Starting phenix.real_space_refine on Sat Jun 6 06:35:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y0c_72391/06_2026/9y0c_72391.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y0c_72391/06_2026/9y0c_72391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y0c_72391/06_2026/9y0c_72391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y0c_72391/06_2026/9y0c_72391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y0c_72391/06_2026/9y0c_72391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y0c_72391/06_2026/9y0c_72391.map" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 144 5.16 5 C 16254 2.51 5 N 4566 2.21 5 O 4986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25998 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "B" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "C" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "D" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "E" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "F" Number of atoms: 4269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4269 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 520} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.39, per 1000 atoms: 0.25 Number of scatterers: 25998 At special positions: 0 Unit cell: (147, 139, 96, 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 144 16.00 P 36 15.00 Mg 12 11.99 O 4986 8.00 N 4566 7.00 C 16254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6120 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 12 sheets defined 59.6% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 210 through 226 removed outlier: 4.375A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 234 removed outlier: 4.389A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.529A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.978A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 Processing helix chain 'A' and resid 336 through 339 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.660A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.546A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.702A pdb=" N LEU A 429 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 3.977A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.773A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 544 through 550 Processing helix chain 'A' and resid 556 through 569 removed outlier: 4.430A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 584 removed outlier: 4.180A pdb=" N ILE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 599 through 610 removed outlier: 4.035A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 678 removed outlier: 3.683A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 705 Processing helix chain 'A' and resid 732 through 743 removed outlier: 3.683A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 210 through 226 removed outlier: 4.390A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 removed outlier: 4.381A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.536A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.943A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 336 through 339 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.673A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.544A pdb=" N LYS B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.631A pdb=" N LEU B 429 " --> pdb=" O LYS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 456 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.078A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.813A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 544 through 550 Processing helix chain 'B' and resid 556 through 569 removed outlier: 4.278A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 584 removed outlier: 4.143A pdb=" N ILE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 587 No H-bonds generated for 'chain 'B' and resid 585 through 587' Processing helix chain 'B' and resid 599 through 610 removed outlier: 3.997A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 678 Processing helix chain 'B' and resid 683 through 707 removed outlier: 3.635A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE B 707 " --> pdb=" O ILE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.702A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 761 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 210 through 226 removed outlier: 4.470A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.380A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.543A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.051A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 Processing helix chain 'C' and resid 336 through 339 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.649A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 426 through 430 removed outlier: 3.630A pdb=" N LEU C 429 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 456 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 3.980A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.752A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 544 through 550 