helix chain 'D' and resid 96 through 119 removed outlier: 4.058A pdb=" N HIS D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ASN D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 153 removed outlier: 4.171A pdb=" N ALA D 153 " --> pdb=" O GLU D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 221 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 224 through 242 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 273 through 278 Processing helix chain 'D' and resid 293 through 295 No H-bonds generated for 'chain 'D' and resid 293 through 295' Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 314 through 319 Processing helix chain 'D' and resid 322 through 332 Processing helix chain 'D' and resid 363 through 369 removed outlier: 3.688A pdb=" N GLY D 369 " --> pdb=" O GLU D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 379 Processing helix chain 'D' and resid 393 through 408 removed outlier: 3.518A pdb=" N GLY D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 427 Processing helix chain 'D' and resid 436 through 451 Processing helix chain 'D' and resid 456 through 471 removed outlier: 3.706A pdb=" N SER D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 539 through 557 Processing helix chain 'D' and resid 583 through 597 Processing helix chain 'D' and resid 621 through 636 Processing helix chain 'D' and resid 649 through 654 removed outlier: 4.651A pdb=" N ALA D 652 " --> pdb=" O ALA D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 666 Processing helix chain 'D' and resid 676 through 686 Processing helix chain 'D' and resid 694 through 719 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 58 through 70 Processing helix chain 'C' and resid 96 through 119 removed outlier: 4.064A pdb=" N HIS C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ASN C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 153 removed outlier: 4.171A pdb=" N ALA C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 221 Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 224 through 242 Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 273 through 278 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 314 through 321 removed outlier: 3.702A pdb=" N GLU C 320 " --> pdb=" O SER C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 332 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.699A pdb=" N GLY C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 Processing helix chain 'C' and resid 393 through 408 removed outlier: 3.512A pdb=" N GLY C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 427 Processing helix chain 'C' and resid 436 through 451 Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.706A pdb=" N SER C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 539 through 557 Processing helix chain 'C' and resid 583 through 597 Processing helix chain 'C' and resid 621 through 636 Processing helix chain 'C' and resid 649 through 654 removed outlier: 4.637A pdb=" N ALA C 652 " --> pdb=" O ALA C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 666 Processing helix chain 'C' and resid 676 through 686 removed outlier: 3.542A pdb=" N ALA C 680 " --> pdb=" O THR C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 719 Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 58 through 70 Processing helix chain 'B' and resid 96 through 119 removed outlier: 4.058A pdb=" N HIS B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 153 removed outlier: 4.173A pdb=" N ALA B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 221 Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 224 through 242 Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 314 through 321 removed outlier: 3.560A pdb=" N GLU B 320 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 332 Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.646A pdb=" N GLY B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 379 Processing helix chain 'B' and resid 393 through 408 removed outlier: 3.508A pdb=" N GLY B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 436 through 451 Processing helix chain 'B' and resid 456 through 471 removed outlier: 3.721A pdb=" N SER B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 539 through 557 Processing helix chain 'B' and resid 583 through 597 Processing helix chain 'B' and resid 621 through 636 Processing helix chain 'B' and resid 649 through 654 removed outlier: 4.622A pdb=" N ALA B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 676 through 686 removed outlier: 3.528A pdb=" N ALA B 680 " --> pdb=" O THR B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 269 removed outlier: 4.675A pdb=" N ASP A 313 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU A 310 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL A 361 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU A 312 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N HIS A 48 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 382 " --> pdb=" O HIS A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 253 through 254 Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 157 Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 286 removed outlier: 3.904A pdb=" N LEU A 284 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA7, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AA8, first strand: chain 'A' and resid 527 through 530 removed outlier: 6.705A pdb=" N HIS A 527 " --> pdb=" O ILE A 567 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU A 569 " --> pdb=" O HIS A 527 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A 529 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N PHE A 571 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N GLU A 498 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N VAL A 606 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASN A 500 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA A 605 " --> pdb=" O ILE A 645 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 609 through 610 Processing sheet with id=AB1, first strand: chain 'F' and resid 266 through 269 removed outlier: 4.636A pdb=" N ASP F 313 " --> pdb=" O GLU F 269 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU F 310 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL F 361 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU F 312 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N HIS F 48 " --> pdb=" O PHE F 380 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE F 382 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 253 through 254 Processing sheet with id=AB3, first strand: chain 'F' and resid 156 through 157 Processing sheet with id=AB4, first strand: chain 'F' and resid 280 through 281 Processing sheet with id=AB5, first strand: chain 'F' and resid 284 through 286 removed outlier: 3.918A pdb=" N LEU F 284 " --> pdb=" O SER F 291 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 389 through 391 Processing sheet with id=AB7, first strand: chain 'F' and resid 494 through 496 Processing sheet with id=AB8, first strand: chain 'F' and resid 527 through 530 removed outlier: 6.691A pdb=" N HIS F 527 " --> pdb=" O ILE F 567 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU F 569 " --> pdb=" O HIS F 527 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE F 529 " --> pdb=" O LEU F 569 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N PHE F 571 " --> pdb=" O ILE F 529 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N GLU F 498 " --> pdb=" O LEU F 604 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N VAL F 606 " --> pdb=" O GLU F 498 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASN F 500 " --> pdb=" O VAL F 606 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA F 605 " --> pdb=" O ILE F 645 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL F 644 " --> pdb=" O TYR F 672 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL F 674 " --> pdb=" O VAL F 644 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU F 646 " --> pdb=" O VAL F 674 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 609 through 610 Processing sheet with id=AC1, first strand: chain 'E' and resid 266 through 269 removed outlier: 4.672A pdb=" N ASP E 313 " --> pdb=" O GLU E 269 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU E 310 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL E 361 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU E 312 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N HIS E 48 " --> pdb=" O PHE E 380 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE E 382 " --> pdb=" O HIS E 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 253 through 254 Processing sheet with id=AC3, first strand: chain 'E' and resid 156 through 157 Processing sheet with id=AC4, first strand: chain 'E' and resid 280 through 281 Processing sheet with id=AC5, first strand: chain 'E' and resid 284 through 286 removed outlier: 3.914A pdb=" N LEU E 284 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AC7, first strand: chain 'E' and resid 494 through 496 Processing sheet with id=AC8, first strand: chain 'E' and resid 527 through 530 removed outlier: 6.697A pdb=" N HIS E 527 " --> pdb=" O ILE E 567 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU E 569 " --> pdb=" O HIS E 527 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE E 529 