Processing helix chain 'C' and resid 556 through 569 removed outlier: 4.523A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 584 removed outlier: 4.150A pdb=" N ILE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 587 No H-bonds generated for 'chain 'C' and resid 585 through 587' Processing helix chain 'C' and resid 599 through 610 removed outlier: 4.083A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.600A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.845A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 707 removed outlier: 3.575A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE C 707 " --> pdb=" O ILE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.554A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 761 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 210 through 226 removed outlier: 4.283A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 4.389A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.589A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.981A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 Processing helix chain 'D' and resid 336 through 339 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.663A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 386 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 425 removed outlier: 3.548A pdb=" N LYS D 425 " --> pdb=" O GLN D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 430 removed outlier: 3.672A pdb=" N LEU D 429 " --> pdb=" O LYS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 456 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 removed outlier: 3.984A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.727A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 544 through 550 Processing helix chain 'D' and resid 556 through 569 removed outlier: 4.399A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 584 removed outlier: 4.175A pdb=" N ILE D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 587 No H-bonds generated for 'chain 'D' and resid 585 through 587' Processing helix chain 'D' and resid 599 through 610 removed outlier: 4.031A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 678 removed outlier: 3.598A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 705 Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.705A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 761 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 210 through 226 removed outlier: 4.397A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 removed outlier: 4.376A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.524A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.939A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 334 Processing helix chain 'E' and resid 336 through 339 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.674A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 386 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 425 removed outlier: 3.541A pdb=" N LYS E 425 " --> pdb=" O GLN E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 430 removed outlier: 3.668A pdb=" N LEU E 429 " --> pdb=" O LYS E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 456 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.039A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.808A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 544 through 550 Processing helix chain 'E' and resid 556 through 569 removed outlier: 4.279A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 584 removed outlier: 4.143A pdb=" N ILE E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 587 No H-bonds generated for 'chain 'E' and resid 585 through 587' Processing helix chain 'E' and resid 599 through 610 removed outlier: 3.992A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 649 through 661 removed outlier: 3.634A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.781A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 707 removed outlier: 3.662A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE E 707 " --> pdb=" O ILE E 703 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 743 removed outlier: 3.719A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 761 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 210 through 226 removed outlier: 4.520A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.374A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 280 through 296 Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.053A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 334 Processing helix chain 'F' and resid 336 through 339 Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.649A pdb=" N ARG F 359 " --> pdb=" O ALA F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 386 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 425 removed outlier: 3.520A pdb=" N LYS F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 430 removed outlier: 3.573A pdb=" N LEU F 429 " --> pdb=" O LYS F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 456 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.009A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 