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N PHE E 571 " --> pdb=" O ILE E 529 " (cutoff:3.500A) removed outlier: 9.473A pdb=" N GLU E 498 " --> pdb=" O LEU E 604 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N VAL E 606 " --> pdb=" O GLU E 498 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASN E 500 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA E 605 " --> pdb=" O ILE E 645 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 609 through 611 removed outlier: 3.911A pdb=" N LYS E 615 " --> pdb=" O ASP E 611 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 266 through 269 removed outlier: 4.669A pdb=" N ASP D 313 " --> pdb=" O GLU D 269 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU D 310 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL D 361 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU D 312 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N HIS D 48 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 382 " --> pdb=" O HIS D 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD3, first strand: chain 'D' and resid 156 through 157 Processing sheet with id=AD4, first strand: chain 'D' and resid 280 through 281 Processing sheet with id=AD5, first strand: chain 'D' and resid 284 through 286 removed outlier: 3.941A pdb=" N LEU D 284 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AD7, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AD8, first strand: chain 'D' and resid 527 through 530 removed outlier: 6.695A pdb=" N HIS D 527 " --> pdb=" O ILE D 567 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU D 569 " --> pdb=" O HIS D 527 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE D 529 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N PHE D 571 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N GLU D 498 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N VAL D 606 " --> pdb=" O GLU D 498 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASN D 500 " --> pdb=" O VAL D 606 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA D 605 " --> pdb=" O ILE D 645 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 609 through 610 Processing sheet with id=AE1, first strand: chain 'C' and resid 266 through 269 removed outlier: 4.639A pdb=" N ASP C 313 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU C 310 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL C 361 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU C 312 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N HIS C 48 " --> pdb=" O PHE C 380 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 382 " --> pdb=" O HIS C 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 253 through 254 Processing sheet with id=AE3, first strand: chain 'C' and resid 156 through 157 Processing sheet with id=AE4, first strand: chain 'C' and resid 280 through 281 Processing sheet with id=AE5, first strand: chain 'C' and resid 284 through 286 removed outlier: 3.922A pdb=" N LEU C 284 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 389 through 391 Processing sheet with id=AE7, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AE8, first strand: chain 'C' and resid 527 through 530 removed outlier: 6.706A pdb=" N HIS C 527 " --> pdb=" O ILE C 567 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU C 569 " --> pdb=" O HIS C 527 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE C 529 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N PHE C 571 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N GLU C 498 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N VAL C 606 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN C 500 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA C 605 " --> pdb=" O ILE C 645 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 609 through 610 Processing sheet with id=AF1, first strand: chain 'B' and resid 266 through 269 removed outlier: 4.641A pdb=" N ASP B 313 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU B 310 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL B 361 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU B 312 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N HIS B 48 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 382 " --> pdb=" O HIS B 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 253 through 254 Processing sheet with id=AF3, first strand: chain 'B' and resid 156 through 157 Processing sheet with id=AF4, first strand: chain 'B' and resid 280 through 281 Processing sheet with id=AF5, first strand: chain 'B' and resid 284 through 286 removed outlier: 3.870A pdb=" N LEU B 284 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AF7, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AF8, first strand: chain 'B' and resid 527 through 530 removed outlier: 6.700A pdb=" N HIS B 527 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU B 569 " --> pdb=" O HIS B 527 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE B 529 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N PHE B 571 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 9.472A pdb=" N GLU B 498 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N VAL B 606 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASN B 500 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA B 605 " --> pdb=" O ILE B 645 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 609 through 611 removed outlier: 3.960A pdb=" N LYS B 615 " --> pdb=" O ASP B 611 " (cutoff:3.500A) 1931 hydrogen bonds defined for protein. 5613 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: 7.77 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 11867 1.37 - 1.51: 10590 1.51 - 1.66: 11785 1.66 - 1.80: 63 1.80 - 1.95: 15 Bond restraints: 34320 Sorted by residual: bond pdb=" O4 PO4 C 801 " pdb=" P PO4 C 801 " ideal model delta sigma weight residual 1.568 1.947 -0.379 2.00e-02 2.50e+03 3.60e+02 bond pdb=" O4 PO4 B 801 " pdb=" P PO4 B 801 " ideal model delta sigma weight residual 1.568 1.947 -0.379 2.00e-02 2.50e+03 3.59e+02 bond pdb=" O4 PO4 D 801 " pdb=" P PO4 D 801 " ideal model delta sigma weight residual 1.568 1.947 -0.379 2.00e-02 2.50e+03 3.58e+02 bond pdb=" O4 PO4 A 801 " pdb=" P PO4 A 801 " ideal model delta sigma weight residual 1.568 1.946 -0.378 2.00e-02 2.50e+03 3.58e+02 bond pdb=" O4 PO4 F 801 " pdb=" P PO4 F 801 " ideal model delta sigma weight residual 1.568 1.946 -0.378 2.00e-02 2.50e+03 3.58e+02 ... (remaining 34315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 45958 2.35 - 4.70: 567 4.70 - 7.06: 45 7.06 - 9.41: 14 9.41 - 11.76: 6 Bond angle restraints: 46590 Sorted by residual: angle pdb=" N ILE E 558 " pdb=" CA ILE E 558 " pdb=" C ILE E 558 " ideal model delta sigma weight residual 113.47 109.16 4.31 1.01e+00 9.80e-01 1.82e+01 angle pdb=" C VAL E 349 " pdb=" N GLU E 350 " pdb=" CA GLU E 350 " ideal model delta sigma weight residual 120.49 125.34 -4.85 1.42e+00 4.96e-01 1.17e+01 angle pdb=" N GLU D 195 " pdb=" CA GLU D 195 " pdb=" CB GLU D 195 " ideal model delta sigma weight residual 110.12 115.14 -5.02 1.47e+00 4.63e-01 1.17e+01 angle pdb=" N GLU E 195 " pdb=" CA GLU E 195 " pdb=" CB GLU E 195 " ideal model delta sigma weight residual 110.12 115.09 -4.97 1.47e+00 4.63e-01 1.15e+01 angle pdb=" N GLU F 195 " pdb=" CA GLU F 195 " pdb=" CB GLU F 195 " ideal model delta sigma weight residual 110.12 115.09 -4.97 1.47e+00 4.63e-01 1.14e+01 ... (remaining 46585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 18823 17.92 - 35.84: 1627 35.84 - 53.76: 253 53.76 - 71.68: 65 71.68 - 89.60: 70 Dihedral angle restraints: 20838 sinusoidal: 8508 harmonic: 12330 Sorted by residual: dihedral pdb=" CA ALA E 508 " pdb=" C ALA E 508 " pdb=" N PRO E 509 " pdb=" CA PRO E 509 " ideal model delta harmonic sigma weight residual -180.00 -139.43 -40.57 0 5.00e+00 4.00e-02 6.58e+01 dihedral pdb=" CA ALA B 508 " pdb=" C ALA B 508 " pdb=" N PRO B 509 " pdb=" CA PRO B 509 " ideal model delta harmonic sigma weight residual 180.00 -139.47 -40.53 0 5.00e+00 4.00e-02 6.57e+01 dihedral pdb=" CA ALA A 508 " pdb=" C ALA A 508 " pdb=" N PRO A 509 " pdb=" CA PRO A 509 " ideal model delta harmonic sigma weight residual -180.00 -139.47 -40.53 0 5.00e+00 4.00e-02 6.57e+01 ... (remaining 20835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3479 0.033 - 0.067: 1139 0.067 - 0.100: 383 0.100 - 0.133: 157 0.133 - 0.166: 20 Chirality restraints: 5178 Sorted by residual: chirality pdb=" C21 BO2 A 802 " pdb=" B26 BO2 A 802 " pdb=" C22 BO2 A 802 " pdb=" N20 BO2 A 802 " both_signs ideal model delta sigma weight residual False 2.49 2.65 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CG LEU F 617 " pdb=" CB LEU F 617 " pdb=" CD1 LEU F 617 " pdb=" CD2 LEU F 617 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CG LEU C 617 " pdb=" CB LEU C 617 " pdb=" CD1 LEU C 617 " pdb=" CD2 LEU C 617 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.24e-01 ... (remaining 5175 not shown) Planarity restraints: 6210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BO2 C 802 " 0.101 2.00e-02 2.50e+03 1.12e-01 1.58e+02 pdb=" C18 BO2 C 802 " -0.035 2.00e-02 2.50e+03 pdb=" C21 BO2 C 802 " 0.137 2.00e-02 2.50e+03 pdb=" N20 BO2 C 802 " -0.180 2.00e-02 2.50e+03 pdb=" O19 BO2 C 802 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 C 802 " 0.115 2.00e-02 2.50e+03 9.54e-02 1.14e+02 pdb=" C2 BO2 C 802 " 0.091 2.00e-02 2.50e+03 pdb=" C7 BO2 C 802 " -0.048 2.00e-02 2.50e+03 pdb=" N9 BO2 C 802 " -0.146 2.00e-02 2.50e+03 pdb=" O8 BO2 C 802 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 F 802 " -0.096 2.00e-02 2.50e+03 7.96e-02 7.92e+01 pdb=" C2 BO2 F 802 " -0.077 2.00e-02 2.50e+03 pdb=" C7 BO2 F 802 " 0.042 2.00e-02 2.50e+03 pdb=" N9 BO2 F 802 " 0.121 2.00e-02 2.50e+03 pdb=" O8 BO2 F 802 " 0.010 2.00e-02 2.50e+03 ... (remaining 6207 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.85: 5 1.85 - 2.61: 419 2.61 - 3.37: 46705 3.37 - 4.14: 85906 4.14 - 4.90: 158383 Nonbonded interactions: 291418 Sorted by model distance: nonbonded pdb=" OG SER C 582 " pdb=" O27 BO2 C 802 " model vdw 1.086 3.040 nonbonded pdb=" OG SER F 582 " pdb=" O28 BO2 F 802 " model vdw 1.436 3.040 nonbonded pdb=" OG SER F 582 " pdb=" B26 BO2 F 802 " model vdw 1.445 2.370 nonbonded pdb=" OG SER C 582 " pdb=" B26 BO2 C 802 " model vdw 1.445 2.370 nonbonded pdb=" OG SER F 582 " pdb=" O27 BO2 F 802 " model vdw 1.590 3.040 ... (remaining 291413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 31.070 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 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 : 0.006 0.379 34324 Z= 0.307 Angle : 0.640 11.759 46590 Z= 0.333 Chirality : 0.040 0.166 5178 Planarity : 0.005 0.112 6210 Dihedral : 14.649 89.601 12918 Min Nonbonded Distance : 1.086 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.13), residues: 4302 helix: 1.21 (0.11), residues: 2304 sheet: 0.08 (0.25), residues: 480 loop : -0.55 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 86 TYR 0.018 0.002 TYR A 80 PHE 0.026 0.001 PHE A 352 TRP 0.018 0.001 TRP C 205 HIS 0.005 0.001 HIS B 560 Details of bonding type rmsd covalent geometry : bond 0.00629 (34320) covalent geometry : angle 0.63981 (46590) hydrogen bonds : bond 0.14023 ( 1931) hydrogen bonds : angle 5.85208 ( 5613) Misc. bond : bond 0.00330 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7114 (m-30) cc_final: 0.6902 (m-30) REVERT: A 256 THR cc_start: 0.5893 (m) cc_final: 0.5387 (p) REVERT: A 296 LEU cc_start: 0.6771 (mt) cc_final: 0.6461 (mp) REVERT: A 410 GLN cc_start: 0.6664 (mt0) cc_final: 0.5867 (mm-40) REVERT: A 474 SER cc_start: 0.7346 (m) cc_final: 0.7023 (p) REVERT: A 506 GLU cc_start: 0.7632 (mp0) cc_final: 0.6954 (mp0) REVERT: A 556 ARG cc_start: 0.6925 (tpt90) cc_final: 0.6580 (tpt90) REVERT: A 639 SER cc_start: 0.7926 (t) cc_final: 0.7644 (p) REVERT: A 659 GLU cc_start: 0.7539 (pt0) cc_final: 0.6854 (pm20) REVERT: A 675 GLU cc_start: 0.7000 (pm20) cc_final: 0.5786 (mm-30) REVERT: A 688 ARG cc_start: 0.5899 (mtm110) cc_final: 0.4880 (pmm150) REVERT: F 77 ASP cc_start: 0.6970 (m-30) cc_final: 0.6742 (m-30) REVERT: F 256 THR cc_start: 0.5655 (m) cc_final: 0.5192 (p) REVERT: F 319 ARG cc_start: 0.6685 (ttp-110) cc_final: 0.6280 (mtm110) REVERT: F 331 ARG cc_start: 0.6487 (mtp180) cc_final: 0.6264 (mtm180) REVERT: F 410 GLN cc_start: 0.6535 (mt0) cc_final: 0.5733 (mm110) REVERT: F 474 SER cc_start: 0.7328 (m) cc_final: 0.7105 (p) REVERT: F 506 GLU cc_start: 0.7668 (mp0) cc_final: 0.7039 (mp0) REVERT: F 688 ARG cc_start: 0.6085 (ptp90) cc_final: 0.5784 (ptp90) REVERT: F 697 GLU cc_start: 0.6191 (tm-30) cc_final: 0.5775 (tm-30) REVERT: E 77 ASP cc_start: 0.7158 (m-30) cc_final: 0.6946 (m-30) REVERT: E 256 THR cc_start: 0.6090 (m) cc_final: 0.5676 (p) REVERT: E 331 ARG cc_start: 0.6521 (mtp180) cc_final: 0.6251 (mtm180) REVERT: E 410 GLN cc_start: 0.6503 (mt0) cc_final: 0.5658 (mm-40) REVERT: E 426 MET cc_start: 0.6737 (mtt) cc_final: 0.6427 (mtp) REVERT: E 474 SER cc_start: 0.7183 (m) cc_final: 0.6932 (p) REVERT: E 498 GLU cc_start: 0.7182 (tt0) cc_final: 0.6473 (mm-30) REVERT: E 556 ARG cc_start: 0.6843 (tpt90) cc_final: 0.6319 (tpt90) REVERT: E 659 GLU cc_start: 0.7508 (pt0) cc_final: 0.6808 (pm20) REVERT: E 688 ARG cc_start: 0.5992 (ttp-110) cc_final: 0.5745 (ptp90) REVERT: E 697 GLU cc_start: 0.6231 (tm-30) cc_final: 0.5817 (tm-30) REVERT: E 698 LYS cc_start: 0.5890 (mtmt) cc_final: 0.5645 (mttt) REVERT: D 77 ASP cc_start: 0.7111 (m-30) cc_final: 0.6886 (m-30) REVERT: D 256 THR cc_start: 0.5871 (m) cc_final: 0.5423 (p) REVERT: D 410 GLN cc_start: 0.6642 (mt0) cc_final: 0.5858 (mm-40) REVERT: D 474 SER cc_start: 0.7359 (m) cc_final: 0.7035 (p) REVERT: D 506 GLU cc_start: 0.7614 (mp0) cc_final: 0.6908 (mp0) REVERT: D 556 ARG cc_start: 0.6941 (tpt90) cc_final: 0.6602 (tpt90) REVERT: D 639 SER cc_start: 0.7927 (t) cc_final: 0.7646 (p) REVERT: D 659 GLU cc_start: 0.7541 (pt0) cc_final: 0.6859 (pm20) REVERT: D 675 GLU cc_start: 0.6995 (pm20) cc_final: 0.5778 (mm-30) REVERT: D 688 ARG cc_start: 0.5903 (mtm110) cc_final: 0.4853 (pmm150) REVERT: C 77 ASP cc_start: 0.6982 (m-30) cc_final: 0.6742 (m-30) REVERT: C 256 THR cc_start: 0.5762 (m) cc_final: 0.5309 (p) REVERT: C 319 ARG cc_start: 0.6643 (ttp-110) cc_final: 0.6253 (mtm110) REVERT: C 331 ARG cc_start: 0.6449 (mtp180) cc_final: 0.6226 (mtm180) REVERT: C 410 GLN cc_start: 0.6530 (mt0) cc_final: 0.5726 (mm110) REVERT: C 474 SER cc_start: 0.7312 (m) cc_final: 0.7090 (p) REVERT: C 506 GLU cc_start: 0.7661 (mp0) cc_final: 0.7020 (mp0) REVERT: C 688 ARG cc_start: 0.6102 (ptp90) cc_final: 0.5798 (ptp90) REVERT: C 697 GLU cc_start: 0.6182 (tm-30) cc_final: 0.5710 (tm-30) REVERT: B 77 ASP cc_start: 0.7149 (m-30) cc_final: 0.6934 (m-30) REVERT: B 229 GLU cc_start: 0.7580 (pp20) cc_final: 0.7225 (pt0) REVERT: B 256 THR cc_start: 0.6080 (m) cc_final: 0.5665 (p) REVERT: B 331 ARG cc_start: 0.6510 (mtp180) cc_final: 0.6255 (mtm180) REVERT: B 410 GLN cc_start: 0.6495 (mt0) cc_final: 0.5647 (mm-40) REVERT: B 474 SER cc_start: 0.7161 (m) cc_final: 0.6908 (p) REVERT: B 540 GLN cc_start: 0.7027 (mt0) cc_final: 0.6760 (mt0) REVERT: B 556 ARG cc_start: 0.6839 (tpt90) cc_final: 0.6312 (tpt90) REVERT: B 659 GLU cc_start: 0.7510 (pt0) cc_final: 0.6812 (pm20) REVERT: B 688 ARG cc_start: 0.6041 (ttp-110) cc_final: 0.5804 (ptp90) REVERT: B 697 GLU cc_start: 0.6192 (tm-30) cc_final: 0.5734 (tm-30) REVERT: B 698 LYS cc_start: 0.5906 (mtmt) cc_final: 0.5646 (mttt) REVERT: B 708 ARG cc_start: 0.6574 (tpp80) cc_final: 0.6308 (ttm170) outliers start: 0 outliers final: 2 residues processed: 428 average time/residue: 0.8059 time to fit residues: 400.3190 Evaluate side-chains 270 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 268 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain B residue 431 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** E 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 ASN E 540 GLN ** E 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 HIS D 121 GLN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 HIS C 121 GLN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN C 540 GLN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN ** B 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.195547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.137486 restraints weight = 38228.443| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.92 r_work: 0.3715 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34324 Z= 0.190 Angle : 0.656 13.152 46590 Z= 0.320 Chirality : 0.041 0.221 5178 Planarity : 0.005 0.070 6210 Dihedral : 7.450 81.659 4918 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.91 % Allowed : 7.78 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.13), residues: 4302 helix: 1.32 (0.11), residues: 2322 sheet: 0.44 (0.25), residues: 444 loop : -0.56 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 86 TYR 0.017 0.002 TYR A 557 PHE 0.017 0.002 PHE A 692 TRP 0.009 0.002 TRP D 290 HIS 0.004 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00440 (34320) covalent geometry : angle 0.65597 (46590) hydrogen bonds : bond 0.04480 ( 1931) hydrogen bonds : angle 4.84928 ( 5613) Misc. bond : bond 0.00110 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 304 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7773 (m-30) cc_final: 0.7503 (m-30) REVERT: A 256 THR cc_start: 0.6786 (m) cc_final: 0.6520 (p) REVERT: A 298 ARG cc_start: 0.8322 (mmt180) cc_final: 0.8056 (mmt180) REVERT: A 410 GLN cc_start: 0.7805 (mt0) cc_final: 0.7262 (mm-40) REVERT: A 506 GLU cc_start: 0.7386 (mp0) cc_final: 0.7073 (mp0) REVERT: A 648 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7621 (tt0) REVERT: A 659 GLU cc_start: 0.8272 (pt0) cc_final: 0.7992 (pm20) REVERT: A 675 GLU cc_start: 0.7866 (pm20) cc_final: 0.7279 (mm-30) REVERT: A 688 ARG cc_start: 0.7145 (mtm110) cc_final: 0.6099 (pmm150) REVERT: F 77 ASP cc_start: 0.7650 (m-30) cc_final: 0.7426 (m-30) REVERT: F 98 GLU cc_start: 0.6015 (tt0) cc_final: 0.5794 (tm-30) REVERT: F 256 THR cc_start: 0.6743 (m) cc_final: 0.6531 (p) REVERT: F 410 GLN cc_start: 0.7742 (mt0) cc_final: 0.7238 (mm110) REVERT: F 506 GLU cc_start: 0.7522 (mp0) cc_final: 0.7125 (mp0) REVERT: F 659 GLU cc_start: 0.8271 (pt0) cc_final: 0.7937 (pm20) REVERT: F 688 ARG cc_start: 0.7251 (ptp90) cc_final: 0.7013 (ptp90) REVERT: F 697 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7240 (tm-30) REVERT: E 77 ASP cc_start: 0.7625 (m-30) cc_final: 0.7409 (m-30) REVERT: E 256 THR cc_start: 0.7026 (m) cc_final: 0.6756 (p) REVERT: E 296 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7685 (mp) REVERT: E 298 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7798 (mmt180) REVERT: E 356 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7151 (ptt) REVERT: E 410 GLN