removed outlier: 3.752A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 544 through 550 Processing helix chain 'F' and resid 556 through 569 removed outlier: 4.470A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 584 removed outlier: 4.163A pdb=" N ILE F 582 " --> pdb=" O GLU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 587 No H-bonds generated for 'chain 'F' and resid 585 through 587' Processing helix chain 'F' and resid 599 through 610 removed outlier: 4.118A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.605A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.831A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 707 removed outlier: 3.605A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE F 707 " --> pdb=" O ILE F 703 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.564A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 761 Processing helix chain 'F' and resid 762 through 766 removed outlier: 3.872A pdb=" N ARG F 766 " --> pdb=" O GLN F 763 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.464A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 543 removed outlier: 6.543A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.504A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 543 removed outlier: 6.577A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.150A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 538 through 543 removed outlier: 6.571A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.490A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 538 through 543 removed outlier: 6.571A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.505A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 538 through 543 removed outlier: 6.578A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.161A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 538 through 543 removed outlier: 6.574A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) 1258 hydrogen bonds defined for protein. 3522 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: 4.95 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 8999 1.37 - 1.52: 7478 1.52 - 1.66: 9719 1.66 - 1.80: 190 1.80 - 1.95: 44 Bond restraints: 26430 Sorted by residual: bond pdb=" CG1 ILE B 324 " pdb=" CD1 ILE B 324 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.14e+00 bond pdb=" CG1 ILE E 324 " pdb=" CD1 ILE E 324 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.14e+00 bond pdb=" CB TRP D 551 " pdb=" CG TRP D 551 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 8.26e-01 bond pdb=" N PRO A 519 " pdb=" CA PRO A 519 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.31e-02 5.83e+03 8.14e-01 bond pdb=" CG1 ILE A 752 " pdb=" CD1 ILE A 752 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 8.12e-01 ... (remaining 26425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 34485 1.31 - 2.63: 996 2.63 - 3.94: 209 3.94 - 5.25: 34 5.25 - 6.57: 30 Bond angle restraints: 35754 Sorted by residual: angle pdb=" N GLY A 318 " pdb=" CA GLY A 318 " pdb=" C GLY A 318 " ideal model delta sigma weight residual 111.36 116.73 -5.37 1.17e+00 7.31e-01 2.11e+01 angle pdb=" N GLY F 318 " pdb=" CA GLY F 318 " pdb=" C GLY F 318 " ideal model delta sigma weight residual 111.03 116.91 -5.88 1.40e+00 5.10e-01 1.77e+01 angle pdb=" N GLY C 318 " pdb=" CA GLY C 318 " pdb=" C GLY C 318 " ideal model delta sigma weight residual 111.03 116.82 -5.79 1.40e+00 5.10e-01 1.71e+01 angle pdb=" C TRP C 551 " pdb=" N PHE C 552 " pdb=" CA PHE C 552 " ideal model delta sigma weight residual 120.72 116.56 4.16 1.67e+00 3.59e-01 6.22e+00 angle pdb=" C TRP F 551 " pdb=" N PHE F 552 " pdb=" CA PHE F 552 " ideal model delta sigma weight residual 120.72 116.60 4.12 1.67e+00 3.59e-01 6.10e+00 ... (remaining 35749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 14945 17.79 - 35.58: 1116 35.58 - 53.38: 234 53.38 - 71.17: 38 71.17 - 88.96: 17 Dihedral angle restraints: 16350 sinusoidal: 6912 harmonic: 9438 Sorted by residual: dihedral pdb=" CA ALA E 297 " pdb=" C ALA E 297 " pdb=" N PRO E 298 " pdb=" CA PRO E 298 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ALA B 297 " pdb=" C ALA B 297 " pdb=" N PRO B 298 " pdb=" CA PRO B 298 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ALA D 297 " pdb=" C ALA D 297 " pdb=" N PRO D 298 " pdb=" CA PRO D 298 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 16347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2520 0.034 - 0.067: 1012 0.067 - 0.101: 318 0.101 - 0.134: 158 0.134 - 0.168: 12 Chirality restraints: 4020 Sorted by residual: chirality pdb=" CB ILE C 301 " pdb=" CA ILE C 301 " pdb=" CG1 ILE C 301 " pdb=" CG2 ILE C 301 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" CB ILE F 301 " pdb=" CA ILE F 301 " pdb=" CG1 ILE F 301 " pdb=" CG2 ILE F 301 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CB ILE E 301 " pdb=" CA ILE E 301 " pdb=" CG1 ILE E 301 " pdb=" CG2 ILE E 301 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 4017 not shown) Planarity restraints: 4668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 460 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.24e+00 pdb=" N PRO E 461 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 461 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 461 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 460 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO D 461 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 461 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 461 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 460 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 461 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 461 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 461 " 0.030 5.00e-02 4.00e+02 ... (remaining 4665 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 279 2.60 - 3.18: 22567 3.18 - 3.75: 42174 3.75 - 4.33: 59400 4.33 - 4.90: 94622 Nonbonded interactions: 219042 Sorted by model distance: nonbonded pdb=" OG1 THR D 525 " pdb="MG MG D 904 " model vdw 2.029 2.170 nonbonded pdb=" O1B AGS B 902 " pdb="MG MG B 903 " model vdw 2.042 2.170 nonbonded pdb=" O1B AGS E 901 " pdb="MG MG E 903 " model vdw 2.042 2.170 nonbonded pdb=" OG1 THR A 525 " pdb="MG MG A 904 " model vdw 2.045 2.170 nonbonded pdb=" OG1 THR A 252 " pdb="MG MG A 903 " model vdw 2.046 2.170 ... (remaining 219037 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 200 through 901 or resid 903)) selection = (chain 'B' and (resid 200 through 901 or resid 903)) selection = (chain 'C' and (resid 200 through 901 or resid 903)) selection = (chain 'D' and (resid 200 through 901 or resid 903)) selection = (chain 'E' and (resid 200 through 901 or resid 903)) selection = (chain 'F' and (resid 200 through 901 or resid 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.440 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 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:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26430 Z= 0.122 Angle : 0.569 6.565 35754 Z= 0.302 Chirality : 0.043 0.168 4020 Planarity : 0.005 0.062 4668 Dihedral : 13.265 88.962 10230 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.75 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.04 (0.15), residues: 3270 helix: 0.75 (0.13), residues: 1668 sheet: 0.49 (0.25), residues: 396 loop : 0.98 (0.21), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 753 TYR 0.013 0.002 TYR F 244 PHE 0.015 0.001 PHE C 267 TRP 0.027 0.003 TRP E 551 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (26430) covalent geometry : angle 0.56872 / 0.30 (35754) hydrogen bonds : bond 0.13654 / 8.94 ( 1258) hydrogen bonds : angle 5.18880 / 3.73 ( 3522) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 634 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 677 LYS cc_start: 0.8429 (pttm) cc_final: 0.7794 (ptmm) REVERT: B 352 SER cc_start: 0.9344 (m) cc_final: 0.9141 (p) REVERT: B 389 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8278 (tptm) REVERT: B 397 GLU cc_start: 0.8581 (tp30) cc_final: 0.8043 (tp30) REVERT: B 417 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7740 (mp0) REVERT: B 498 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8334 (mm-30) REVERT: B 603 GLN cc_start: 0.8529 (tp40) cc_final: 0.8116 (tt0) REVERT: B 607 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8612 (mm-30) REVERT: B 689 GLU cc_start: 0.8568 (tt0) cc_final: 0.8343 (tp30) REVERT: C 389 LYS cc_start: 0.8576 (ttmt) cc_final: 0.8280 (tptm) REVERT: C 398 GLN cc_start: 0.9026 (tp-100) cc_final: 0.8531 (tp-100) REVERT: C 468 VAL cc_start: 0.9132 (p) cc_final: 0.8906 (m) REVERT: C 542 ILE cc_start: 0.9251 (mm) cc_final: 0.9049 (mm) REVERT: C 548 LEU cc_start: 0.9094 (mt) cc_final: 0.8813 (mt) REVERT: C 677 LYS cc_start: 0.8495 (pttm) cc_final: 0.8293 (ttmm) REVERT: C 689 GLU cc_start: 0.8645 (tt0) cc_final: 0.8287 (tp30) REVERT: D 677 LYS cc_start: 0.8465 (pttm) cc_final: 0.7853 (ptmm) REVERT: D 689 GLU cc_start: 0.8541 (tt0) cc_final: 0.8318 (tp30) REVERT: E 352 SER cc_start: 0.9327 (m) cc_final: 0.9122 (p) REVERT: E 442 MET cc_start: 0.6375 (tmm) cc_final: 0.6079 (pmm) REVERT: E 498 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8349 (mm-30) REVERT: E 603 GLN cc_start: 0.8549 (tp40) cc_final: 0.8042 (tt0) REVERT: E 607 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8620 (mm-30) REVERT: E 689 GLU cc_start: 0.8656 (tt0) cc_final: 0.8437 (tp30) REVERT: F 203 TYR cc_start: 0.8644 (m-10) cc_final: 0.8403 (m-80) REVERT: F 389 LYS cc_start: 0.8558 (ttmt) cc_final: 0.8223 (tptm) REVERT: F 398 GLN cc_start: 0.9020 (tp-100) cc_final: 0.8513 (tp-100) REVERT: F 468 VAL cc_start: 0.9137 (p) cc_final: 0.8894 (m) REVERT: F 542 ILE cc_start: 0.9242 (mm) cc_final: 0.9029 (mm) REVERT: F 548 LEU cc_start: 0.9115 (mt) cc_final: 0.8839 (mt) REVERT: F 560 ARG cc_start: 0.7616 (mmm-85) cc_final: 0.7164 (mmt180) REVERT: F 677 LYS cc_start: 0.8429 (pttm) cc_final: 0.8145 (ptmm) REVERT: F 689 GLU cc_start: 0.8704 (tt0) cc_final: 0.8388 (tp30) outliers start: 0 outliers final: 1 residues processed: 634 average time/residue: 0.8526 time to fit residues: 603.5519 Evaluate side-chains 358 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 