cc_start: 0.7714 (mt0) cc_final: 0.7161 (mm-40) REVERT: E 556 ARG cc_start: 0.8055 (tpt90) cc_final: 0.7683 (tpt90) REVERT: E 615 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8091 (mttp) REVERT: E 659 GLU cc_start: 0.8223 (pt0) cc_final: 0.7946 (pm20) REVERT: E 698 LYS cc_start: 0.7781 (mtmt) cc_final: 0.7533 (mttt) REVERT: D 77 ASP cc_start: 0.7791 (m-30) cc_final: 0.7497 (m-30) REVERT: D 86 ARG cc_start: 0.7299 (ttp-110) cc_final: 0.6035 (ttt180) REVERT: D 296 LEU cc_start: 0.8072 (mp) cc_final: 0.7655 (mp) REVERT: D 298 ARG cc_start: 0.8264 (mmt180) cc_final: 0.7863 (mmt180) REVERT: D 410 GLN cc_start: 0.7784 (mt0) cc_final: 0.7262 (mm-40) REVERT: D 506 GLU cc_start: 0.7403 (mp0) cc_final: 0.7043 (mp0) REVERT: D 648 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7603 (tt0) REVERT: D 659 GLU cc_start: 0.8272 (pt0) cc_final: 0.7973 (pm20) REVERT: D 675 GLU cc_start: 0.7863 (pm20) cc_final: 0.7267 (mm-30) REVERT: C 77 ASP cc_start: 0.7649 (m-30) cc_final: 0.7449 (m-30) REVERT: C 256 THR cc_start: 0.6682 (m) cc_final: 0.6480 (p) REVERT: C 296 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7633 (mp) REVERT: C 410 GLN cc_start: 0.7724 (mt0) cc_final: 0.7213 (mm110) REVERT: C 506 GLU cc_start: 0.7526 (mp0) cc_final: 0.7168 (mp0) REVERT: C 659 GLU cc_start: 0.8281 (pt0) cc_final: 0.7953 (pm20) REVERT: C 688 ARG cc_start: 0.7211 (ptp90) cc_final: 0.6973 (ptp90) REVERT: C 697 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7231 (tm-30) REVERT: B 77 ASP cc_start: 0.7671 (m-30) cc_final: 0.7457 (m-30) REVERT: B 256 THR cc_start: 0.7033 (m) cc_final: 0.6750 (p) REVERT: B 296 LEU cc_start: 0.7806 (mp) cc_final: 0.7352 (mp) REVERT: B 410 GLN cc_start: 0.7652 (mt0) cc_final: 0.7099 (mm-40) REVERT: B 556 ARG cc_start: 0.8078 (tpt90) cc_final: 0.7713 (tpt90) REVERT: B 615 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8112 (mttp) REVERT: B 659 GLU cc_start: 0.8243 (pt0) cc_final: 0.7961 (pm20) REVERT: B 698 LYS cc_start: 0.7741 (mtmt) cc_final: 0.7472 (mttt) outliers start: 65 outliers final: 30 residues processed: 347 average time/residue: 0.7210 time to fit residues: 295.8475 Evaluate side-chains 280 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 615 LYS Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 498 GLU Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 615 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 282 optimal weight: 5.9990 chunk 173 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 289 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 414 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 331 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 GLN E 574 ASN ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 ASN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.195434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.131811 restraints weight = 36345.640| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.03 r_work: 0.3486 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34324 Z= 0.135 Angle : 0.579 12.051 46590 Z= 0.285 Chirality : 0.039 0.144 5178 Planarity : 0.004 0.069 6210 Dihedral : 7.129 81.340 4914 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.11 % Allowed : 11.85 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.13), residues: 4302 helix: 1.50 (0.11), residues: 2328 sheet: 0.45 (0.25), residues: 474 loop : -0.36 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 86 TYR 0.017 0.002 TYR C 557 PHE 0.016 0.001 PHE B 352 TRP 0.008 0.001 TRP A 10 HIS 0.002 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00302 (34320) covalent geometry : angle 0.57883 (46590) hydrogen bonds : bond 0.04225 ( 1931) hydrogen bonds : angle 4.62275 ( 5613) Misc. bond : bond 0.00049 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 264 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: A 256 THR cc_start: 0.6663 (m) cc_final: 0.6415 (p) REVERT: A 296 LEU cc_start: 0.7825 (mp) cc_final: 0.7410 (mp) REVERT: A 410 GLN cc_start: 0.7827 (mt0) cc_final: 0.7283 (mm-40) REVERT: A 506 GLU cc_start: 0.7635 (mp0) cc_final: 0.7229 (mp0) REVERT: A 648 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7540 (tt0) REVERT: A 659 GLU cc_start: 0.8206 (pt0) cc_final: 0.7874 (pm20) REVERT: A 675 GLU cc_start: 0.7889 (pm20) cc_final: 0.7262 (mm-30) REVERT: F 77 ASP cc_start: 0.7562 (m-30) cc_final: 0.7305 (m-30) REVERT: F 256 THR cc_start: 0.6554 (m) cc_final: 0.6338 (p) REVERT: F 320 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: F 410 GLN cc_start: 0.7600 (mt0) cc_final: 0.7112 (mp10) REVERT: F 506 GLU cc_start: 0.7627 (mp0) cc_final: 0.7240 (mp0) REVERT: F 659 GLU cc_start: 0.8243 (pt0) cc_final: 0.7923 (pm20) REVERT: F 675 GLU cc_start: 0.8161 (pt0) cc_final: 0.7116 (mm-30) REVERT: F 688 ARG cc_start: 0.7168 (ptp90) cc_final: 0.6902 (ptp90) REVERT: F 697 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7261 (tm-30) REVERT: E 256 THR cc_start: 0.6930 (m) cc_final: 0.6634 (p) REVERT: E 296 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7503 (mp) REVERT: E 410 GLN cc_start: 0.7471 (mt0) cc_final: 0.6892 (mm-40) REVERT: E 556 ARG cc_start: 0.8068 (tpt90) cc_final: 0.7658 (tpt90) REVERT: E 573 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7541 (mp10) REVERT: E 615 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8017 (mttp) REVERT: E 659 GLU cc_start: 0.8277 (pt0) cc_final: 0.7978 (pm20) REVERT: E 675 GLU cc_start: 0.8177 (pt0) cc_final: 0.7044 (mm-30) REVERT: E 698 LYS cc_start: 0.7684 (mtmt) cc_final: 0.7411 (mttm) REVERT: D 86 ARG cc_start: 0.7292 (ttp-110) cc_final: 0.5794 (ttt180) REVERT: D 296 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7401 (mp) REVERT: D 298 ARG cc_start: 0.8289 (mmt180) cc_final: 0.7926 (mmt180) REVERT: D 410 GLN cc_start: 0.7825 (mt0) cc_final: 0.7293 (mm-40) REVERT: D 506 GLU cc_start: 0.7587 (mp0) cc_final: 0.7179 (mp0) REVERT: D 648 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7520 (tt0) REVERT: D 659 GLU cc_start: 0.8179 (pt0) cc_final: 0.7862 (pm20) REVERT: D 675 GLU cc_start: 0.7879 (pm20) cc_final: 0.7256 (mm-30) REVERT: C 256 THR cc_start: 0.6527 (m) cc_final: 0.6313 (p) REVERT: C 350 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: C 356 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8289 (pp-130) REVERT: C 410 GLN cc_start: 0.7580 (mt0) cc_final: 0.7092 (mp10) REVERT: C 506 GLU cc_start: 0.7672 (mp0) cc_final: 0.7284 (mp0) REVERT: C 659 GLU cc_start: 0.8299 (pt0) cc_final: 0.7974 (pm20) REVERT: C 688 ARG cc_start: 0.7137 (ptp90) cc_final: 0.6875 (ptp90) REVERT: C 697 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7294 (tm-30) REVERT: B 256 THR cc_start: 0.6899 (m) cc_final: 0.6610 (p) REVERT: B 296 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7323 (mp) REVERT: B 410 GLN cc_start: 0.7483 (mt0) cc_final: 0.6884 (mm-40) REVERT: B 426 MET cc_start: 0.8215 (mtt) cc_final: 0.7985 (mtp) REVERT: B 556 ARG cc_start: 0.8023 (tpt90) cc_final: 0.7586 (tpt90) REVERT: B 573 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7535 (mp10) REVERT: B 615 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7980 (mttp) REVERT: B 659 GLU cc_start: 0.8295 (pt0) cc_final: 0.7983 (pm20) REVERT: B 675 GLU cc_start: 0.8184 (pt0) cc_final: 0.7079 (mm-30) REVERT: B 698 LYS cc_start: 0.7671 (mtmt) cc_final: 0.7381 (mttm) outliers start: 72 outliers final: 33 residues processed: 312 average time/residue: 0.7579 time to fit residues: 279.8712 Evaluate side-chains 271 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 228 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 320 GLU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 474 SER Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 573 GLN Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 615 LYS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 498 GLU Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 615 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 336 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 371 optimal weight: 5.9990 chunk 259 optimal weight: 6.9990 chunk 298 optimal weight: 30.0000 chunk 44 optimal weight: 3.9990 chunk 406 optimal weight: 1.9990 chunk 411 optimal weight: 1.9990 chunk 337 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 212 ASN ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 GLN ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 GLN D 212 ASN ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.189257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124998 restraints weight = 36561.009| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.99 r_work: 0.3395 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 34324 Z= 0.268 Angle : 0.689 12.419 46590 Z= 0.337 Chirality : 0.043 0.197 5178 Planarity : 0.005 0.069 6210 Dihedral : 7.323 86.747 4914 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.90 % Allowed : 13.76 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.13), residues: 4302 helix: 1.19 (0.11), residues: 2250 sheet: -0.09 (0.23), residues: 516 loop : -0.45 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 693 TYR 0.020 0.002 TYR E 557 PHE 0.024 0.002 PHE F 692 TRP 0.011 0.002 TRP E 290 HIS 0.005 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00632 (34320) covalent geometry : angle 0.68937 (46590) hydrogen bonds : bond 0.04538 ( 1931) hydrogen bonds : angle 4.82659 ( 5613) Misc. bond : bond 0.00127 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 251 time to evaluate : 1.288 Fit side-chains REVERT: A 296 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7395 (mp) REVERT: A 410 GLN cc_start: 0.7844 (mt0) cc_final: 0.7335 (mp10) REVERT: A 445 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7681 (mt-10) REVERT: A 506 GLU cc_start: 0.7540 (mp0) cc_final: 0.7322 (mp0) REVERT: A 648 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7567 (tt0) REVERT: A 659 GLU cc_start: 0.8336 (pt0) cc_final: 0.7977 (pm20) REVERT: A 675 GLU cc_start: 0.7895 (pm20) cc_final: 0.7384 (mm-30) REVERT: A 688 ARG cc_start: 0.7100 (mtm110) cc_final: 0.5956 (pmm150) REVERT: F 256 THR cc_start: 0.6557 (m) cc_final: 0.6119 (p) REVERT: F 368 GLU cc_start: 0.6778 (pp20) cc_final: 0.6473 (mt-10) REVERT: F 410 GLN cc_start: 0.7639 (mt0) cc_final: 0.7163 (mp10) REVERT: F 506 GLU cc_start: 0.7670 (mp0) cc_final: 0.7290 (mp0) REVERT: F 659 GLU cc_start: 0.8375 (pt0) cc_final: 0.7967 (pm20) REVERT: F 675 GLU cc_start: 0.8275 (pt0) cc_final: 0.7250 (mm-30) REVERT: F 688 ARG cc_start: 0.7336 (ptp90) cc_final: 0.7052 (ptp90) REVERT: F 697 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7375 (tm-30) REVERT: E 57 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8594 (tp) REVERT: E 90 VAL cc_start: 0.6859 (OUTLIER) cc_final: 0.6609 (p) REVERT: E 220 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7093 (ttp-170) REVERT: E 256 THR cc_start: 0.6895 (m) cc_final: 0.6659 (p) REVERT: E 296 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7479 (mp) REVERT: E 356 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7294 (ptt) REVERT: E 368 GLU cc_start: 0.6787 (pp20) cc_final: 0.6570 (mt-10) REVERT: E 410 GLN cc_start: 0.7469 (mt0) cc_final: 0.6904 (mm-40) REVERT: E 556 ARG cc_start: 0.8155 (tpt90) cc_final: 0.7911 (tpt90) REVERT: E 573 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7978 (mp10) REVERT: E 659 GLU cc_start: 0.8397 (pt0) cc_final: 0.8053 (pm20) REVERT: E 675 GLU cc_start: 0.8325 (pt0) cc_final: 0.7218 (mm-30) REVERT: E 698 LYS cc_start: 0.7813 (mtmt) cc_final: 0.7451 (mttp) REVERT: D 280 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7576 (ttm-80) REVERT: D 296 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7469 (mp) REVERT: D 298 ARG cc_start: 0.8339 (mmt180) cc_final: 0.7979 (mmt180) REVERT: D 368 GLU cc_start: 0.6883 (pp20) cc_final: 0.6624 (mt-10) REVERT: D 410 GLN cc_start: 0.7848 (mt0) cc_final: 0.7343 (mp10) REVERT: D 445 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7681 (mt-10) REVERT: D 506 GLU cc_start: 0.7522 (mp0) cc_final: 0.7303 (mp0) REVERT: D 648 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7570 (tt0) REVERT: D 659 GLU cc_start: 0.8315 (pt0) cc_final: 0.7956 (pm20) REVERT: D 675 GLU cc_start: 0.7907 (pm20) cc_final: 0.7406 (mm-30) REVERT: D 688 ARG cc_start: 0.7045 (mtm110) cc_final: 0.5892 (pmm150) REVERT: C 256 THR cc_start: 0.6488 (m) cc_final: 0.6147 (p) REVERT: C 368 GLU cc_start: 0.6792 (pp20) cc_final: 0.6496 (mt-10) REVERT: C 410 GLN cc_start: 0.7622 (mt0) cc_final: 0.7135 (mp10) REVERT: C 506 GLU cc_start: 0.7649 (mp0) cc_final: 0.7299 (mp0) REVERT: C 659 GLU cc_start: 0.8385 (pt0) cc_final: 0.7983 (pm20) REVERT: C 675 GLU cc_start: 0.8340 (pt0) cc_final: 0.7238 (mm-30) REVERT: C 688 ARG cc_start: 0.7251 (ptp90) cc_final: 0.6954 (ptp90) REVERT: C 697 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7364 (tm-30) REVERT: B 57 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8599 (tp) REVERT: B 256 THR cc_start: 0.6801 (m) cc_final: 0.6586 (p) REVERT: B 296 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7478 (mp) REVERT: B 368 GLU cc_start: 0.6789 (pp20) cc_final: 0.6577 (mt-10) REVERT: B 410 GLN cc_start: 0.7493 (mt0) cc_final: 0.6883 (mm-40) REVERT: B 556 ARG cc_start: 0.8144 (tpt90) cc_final: 0.7869 (tpt90) REVERT: B 573 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7993 (mp10) REVERT: B 659 GLU cc_start: 0.8412 (pt0) cc_final: 0.8070 (pm20) REVERT: B 675 GLU cc_start: 0.8314 (pt0) cc_final: 0.7214 (mm-30) REVERT: B 698 LYS cc_start: 0.7828 (mtmt) cc_final: 0.7471 (mttp) outliers start: 99 outliers final: 45 residues processed: 319 average time/residue: 0.7747 time to fit residues: 292.1801 Evaluate side-chains 274 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 217 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 474 SER Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 573 GLN Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 498 GLU Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 603 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 377 optimal weight: 9.9990 chunk 143 optimal weight: 0.1980 chunk 347 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 267 optimal weight: 0.9990 chunk 361 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 421 optimal weight: 0.9990 chunk 381 optimal weight: 0.0980 chunk 387 optimal weight: 0.7980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 GLN E 212 ASN E 223 GLN E 540 GLN ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN B 212 ASN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.194478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.131008 restraints weight = 36578.301| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.03 r_work: 0.3473 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34324 Z= 0.120 Angle : 0.564 12.236 46590 Z= 0.276 Chirality : 0.038 0.137 5178 Planarity : 0.004 0.053 6210 Dihedral : 7.005 82.733 4914 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.29 % Allowed : 15.55 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.13), residues: 4302 helix: 1.55 (0.11), residues: 2274 sheet: 0.09 (0.23), residues: 516 loop : -0.22 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 86 TYR 0.018 0.002 TYR A 557 PHE 0.013 0.001 PHE D 571 TRP 0.009 0.001 TRP C 10 HIS 0.002 0.000 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00266 (34320) covalent geometry : angle 0.56430 (46590) hydrogen bonds : bond 0.04027 ( 1931) hydrogen bonds : angle 4.46950 ( 5613) Misc. bond : bond 0.00042 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 239 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7329 (mp) REVERT: A 410 GLN cc_start: 0.7781 (mt0) cc_final: 0.7251 (mp10) REVERT: A 648 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7590 (tt0) REVERT: A 659 GLU cc_start: 0.8322 (pt0) cc_final: 0.8037 (pm20) REVERT: A 675 GLU cc_start: 0.7831 (pm20) cc_final: 0.7323 (mm-30) REVERT: F 368 GLU cc_start: 0.6791 (pp20) cc_final: 0.6496 (mt-10) REVERT: F 410 GLN cc_start: 0.7494 (mt0) cc_final: 0.7065 (mp10) REVERT: F 506 GLU cc_start: 0.7486 (mp0) cc_final: 0.7230 (mp0) REVERT: F 659 GLU cc_start: 0.8363 (pt0) cc_final: 0.8023 (pm20) REVERT: F 675 GLU cc_start: 0.8106 (pt0) cc_final: 0.7081 (mm-30) REVERT: F 688 ARG cc_start: 0.7325 (ptp90) cc_final: 0.7115 (ptp90) REVERT: F 697 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7349 (tm-30) REVERT: E 57 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8508 (tp) REVERT: E 193 GLU cc_start: 0.4578 (OUTLIER) cc_final: 0.4377 (mm-30) REVERT: E 296 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7495 (mp) REVERT: E 410 GLN cc_start: 0.7265 (mt0) cc_final: 0.6778 (mp10) REVERT: E 573 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7617 (mp10) REVERT: E 659 GLU cc_start: 0.8326 (pt0) cc_final: 0.8038 (pm20) REVERT: E 675 GLU cc_start: 0.8177 (pt0) cc_final: 0.7141 (mm-30) REVERT: E 698 LYS cc_start: 0.7829 (mtmt) cc_final: 0.7506 (mttp) REVERT: D 229 GLU cc_start: 0.7765 (pp20) cc_final: 0.7334 (pt0) REVERT: D 296 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7372 (mp) REVERT: D 298 ARG cc_start: 0.8308 (mmt180) cc_final: 0.8025 (mmt180) REVERT: D 410 GLN cc_start: 0.7781 (mt0) cc_final: 0.7261 (mp10) REVERT: D 659 GLU cc_start: 0.8308 (pt0) cc_final: 0.8026 (pm20) REVERT: D 675 GLU cc_start: 0.7849 (pm20) cc_final: 0.7345 (mm-30) REVERT: D 688 ARG cc_start: 0.7090 (mtm110) cc_final: 0.5996 (pmm150) REVERT: C 256 THR cc_start: 0.6657 (m) cc_final: 0.6410 (p) REVERT: C 320 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7125 (mt-10) REVERT: C 368 GLU cc_start: 0.6794 (pp20) cc_final: 0.6505 (mt-10) REVERT: C 410 GLN cc_start: 0.7469 (mt0) cc_final: 0.7036 (mp10) REVERT: C 506 GLU cc_start: 0.7521 (mp0) cc_final: 0.7245 (mp0) REVERT: C 659 GLU cc_start: 0.8367 (pt0) cc_final: 0.8035 (pm20) REVERT: C 675 GLU cc_start: 0.8174 (pt0) cc_final: 0.7115 (mm-30) REVERT: C 688 ARG cc_start: 0.7276 (ptp90) cc_final: 0.6988 (ptp90) REVERT: B 57 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8509 (tp) REVERT: B 193 GLU cc_start: 0.4579 (OUTLIER) cc_final: 0.4378 (mm-30) REVERT: B 281 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7972 (tp) REVERT: B 296 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7445 (mp) REVERT: B 336 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6401 (pm20) REVERT: B 410 GLN cc_start: 0.7227 (mt0) cc_final: 0.6767 (mp10) REVERT: B 559 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: B 573 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7622 (mp10) REVERT: B 659 GLU cc_start: 0.8363 (pt0) cc_final: 0.8060 (pm20) REVERT: B 675 GLU cc_start: 0.8182 (pt0) cc_final: 0.7104 (mm-30) REVERT: B 698 LYS cc_start: 0.7836 (mtmt) cc_final: 0.7511 (mttp) outliers start: 78 outliers final: 35 residues processed: 295 average time/residue: 0.7667 time to fit residues: 267.6756 Evaluate side-chains 251 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 203 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 573 GLN Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 498 GLU Chi-restraints excluded: chain D residue 582 SER Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 603 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 116 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 420 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 329 optimal weight: 3.9990 chunk 279 optimal weight: 0.7980 chunk 374 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 246 optimal weight: 0.5980 chunk 320 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN F 70 GLN F 223 GLN E 540 GLN ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.194118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.130689 restraints weight = 36278.537| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.03 r_work: 0.3468 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34324 Z= 0.136 Angle : 0.568 12.166 46590 Z= 0.276 Chirality : 0.038 0.138 5178 Planarity : 0.004 0.069 6210 Dihedral : 6.863 83.561 4914 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.79 % Allowed : 16.20 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.13), residues: 4302 helix: 1.63 (0.11), residues: 2274 sheet: 0.14 (0.22), residues: 516 loop : -0.12 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 86 TYR 0.018 0.002 TYR A 557 PHE 0.016 0.001 PHE A 221 TRP 0.010 0.001 TRP F 205 HIS 0.002 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00308 (34320) covalent geometry : angle 0.56836 (46590) hydrogen bonds : bond 0.03969 ( 1931) hydrogen bonds : angle 4.37668 ( 5613) Misc. bond : bond 0.00051 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 209 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7367 (mp) REVERT: A 410 GLN cc_start: 0.7776 (mt0) cc_final: 0.7274 (mp10) REVERT: A 659 GLU cc_start: 0.8341 (pt0) cc_final: 0.8034 (pm20) REVERT: A 675 GLU cc_start: 0.7865 (pm20) cc_final: 0.7353 (mm-30) REVERT: A 688 ARG cc_start: 0.7071 (mtm110) cc_final: 0.6505 (ptp90) REVERT: F 368 GLU cc_start: 0.6856 (pp20) cc_final: 0.6534 (mt-10) REVERT: F 410 GLN cc_start: 0.7480 (mt0) cc_final: 0.7034 (mp10) REVERT: F 506 GLU cc_start: 0.7496 (mp0) cc_final: 0.7140 (mp0) REVERT: F 659 GLU cc_start: 0.8369 (pt0) cc_final: 0.8034 (pm20) REVERT: F 675 GLU cc_start: 0.8128 (pt0) cc_final: 0.7133 (mm-30) REVERT: F 688 ARG cc_start: 0.7339 (ptp90) cc_final: 0.6879 (mtm-85) REVERT: F 697 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7340 (tm-30) REVERT: E 57 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8497 (tp) REVERT: E 193 GLU cc_start: 0.4507 (OUTLIER) cc_final: 0.4271 (mm-30) REVERT: E 296 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7517 (mp) REVERT: E 410 GLN cc_start: 0.7204 (mt0) cc_final: 0.6754 (mp10) REVERT: E 559 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7155 (tt0) REVERT: E 573 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7811 (mp10) REVERT: E 648 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: E 659 GLU cc_start: 0.8349 (pt0) cc_final: 0.8026 (pm20) REVERT: E 675 GLU cc_start: 0.8213 (pt0) cc_final: 0.7176 (mm-30) REVERT: E 698 LYS cc_start: 0.7865 (mtmt) cc_final: 0.7542 (mttp) REVERT: D 229 GLU cc_start: 0.7770 (pp20) cc_final: 0.7340 (pt0) REVERT: D 296 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7421 (mp) REVERT: D 410 GLN cc_start: 0.7804 (mt0) cc_final: 0.7266 (mp10) REVERT: D 659 GLU cc_start: 0.8341 (pt0) cc_final: 0.8041 (pm20) REVERT: D 675 GLU cc_start: 0.7806 (pm20) cc_final: 0.7397 (mm-30) REVERT: D 688 ARG cc_start: 0.7090 (mtm110) cc_final: 0.6512 (ptp90) REVERT: C 256 THR cc_start: 0.6725 (m) cc_final: 0.6500 (p) REVERT: C 368 GLU cc_start: 0.6853 (pp20) cc_final: 0.6535 (mt-10) REVERT: C 410 GLN cc_start: 0.7460 (mt0) cc_final: 0.7005 (mp10) REVERT: C 506 GLU cc_start: 0.7514 (mp0) cc_final: 0.7187 (mp0) REVERT: C 646 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7716 (pp) REVERT: C 659 GLU cc_start: 0.8388 (pt0) cc_final: 0.8058 (pm20) REVERT: C 675 GLU cc_start: 0.8211 (pt0) cc_final: 0.7167 (mm-30) REVERT: C 688 ARG cc_start: 0.7305 (ptp90) cc_final: 0.6989 (ptp90) REVERT: C 697 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7672 (tm-30) REVERT: B 57 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8506 (tp) REVERT: B 193 GLU cc_start: 0.4491 (OUTLIER) cc_final: 0.4263 (mm-30) REVERT: B 281 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7949 (tp) REVERT: B 296 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7442 (mp) REVERT: B 336 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6455 (pm20) REVERT: B 410 GLN cc_start: 0.7273 (mt0) cc_final: 0.6800 (mp10) REVERT: B 573 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7807 (mp10) REVERT: B 648 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: B 659 GLU cc_start: 0.8389 (pt0) cc_final: 0.8050 (pm20) REVERT: B 675 GLU cc_start: 0.8213 (pt0) cc_final: 0.7130 (mm-30) REVERT: B 698 LYS cc_start: 0.7876 (mtmt) cc_final: 0.7544 (mttp) outliers start: 95 outliers final: 46 residues processed: 281 average time/residue: 0.7529 time to fit residues: 251.9551 Evaluate side-chains 262 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 201 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 474 SER Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 559 GLU Chi-restraints excluded: chain E residue 573 GLN Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 648 GLU Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 498 GLU Chi-restraints excluded: chain D residue 582 SER Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 648 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 127 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 329 optimal weight: 3.9990 chunk 314 optimal weight: 5.9990 chunk 410 optimal weight: 2.9990 chunk 297 optimal weight: 20.0000 chunk 374 optimal weight: 40.0000 chunk 340 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 330 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 142 GLN F 396 ASN E 142 GLN E 540 GLN ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN C 142 GLN B 142 GLN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.188217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.124910 restraints weight = 36854.455| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.96 r_work: 0.3379 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 34324 Z= 0.314 Angle : 0.698 12.619 46590 Z= 0.341 Chirality : 0.043 0.172 5178 Planarity : 0.005 0.064 6210 Dihedral : 7.163 89.801 4914 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.14 % Allowed : 17.02 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.13), residues: 4302 helix: 1.16 (0.11), residues: 2268 sheet: -0.08 (0.22), residues: 516 loop : -0.38 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 556 TYR 0.021 0.003 TYR E 557 PHE 0.025 0.002 PHE F 352 TRP 0.015 0.002 TRP B 290 HIS 0.004 0.001 HIS F 560 Details of bonding type rmsd covalent geometry : bond 0.00747 (34320) covalent geometry : angle 0.69816 (46590) hydrogen bonds : bond 0.04529 ( 1931) hydrogen bonds : angle 4.72612 ( 5613) Misc. bond : bond 0.00106 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 203 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7370 (mp) REVERT: A 410 GLN cc_start: 0.7767 (mt0) cc_final: 0.7242 (mp10) REVERT: A 445 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7743 (mt-10) REVERT: A 567 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8478 (mm) REVERT: A 615 LYS cc_start: 0.8579 (mptp) cc_final: 0.8265 (mmtp) REVERT: A 659 GLU cc_start: 0.8394 (pt0) cc_final: 0.8054 (pm20) REVERT: A 675 GLU cc_start: 0.7819 (pm20) cc_final: 0.7470 (mm-30) REVERT: A 688 ARG cc_start: 0.7092 (mtm110) cc_final: 0.5986 (pmm150) REVERT: F 368 GLU cc_start: 0.6790 (pp20) cc_final: 0.6495 (mt-10) REVERT: F 410 GLN cc_start: 0.7638 (mt0) cc_final: 0.7132 (mp10) REVERT: F 506 GLU cc_start: 0.7653 (mp0) cc_final: 0.7196 (mp0) REVERT: F 646 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7788 (pp) REVERT: F 659 GLU cc_start: 0.8418 (pt0) cc_final: 0.8030 (pm20) REVERT: F 675 GLU cc_start: 0.8200 (pt0) cc_final: 0.7227 (mm-30) REVERT: F 688 ARG cc_start: 0.7358 (ptp90) cc_final: 0.7035 (ptp90) REVERT: F 697 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7319 (tm-30) REVERT: E 57 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8662 (tp) REVERT: E 296 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7478 (mp) REVERT: E 410 GLN cc_start: 0.7340 (mt0) cc_final: 0.6854 (mp10) REVERT: E 573 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8000 (mp10) REVERT: E 615 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8036 (mttp) REVERT: E 659 GLU cc_start: 0.8442 (pt0) cc_final: 0.8034 (pm20) REVERT: E 675 GLU cc_start: 0.8291 (pt0) cc_final: 0.7274 (mm-30) REVERT: E 698 LYS cc_start: 0.7733 (mtmt) cc_final: 0.7402 (mttp) REVERT: D 296 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7437 (mp) REVERT: D 410 GLN cc_start: 0.7793 (mt0) cc_final: 0.7270 (mp10) REVERT: D 445 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7751 (mt-10) REVERT: D 659 GLU