562 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 558 ASN A 603 GLN B 226 HIS B 337 GLN B 499 HIS ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN C 337 GLN ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS D 337 GLN D 460 ASN D 558 ASN D 603 GLN E 226 HIS E 337 GLN E 499 HIS ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 ASN F 337 GLN F 499 HIS ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 764 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.132698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.099300 restraints weight = 39739.150| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.03 r_work: 0.3176 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26430 Z= 0.154 Angle : 0.608 7.251 35754 Z= 0.304 Chirality : 0.044 0.144 4020 Planarity : 0.006 0.063 4668 Dihedral : 8.593 59.740 3782 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.97 % Favored : 96.85 % Rotamer: Outliers : 2.86 % Allowed : 10.73 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.19 (0.15), residues: 3270 helix: 0.86 (0.13), residues: 1674 sheet: 0.65 (0.25), residues: 360 loop : 1.02 (0.20), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 465 TYR 0.015 0.001 TYR F 203 PHE 0.015 0.001 PHE F 742 TRP 0.018 0.002 TRP F 551 HIS 0.010 0.001 HIS F 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (26430) covalent geometry : angle 0.60837 / 0.30 (35754) hydrogen bonds : bond 0.03796 / 2.57 ( 1258) hydrogen bonds : angle 4.14858 / 2.91 ( 3522) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 362 time to evaluate : 1.078 Fit side-chains REVERT: A 417 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7855 (OUTLIER) REVERT: A 442 MET cc_start: 0.7308 (tmm) cc_final: 0.5898 (mpp) REVERT: A 450 ASP cc_start: 0.8804 (t70) cc_final: 0.8514 (t0) REVERT: A 740 MET cc_start: 0.8850 (mmm) cc_final: 0.8552 (mmm) REVERT: B 352 SER cc_start: 0.9340 (m) cc_final: 0.9127 (p) REVERT: B 389 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8270 (tptm) REVERT: B 397 GLU cc_start: 0.8657 (tp30) cc_final: 0.8151 (tp30) REVERT: B 442 MET cc_start: 0.6977 (tmm) cc_final: 0.6029 (mpp) REVERT: B 498 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8262 (mm-30) REVERT: B 603 GLN cc_start: 0.8533 (tp40) cc_final: 0.7957 (tt0) REVERT: B 677 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8122 (ttmm) REVERT: B 689 GLU cc_start: 0.8471 (tt0) cc_final: 0.8161 (tp30) REVERT: C 389 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8262 (tptm) REVERT: C 508 MET cc_start: 0.8503 (ttt) cc_final: 0.8057 (ttt) REVERT: C 548 LEU cc_start: 0.9092 (mt) cc_final: 0.8790 (mt) REVERT: C 584 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7701 (mtpp) REVERT: C 689 GLU cc_start: 0.8539 (tt0) cc_final: 0.8238 (tp30) REVERT: D 417 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8098 (tp30) REVERT: D 442 MET cc_start: 0.7193 (tmm) cc_final: 0.5797 (mpp) REVERT: D 450 ASP cc_start: 0.8843 (t70) cc_final: 0.8540 (t0) REVERT: D 689 GLU cc_start: 0.8535 (tt0) cc_final: 0.8258 (tp30) REVERT: E 352 SER cc_start: 0.9309 (m) cc_final: 0.9097 (p) REVERT: E 498 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8292 (mm-30) REVERT: E 603 GLN cc_start: 0.8539 (tp40) cc_final: 0.7973 (tt0) REVERT: E 689 GLU cc_start: 0.8503 (tt0) cc_final: 0.8272 (tp30) REVERT: F 389 LYS cc_start: 0.8510 (ttmt) cc_final: 0.8210 (tptm) REVERT: F 508 MET cc_start: 0.8503 (ttt) cc_final: 0.8063 (ttt) REVERT: F 548 LEU cc_start: 0.9099 (mt) cc_final: 0.8800 (mt) REVERT: F 560 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7227 (mmt180) REVERT: F 584 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7740 (mtpp) REVERT: F 689 GLU cc_start: 0.8606 (tt0) cc_final: 0.8283 (tp30) REVERT: F 740 MET cc_start: 0.8635 (mmm) cc_final: 0.8340 (mmm) REVERT: F 745 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.6842 (ttp80) outliers start: 78 outliers final: 34 residues processed: 409 average time/residue: 0.6926 time to fit residues: 325.5140 Evaluate side-chains 364 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 327 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 499 HIS Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 745 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 265 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 292 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 307 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 168 optimal weight: 0.0770 chunk 85 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 250 optimal weight: 0.0970 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS B 460 ASN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 GLN D 226 HIS D 558 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS F 226 HIS ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.132054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.098849 restraints weight = 39782.815| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.03 r_work: 0.3176 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26430 Z= 0.128 Angle : 0.558 7.259 35754 Z= 0.279 Chirality : 0.043 0.140 4020 Planarity : 0.005 0.063 4668 Dihedral : 8.460 59.714 3782 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.54 % Favored : 97.28 % Rotamer: Outliers : 2.89 % Allowed : 11.36 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.25 (0.15), residues: 3270 helix: 1.04 (0.13), residues: 1644 sheet: 0.27 (0.25), residues: 378 loop : 1.00 (0.20), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 359 TYR 0.009 0.001 TYR E 244 PHE 0.009 0.001 PHE E 674 TRP 0.012 0.002 TRP D 551 HIS 0.009 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (26430) covalent geometry : angle 0.55805 / 0.28 (35754) hydrogen bonds : bond 0.03466 / 2.35 ( 1258) hydrogen bonds : angle 4.00877 / 2.81 ( 3522) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 336 time to evaluate : 1.049 Fit side-chains REVERT: A 344 MET cc_start: 0.9323 (mtp) cc_final: 0.9076 (mtt) REVERT: A 417 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7965 (tp30) REVERT: A 442 MET cc_start: 0.7333 (tmm) cc_final: 0.5798 (mpp) REVERT: A 450 ASP cc_start: 0.8868 (t70) cc_final: 0.8533 (t0) REVERT: A 740 MET cc_start: 0.8823 (mmm) cc_final: 0.8535 (mmm) REVERT: B 352 SER cc_start: 0.9347 (m) cc_final: 0.9128 (p) REVERT: B 389 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8297 (tptm) REVERT: B 397 GLU cc_start: 0.8648 (tp30) cc_final: 0.8132 (tp30) REVERT: B 442 MET cc_start: 0.7045 (tmm) cc_final: 0.5969 (mpp) REVERT: B 603 GLN cc_start: 0.8514 (tp40) cc_final: 0.7996 (tt0) REVERT: B 689 GLU cc_start: 0.8454 (tt0) cc_final: 0.8200 (tp30) REVERT: C 389 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8296 (tptm) REVERT: C 442 MET cc_start: 0.6954 (tmm) cc_final: 0.6182 (mpp) REVERT: C 450 ASP cc_start: 0.8784 (t70) cc_final: 0.8440 (t0) REVERT: C 508 MET cc_start: 0.8540 (ttt) cc_final: 0.8088 (ttt) REVERT: C 584 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7741 (mtpp) REVERT: C 689 GLU cc_start: 0.8535 (tt0) cc_final: 0.8227 (tp30) REVERT: D 417 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8098 (tp30) REVERT: D 442 MET cc_start: 0.7226 (tmm) cc_final: 0.5760 (mpp) REVERT: D 450 ASP cc_start: 0.8860 (t70) cc_final: 0.8538 (t0) REVERT: D 689 GLU cc_start: 0.8549 (tt0) cc_final: 0.8257 (tp30) REVERT: E 352 SER cc_start: 0.9323 (m) cc_final: 0.9110 (p) REVERT: E 442 MET cc_start: 0.6997 (tmm) cc_final: 0.5825 (pmm) REVERT: E 584 LYS cc_start: 0.8092 (ttmt) cc_final: 0.7738 (mtpp) REVERT: E 603 GLN cc_start: 0.8533 (tp40) cc_final: 0.8010 (tt0) REVERT: F 389 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8288 (tmtm) REVERT: F 450 ASP cc_start: 0.8764 (t70) cc_final: 0.8446 (t0) REVERT: F 508 MET cc_start: 0.8554 (ttt) cc_final: 0.8107 (ttt) REVERT: F 560 ARG cc_start: 0.7827 (mmm-85) cc_final: 0.7358 (mmt180) REVERT: F 584 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7763 (mtpp) REVERT: F 689 GLU cc_start: 0.8590 (tt0) cc_final: 0.8273 (tp30) REVERT: F 740 MET cc_start: 0.8755 (mmm) cc_final: 0.8369 (mmm) REVERT: F 745 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.6770 (ttp80) outliers start: 79 outliers final: 36 residues processed: 385 average time/residue: 0.6849 time to fit residues: 303.1590 Evaluate side-chains 351 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 312 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 499 HIS Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 745 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 103 optimal weight: 3.9990 chunk 323 optimal weight: 0.8980 chunk 93 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 297 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 266 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 ASN ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN C 226 HIS ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 HIS ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 ASN F 226 HIS ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 735 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.129239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.096434 restraints weight = 39608.520| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.96 r_work: 0.3113 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26430 Z= 0.177 Angle : 0.578 6.742 35754 Z= 0.290 Chirality : 0.044 0.148 4020 Planarity : 0.005 0.063 4668 Dihedral : 8.519 59.974 3782 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.97 % Favored : 96.85 % Rotamer: Outliers : 3.19 % Allowed : 12.01 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.12 (0.15), residues: 3270 helix: 1.02 (0.13), residues: 1680 sheet: -0.05 (0.24), residues: 396 loop : 0.92 (0.21), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 745 TYR 0.009 0.001 TYR A 495 PHE 0.019 0.001 PHE C 674 TRP 0.017 0.002 TRP A 551 HIS 0.009 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (26430) covalent geometry : angle 0.57843 / 0.29 (35754) hydrogen bonds : bond 0.03618 / 2.46 ( 1258) hydrogen bonds : angle 3.93498 / 2.77 ( 3522) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 332 time to evaluate : 0.992 Fit side-chains REVERT: A 344 MET