cc_start: 0.8373 (pt0) cc_final: 0.8039 (pm20) REVERT: D 675 GLU cc_start: 0.7794 (pm20) cc_final: 0.7480 (mm-30) REVERT: D 688 ARG cc_start: 0.7115 (mtm110) cc_final: 0.6028 (pmm150) REVERT: C 256 THR cc_start: 0.6510 (m) cc_final: 0.6171 (p) REVERT: C 368 GLU cc_start: 0.6791 (pp20) cc_final: 0.6492 (mt-10) REVERT: C 410 GLN cc_start: 0.7632 (mt0) cc_final: 0.7117 (mp10) REVERT: C 506 GLU cc_start: 0.7603 (mp0) cc_final: 0.7240 (mp0) REVERT: C 646 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7777 (pp) REVERT: C 659 GLU cc_start: 0.8405 (pt0) cc_final: 0.8023 (pm20) REVERT: C 675 GLU cc_start: 0.8328 (pt0) cc_final: 0.7249 (mm-30) REVERT: C 688 ARG cc_start: 0.7321 (ptp90) cc_final: 0.6991 (ptp90) REVERT: C 697 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7648 (tm-30) REVERT: B 57 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8666 (tp) REVERT: B 281 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8047 (tp) REVERT: B 296 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7478 (mp) REVERT: B 410 GLN cc_start: 0.7314 (mt0) cc_final: 0.6821 (mp10) REVERT: B 573 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8014 (mp10) REVERT: B 615 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8007 (mttp) REVERT: B 659 GLU cc_start: 0.8456 (pt0) cc_final: 0.8040 (pm20) REVERT: B 675 GLU cc_start: 0.8284 (pt0) cc_final: 0.7271 (mm-30) REVERT: B 698 LYS cc_start: 0.7732 (mtmt) cc_final: 0.7414 (mttp) outliers start: 107 outliers final: 56 residues processed: 284 average time/residue: 0.7443 time to fit residues: 251.3447 Evaluate side-chains 266 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 196 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 474 SER Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 573 GLN Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 615 LYS Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 498 GLU Chi-restraints excluded: chain D residue 582 SER Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 615 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 291 optimal weight: 3.9990 chunk 412 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 415 optimal weight: 0.6980 chunk 385 optimal weight: 0.9980 chunk 394 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 97 optimal weight: 0.0870 chunk 371 optimal weight: 9.9990 chunk 230 optimal weight: 20.0000 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 ASN E 540 GLN ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 ASN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.194167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130252 restraints weight = 36403.735| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.04 r_work: 0.3461 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34324 Z= 0.125 Angle : 0.571 12.676 46590 Z= 0.279 Chirality : 0.039 0.362 5178 Planarity : 0.004 0.054 6210 Dihedral : 6.952 88.446 4914 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.41 % Allowed : 18.25 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.13), residues: 4302 helix: 1.56 (0.11), residues: 2274 sheet: 0.10 (0.22), residues: 516 loop : -0.16 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 86 TYR 0.021 0.002 TYR A 557 PHE 0.014 0.001 PHE C 221 TRP 0.015 0.001 TRP B 290 HIS 0.002 0.000 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00276 (34320) covalent geometry : angle 0.57086 (46590) hydrogen bonds : bond 0.03984 ( 1931) hydrogen bonds : angle 4.40355 ( 5613) Misc. bond : bond 0.00039 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 212 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7288 (mp) REVERT: A 410 GLN cc_start: 0.7666 (mt0) cc_final: 0.7163 (mp10) REVERT: A 445 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7698 (mt-10) REVERT: A 659 GLU cc_start: 0.8332 (pt0) cc_final: 0.8008 (pm20) REVERT: A 675 GLU cc_start: 0.7760 (pm20) cc_final: 0.7508 (mm-30) REVERT: A 688 ARG cc_start: 0.7108 (mtm110) cc_final: 0.6501 (ptp90) REVERT: F 368 GLU cc_start: 0.6801 (pp20) cc_final: 0.6516 (mt-10) REVERT: F 410 GLN cc_start: 0.7491 (mt0) cc_final: 0.7048 (mp10) REVERT: F 506 GLU cc_start: 0.7459 (mp0) cc_final: 0.7182 (mp0) REVERT: F 659 GLU cc_start: 0.8367 (pt0) cc_final: 0.8032 (pm20) REVERT: F 675 GLU cc_start: 0.8071 (pt0) cc_final: 0.7126 (mm-30) REVERT: F 688 ARG cc_start: 0.7432 (ptp90) cc_final: 0.7193 (ptp90) REVERT: F 697 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7312 (tm-30) REVERT: E 57 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8554 (tp) REVERT: E 296 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7454 (mp) REVERT: E 410 GLN cc_start: 0.7187 (mt0) cc_final: 0.6731 (mp10) REVERT: E 573 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7773 (mp10) REVERT: E 659 GLU cc_start: 0.8386 (pt0) cc_final: 0.8098 (pm20) REVERT: E 675 GLU cc_start: 0.8186 (pt0) cc_final: 0.7124 (mm-30) REVERT: E 698 LYS cc_start: 0.7802 (mtmt) cc_final: 0.7489 (mttp) REVERT: D 296 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7306 (mp) REVERT: D 410 GLN cc_start: 0.7693 (mt0) cc_final: 0.7192 (mp10) REVERT: D 445 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7725 (mt-10) REVERT: D 659 GLU cc_start: 0.8326 (pt0) cc_final: 0.8008 (pm20) REVERT: D 675 GLU cc_start: 0.7771 (pm20) cc_final: 0.7482 (mm-30) REVERT: D 688 ARG cc_start: 0.7158 (mtm110) cc_final: 0.6091 (pmm150) REVERT: C 254 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8118 (tp) REVERT: C 256 THR cc_start: 0.6722 (m) cc_final: 0.6489 (p) REVERT: C 368 GLU cc_start: 0.6809 (pp20) cc_final: 0.6524 (mt-10) REVERT: C 410 GLN cc_start: 0.7485 (mt0) cc_final: 0.7037 (mp10) REVERT: C 659 GLU cc_start: 0.8366 (pt0) cc_final: 0.8034 (pm20) REVERT: C 675 GLU cc_start: 0.8153 (pt0) cc_final: 0.7103 (mm-30) REVERT: C 688 ARG cc_start: 0.7334 (ptp90) cc_final: 0.7036 (ptp90) REVERT: C 697 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7656 (tm-30) REVERT: B 57 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8563 (tp) REVERT: B 281 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7989 (tp) REVERT: B 296 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7494 (mp) REVERT: B 410 GLN cc_start: 0.7227 (mt0) cc_final: 0.6769 (mp10) REVERT: B 573 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.7778 (mp10) REVERT: B 659 GLU cc_start: 0.8416 (pt0) cc_final: 0.8110 (pm20) REVERT: B 675 GLU cc_start: 0.8191 (pt0) cc_final: 0.7154 (mm-30) REVERT: B 698 LYS cc_start: 0.7779 (mtmt) cc_final: 0.7470 (mttp) outliers start: 82 outliers final: 48 residues processed: 270 average time/residue: 0.6787 time to fit residues: 218.9000 Evaluate side-chains 253 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 474 SER Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 573 GLN Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 498 GLU Chi-restraints excluded: chain D residue 582 SER Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 613 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 87 optimal weight: 40.0000 chunk 93 optimal weight: 0.8980 chunk 263 optimal weight: 0.2980 chunk 238 optimal weight: 0.9990 chunk 277 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 406 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 540 GLN ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.192327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.128129 restraints weight = 36468.375| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.02 r_work: 0.3437 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 34324 Z= 0.172 Angle : 0.600 12.238 46590 Z= 0.292 Chirality : 0.039 0.152 5178 Planarity : 0.004 0.051 6210 Dihedral : 6.919 88.566 4914 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.41 % Allowed : 19.07 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.13), residues: 4302 helix: 1.54 (0.11), residues: 2274 sheet: 0.09 (0.22), residues: 516 loop : -0.14 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 86 TYR 0.023 0.002 TYR E 557 PHE 0.021 0.001 PHE B 221 TRP 0.017 0.002 TRP B 290 HIS 0.002 0.001 HIS F 560 Details of bonding type rmsd covalent geometry : bond 0.00398 (34320) covalent geometry : angle 0.59974 (46590) hydrogen bonds : bond 0.04058 ( 1931) hydrogen bonds : angle 4.41794 ( 5613) Misc. bond : bond 0.00045 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 205 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7308 (mp) REVERT: A 410 GLN cc_start: 0.7657 (mt0) cc_final: 0.7105 (mp10) REVERT: A 445 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7634 (mt-10) REVERT: A 567 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8471 (mm) REVERT: A 659 GLU cc_start: 0.8340 (pt0) cc_final: 0.7971 (pm20) REVERT: A 675 GLU cc_start: 0.7771 (pm20) cc_final: 0.7494 (mm-30) REVERT: A 688 ARG cc_start: 0.7103 (mtm110) cc_final: 0.6009 (pmm150) REVERT: F 368 GLU cc_start: 0.6780 (pp20) cc_final: 0.6492 (mt-10) REVERT: F 410 GLN cc_start: 0.7446 (mt0) cc_final: 0.6993 (mp10) REVERT: F 506 GLU cc_start: 0.7538 (mp0) cc_final: 0.7247 (mp0) REVERT: F 659 GLU cc_start: 0.8380 (pt0) cc_final: 0.8009 (pm20) REVERT: F 675 GLU cc_start: 0.8125 (pt0) cc_final: 0.7103 (mm-30) REVERT: F 688 ARG cc_start: 0.7349 (ptp90) cc_final: 0.6848 (mtm-85) REVERT: F 697 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7259 (tm-30) REVERT: E 57 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8568 (tp) REVERT: E 296 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7424 (mp) REVERT: E 410 GLN cc_start: 0.7227 (mt0) cc_final: 0.6721 (mp10) REVERT: E 573 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7971 (mp10) REVERT: E 659 GLU cc_start: 0.8401 (pt0) cc_final: 0.8053 (pm20) REVERT: E 675 GLU cc_start: 0.8201 (pt0) cc_final: 0.7052 (mm-30) REVERT: E 698 LYS cc_start: 0.7714 (mtmt) cc_final: 0.7387 (mttp) REVERT: D 296 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7328 (mp) REVERT: D 410 GLN cc_start: 0.7669 (mt0) cc_final: 0.7125 (mp10) REVERT: D 445 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7658 (mt-10) REVERT: D 659 GLU cc_start: 0.8342 (pt0) cc_final: 0.7976 (pm20) REVERT: D 675 GLU cc_start: 0.7804 (pm20) cc_final: 0.7465 (mm-30) REVERT: D 688 ARG cc_start: 0.7111 (mtm110) cc_final: 0.6030 (pmm150) REVERT: C 254 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8099 (tp) REVERT: C 256 THR cc_start: 0.6704 (m) cc_final: 0.6453 (p) REVERT: C 368 GLU cc_start: 0.6782 (pp20) cc_final: 0.6476 (mt-10) REVERT: C 410 GLN cc_start: 0.7434 (mt0) cc_final: 0.6978 (mp10) REVERT: C 646 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7691 (pp) REVERT: C 659 GLU cc_start: 0.8376 (pt0) cc_final: 0.8007 (pm20) REVERT: C 675 GLU cc_start: 0.8205 (pt0) cc_final: 0.7139 (mm-30) REVERT: C 688 ARG cc_start: 0.7338 (ptp90) cc_final: 0.7067 (ptp90) REVERT: C 697 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7614 (tm-30) REVERT: B 57 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8554 (tp) REVERT: B 281 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8042 (tp) REVERT: B 296 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7469 (mp) REVERT: B 410 GLN cc_start: 0.7224 (mt0) cc_final: 0.6714 (mp10) REVERT: B 573 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: B 659 GLU cc_start: 0.8432 (pt0) cc_final: 0.8081 (pm20) REVERT: B 675 GLU cc_start: 0.8233 (pt0) cc_final: 0.7134 (mm-30) REVERT: B 698 LYS cc_start: 0.7701 (mtmt) cc_final: 0.7391 (mttp) outliers start: 82 outliers final: 51 residues processed: 264 average time/residue: 0.6912 time to fit residues: 218.2026 Evaluate side-chains 264 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 201 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 474 SER Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 573 GLN Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 498 GLU Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 582 SER Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 603 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 404 optimal weight: 0.8980 chunk 281 optimal weight: 0.7980 chunk 222 optimal weight: 0.0040 chunk 9 optimal weight: 6.9990 chunk 95 optimal weight: 0.3980 chunk 286 optimal weight: 0.0770 chunk 322 optimal weight: 0.5980 chunk 212 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 overall best weight: 0.3750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 HIS E 540 GLN ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.196724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.134497 restraints weight = 36507.686| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.33 r_work: 0.3486 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34324 Z= 0.108 Angle : 0.547 11.877 46590 Z= 0.267 Chirality : 0.038 0.140 5178 Planarity : 0.004 0.050 6210 Dihedral : 6.732 88.887 4914 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.91 % Allowed : 19.66 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.13), residues: 4302 helix: 1.71 (0.11), residues: 2286 sheet: 0.21 (0.22), residues: 516 loop : 0.11 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 86 TYR 0.018 0.001 TYR D 557 PHE 0.012 0.001 PHE C 629 TRP 0.012 0.001 TRP B 290 HIS 0.003 0.001 HIS C 303 Details of bonding type rmsd covalent geometry : bond 0.00230 (34320) covalent geometry : angle 0.54733 (46590) hydrogen bonds : bond 0.03795 ( 1931) hydrogen bonds : angle 4.22022 ( 5613) Misc. bond : bond 0.00015 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8604 Ramachandran restraints generated. 4302 Oldfield, 0 Emsley, 4302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 228 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7285 (mp) REVERT: A 410 GLN cc_start: 0.7608 (mt0) cc_final: 0.7052 (mp10) REVERT: A 659 GLU cc_start: 0.8334 (pt0) cc_final: 0.7990 (pm20) REVERT: A 665 ARG cc_start: 0.8124 (ttm170) cc_final: 0.7836 (ttp-170) REVERT: A 675 GLU cc_start: 0.7771 (pm20) cc_final: 0.7525 (mm-30) REVERT: F 253 ASN cc_start: 0.6942 (t0) cc_final: 0.6741 (t0) REVERT: F 368 GLU cc_start: 0.6749 (pp20) cc_final: 0.6514 (mt-10) REVERT: F 410 GLN cc_start: 0.7339 (mt0) cc_final: 0.6889 (mp10) REVERT: F 506 GLU cc_start: 0.7494 (mp0) cc_final: 0.7213 (mp0) REVERT: F 556 ARG cc_start: 0.8328 (tpt90) cc_final: 0.8086 (tmt170) REVERT: F 659 GLU cc_start: 0.8318 (pt0) cc_final: 0.7995 (pm20) REVERT: F 675 GLU cc_start: 0.8070 (pt0) cc_final: 0.7060 (mm-30) REVERT: F 697 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7259 (tm-30) REVERT: E 57 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8470 (tp) REVERT: E 296 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7435 (mp) REVERT: E 410 GLN cc_start: 0.7146 (mt0) cc_final: 0.6654 (mp10) REVERT: E 573 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: E 659 GLU cc_start: 0.8391 (pt0) cc_final: 0.8023 (pm20) REVERT: E 675 GLU cc_start: 0.8164 (pt0) cc_final: 0.7035 (mm-30) REVERT: E 698 LYS cc_start: 0.7796 (mtmt) cc_final: 0.7460 (mttp) REVERT: D 229 GLU cc_start: 0.7752 (pp20) cc_final: 0.7422 (pt0) REVERT: D 296 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7287 (mp) REVERT: D 410 GLN cc_start: 0.7617 (mt0) cc_final: 0.7065 (mp10) REVERT: D 659 GLU cc_start: 0.8358 (pt0) cc_final: 0.8014 (pm20) REVERT: D 665 ARG cc_start: 0.8115 (ttm170) cc_final: 0.7825 (ttp-170) REVERT: D 675 GLU cc_start: 0.7707 (pm20) cc_final: 0.7441 (mm-30) REVERT: D 688 ARG cc_start: 0.7103 (mtm110) cc_final: 0.6511 (ptp90) REVERT: C 254 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8061 (tp) REVERT: C 368 GLU cc_start: 0.6754 (pp20) cc_final: 0.6515 (mt-10) REVERT: C 410 GLN cc_start: 0.7310 (mt0) cc_final: 0.6860 (mp10) REVERT: C 556 ARG cc_start: 0.8291 (tpt90) cc_final: 0.8042 (tmt170) REVERT: C 646 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7726 (pp) REVERT: C 659 GLU cc_start: 0.8323 (pt0) cc_final: 0.8000 (pm20) REVERT: C 675 GLU cc_start: 0.8125 (pt0) cc_final: 0.7084 (mm-30) REVERT: C 688 ARG cc_start: 0.7370 (ptp90) cc_final: 0.7115 (ptp90) REVERT: C 697 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7594 (tm-30) REVERT: B 57 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8479 (tp) REVERT: B 281 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7971 (tp) REVERT: B 296 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7506 (mp) REVERT: B 336 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6421 (pm20) REVERT: B 410 GLN cc_start: 0.7145 (mt0) cc_final: 0.6652 (mp10) REVERT: B 573 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7857 (mp10) REVERT: B 659 GLU cc_start: 0.8410 (pt0) cc_final: 0.8039 (pm20) REVERT: B 675 GLU cc_start: 0.8138 (pt0) cc_final: 0.6981 (mm-30) REVERT: B 698 LYS cc_start: 0.7751 (mtmt) cc_final: 0.7431 (mttp) outliers start: 65 outliers final: 40 residues processed: 274 average time/residue: 0.6807 time to fit residues: 225.2932 Evaluate side-chains 252 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 474 SER Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain F residue 603 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 474 SER Chi-restraints excluded: chain E residue 573 GLN Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 498 GLU Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 603 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 26 optimal weight: 3.9990 chunk 315 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 0.0010 chunk 132 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 390 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 288 optimal weight: 4.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 100 HIS E 540 GLN ** E 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN B 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.193312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.129496 restraints weight = 36329.979| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.17 r_work: 0.3436 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34324 Z= 0.166 Angle : 0.592 11.714 46590 Z= 0.288 Chirality : 0.039 0.143 5178 Planarity : 0.004 0.048 6210 Dihedral : 6.777 88.712 4914 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.05 % Allowed : 19.89 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.13), residues: 4302 helix: 1.68 (0.11), residues: 2274 sheet: 0.16 (0.22), residues: 516 loop : -0.03 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 86 TYR 0.023 0.002 TYR A 557 PHE 0.018 0.001 PHE B 221 TRP 0.018 0.001 TRP B 290 HIS 0.003 0.001 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00386 (34320) covalent geometry : angle 0.59189 (46590) hydrogen bonds : bond 0.03957 ( 1931) hydrogen bonds : angle 4.31148 ( 5613) Misc. bond : bond 0.00042 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13405.05 seconds wall clock time: 228 minutes 25.62 seconds (13705.62 seconds total)