cc_start: 0.9336 (mtp) cc_final: 0.9034 (mtt) REVERT: A 417 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8087 (tp30) REVERT: A 442 MET cc_start: 0.7192 (tmm) cc_final: 0.5784 (mpp) REVERT: A 450 ASP cc_start: 0.8887 (t70) cc_final: 0.8534 (t0) REVERT: A 465 ARG cc_start: 0.6525 (ttm110) cc_final: 0.6137 (mtt-85) REVERT: A 475 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8236 (p) REVERT: A 558 ASN cc_start: 0.7725 (m-40) cc_final: 0.7363 (m-40) REVERT: A 677 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8687 (ttmm) REVERT: A 744 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7816 (ptp-110) REVERT: B 352 SER cc_start: 0.9339 (m) cc_final: 0.9118 (p) REVERT: B 389 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8295 (tptm) REVERT: B 397 GLU cc_start: 0.8683 (tp30) cc_final: 0.8146 (tp30) REVERT: B 442 MET cc_start: 0.7357 (tmm) cc_final: 0.6257 (mpp) REVERT: B 584 LYS cc_start: 0.8221 (ttmt) cc_final: 0.7769 (mtpt) REVERT: B 603 GLN cc_start: 0.8557 (tp40) cc_final: 0.8006 (tt0) REVERT: B 689 GLU cc_start: 0.8526 (tt0) cc_final: 0.8298 (tp30) REVERT: C 389 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8284 (tptm) REVERT: C 442 MET cc_start: 0.7089 (tmm) cc_final: 0.6229 (mpp) REVERT: C 450 ASP cc_start: 0.8781 (t70) cc_final: 0.8430 (t0) REVERT: C 508 MET cc_start: 0.8597 (ttt) cc_final: 0.8187 (ttt) REVERT: C 689 GLU cc_start: 0.8667 (tt0) cc_final: 0.8329 (tp30) REVERT: D 417 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8148 (tp30) REVERT: D 442 MET cc_start: 0.7167 (tmm) cc_final: 0.5830 (mpp) REVERT: D 450 ASP cc_start: 0.8895 (t70) cc_final: 0.8575 (t0) REVERT: D 465 ARG cc_start: 0.6353 (ttm110) cc_final: 0.5984 (mtt-85) REVERT: D 677 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8656 (ttmm) REVERT: D 689 GLU cc_start: 0.8597 (tt0) cc_final: 0.8313 (tp30) REVERT: E 352 SER cc_start: 0.9329 (m) cc_final: 0.9113 (p) REVERT: E 442 MET cc_start: 0.7197 (tmm) cc_final: 0.6029 (mpp) REVERT: E 465 ARG cc_start: 0.6611 (ttm110) cc_final: 0.6238 (mpt-90) REVERT: E 508 MET cc_start: 0.8530 (ttt) cc_final: 0.8200 (ttt) REVERT: E 584 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7776 (mtpt) REVERT: E 603 GLN cc_start: 0.8551 (tp40) cc_final: 0.8007 (tt0) REVERT: F 389 LYS cc_start: 0.8538 (ttmt) cc_final: 0.8310 (tmtm) REVERT: F 442 MET cc_start: 0.6722 (tmm) cc_final: 0.6166 (mpp) REVERT: F 450 ASP cc_start: 0.8789 (t70) cc_final: 0.8437 (t0) REVERT: F 508 MET cc_start: 0.8595 (ttt) cc_final: 0.8210 (ttt) REVERT: F 560 ARG cc_start: 0.7907 (mmm-85) cc_final: 0.7424 (mmt180) REVERT: F 689 GLU cc_start: 0.8660 (tt0) cc_final: 0.8331 (tp30) REVERT: F 745 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.6682 (ttp80) REVERT: F 764 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7147 (mt0) outliers start: 87 outliers final: 32 residues processed: 395 average time/residue: 0.7001 time to fit residues: 317.0325 Evaluate side-chains 358 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 318 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 499 HIS Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 658 LYS Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 745 ARG Chi-restraints excluded: chain F residue 764 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 268 optimal weight: 6.9990 chunk 226 optimal weight: 2.9990 chunk 134 optimal weight: 0.4980 chunk 231 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 217 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.096529 restraints weight = 39605.200| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.00 r_work: 0.3121 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26430 Z= 0.138 Angle : 0.534 6.666 35754 Z= 0.267 Chirality : 0.043 0.139 4020 Planarity : 0.005 0.063 4668 Dihedral : 8.454 59.633 3780 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.26 % Favored : 97.55 % Rotamer: Outliers : 2.67 % Allowed : 13.22 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.18 (0.15), residues: 3270 helix: 1.08 (0.13), residues: 1680 sheet: -0.08 (0.24), residues: 396 loop : 0.94 (0.21), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 745 TYR 0.009 0.001 TYR E 244 PHE 0.009 0.001 PHE B 674 TRP 0.013 0.001 TRP D 551 HIS 0.009 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (26430) covalent geometry : angle 0.53410 / 0.27 (35754) hydrogen bonds : bond 0.03361 / 2.29 ( 1258) hydrogen bonds : angle 3.92937 / 2.76 ( 3522) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 322 time to evaluate : 1.044 Fit side-chains REVERT: A 344 MET cc_start: 0.9360 (mtp) cc_final: 0.9071 (mtt) REVERT: A 417 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8097 (tp30) REVERT: A 442 MET cc_start: 0.7309 (tmm) cc_final: 0.6003 (mpp) REVERT: A 450 ASP cc_start: 0.8883 (t70) cc_final: 0.8535 (t0) REVERT: A 465 ARG cc_start: 0.6531 (ttm110) cc_final: 0.6153 (mtt-85) REVERT: A 558 ASN cc_start: 0.7707 (m-40) cc_final: 0.7374 (m-40) REVERT: A 744 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7745 (ptp-110) REVERT: B 309 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8844 (pt) REVERT: B 352 SER cc_start: 0.9342 (m) cc_final: 0.9122 (p) REVERT: B 389 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8301 (tptm) REVERT: B 397 GLU cc_start: 0.8662 (tp30) cc_final: 0.8117 (tp30) REVERT: B 442 MET cc_start: 0.7401 (tmm) cc_final: 0.6306 (mpp) REVERT: B 450 ASP cc_start: 0.8852 (t70) cc_final: 0.8493 (t0) REVERT: B 584 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7719 (mtpt) REVERT: B 603 GLN cc_start: 0.8546 (tp40) cc_final: 0.8039 (tt0) REVERT: B 678 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7914 (ptt) REVERT: B 689 GLU cc_start: 0.8505 (tt0) cc_final: 0.8284 (tp30) REVERT: C 389 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8371 (tmtm) REVERT: C 442 MET cc_start: 0.7087 (tmm) cc_final: 0.6240 (mpp) REVERT: C 450 ASP cc_start: 0.8792 (t70) cc_final: 0.8394 (t0) REVERT: C 508 MET cc_start: 0.8563 (ttt) cc_final: 0.8215 (ttt) REVERT: C 689 GLU cc_start: 0.8677 (tt0) cc_final: 0.8378 (tp30) REVERT: D 417 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8151 (tp30) REVERT: D 442 MET cc_start: 0.7330 (tmm) cc_final: 0.6036 (mpp) REVERT: D 450 ASP cc_start: 0.8901 (t70) cc_final: 0.8563 (t0) REVERT: D 465 ARG cc_start: 0.6420 (ttm110) cc_final: 0.6135 (mtt-85) REVERT: D 558 ASN cc_start: 0.7746 (m-40) cc_final: 0.7414 (m-40) REVERT: D 689 GLU cc_start: 0.8601 (tt0) cc_final: 0.8304 (tp30) REVERT: D 744 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7891 (ptp-110) REVERT: E 352 SER cc_start: 0.9333 (m) cc_final: 0.9114 (p) REVERT: E 397 GLU cc_start: 0.8748 (tt0) cc_final: 0.8383 (tm-30) REVERT: E 442 MET cc_start: 0.7202 (tmm) cc_final: 0.6155 (mpp) REVERT: E 450 ASP cc_start: 0.8851 (t70) cc_final: 0.8461 (t0) REVERT: E 465 ARG cc_start: 0.6554 (ttm110) cc_final: 0.6196 (mpt-90) REVERT: E 584 LYS cc_start: 0.8184 (ttmt) cc_final: 0.7798 (mtpp) REVERT: E 603 GLN cc_start: 0.8551 (tp40) cc_final: 0.8015 (tt0) REVERT: F 442 MET cc_start: 0.6629 (tmm) cc_final: 0.6195 (mpp) REVERT: F 450 ASP cc_start: 0.8817 (t70) cc_final: 0.8470 (t0) REVERT: F 508 MET cc_start: 0.8577 (ttt) cc_final: 0.8233 (ttt) REVERT: F 560 ARG cc_start: 0.8019 (mmm-85) cc_final: 0.7461 (mmt180) REVERT: F 603 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8479 (mt0) REVERT: F 689 GLU cc_start: 0.8674 (tt0) cc_final: 0.8384 (tp30) REVERT: F 745 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.6660 (ttp80) outliers start: 73 outliers final: 30 residues processed: 371 average time/residue: 0.7234 time to fit residues: 306.6434 Evaluate side-chains 349 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 311 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 658 LYS Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 658 LYS Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 603 GLN Chi-restraints excluded: chain F residue 745 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 50 optimal weight: 2.9990 chunk 222 optimal weight: 0.0470 chunk 163 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 84 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN C 226 HIS ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN D 558 ASN ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 764 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.130076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.097079 restraints weight = 39624.894| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.03 r_work: 0.3147 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26430 Z= 0.115 Angle : 0.518 8.300 35754 Z= 0.259 Chirality : 0.042 0.135 4020 Planarity : 0.005 0.062 4668 Dihedral : 8.299 59.994 3780 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.51 % Favored : 97.31 % Rotamer: Outliers : 2.42 % Allowed : 14.21 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.32 (0.16), residues: 3270 helix: 1.23 (0.13), residues: 1680 sheet: 0.10 (0.25), residues: 378 loop : 0.89 (0.21), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 744 TYR 0.010 0.001 TYR E 244 PHE 0.021 0.001 PHE C 674 TRP 0.011 0.001 TRP D 551 HIS 0.010 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (26430) covalent geometry : angle 0.51834 / 0.26 (35754) hydrogen bonds : bond 0.03135 / 2.13 ( 1258) hydrogen bonds : angle 3.87909 / 2.73 ( 3522) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 328 time to evaluate : 1.020 Fit side-chains REVERT: A 239 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.6461 (ptt180) REVERT: A 344 MET cc_start: 0.9376 (mtp) cc_final: 0.9062 (mtm) REVERT: A 417 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8111 (tp30) REVERT: A 442 MET cc_start: 0.7280 (tmm) cc_final: 0.6045 (mpp) REVERT: A 449 MET cc_start: 0.8542 (tpt) cc_final: 0.8326 (tpp) REVERT: A 450 ASP cc_start: 0.8876 (t70) cc_final: 0.8535 (t0) REVERT: A 470 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8258 (mt-10) REVERT: A 558 ASN cc_start: 0.7715 (m-40) cc_final: 0.7445 (m-40) REVERT: A 744 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7778 (ptp-110) REVERT: B 352 SER cc_start: 0.9340 (m) cc_final: 0.9128 (p) REVERT: B 389 LYS cc_start: 0.8549 (ttmt) cc_final: 0.8306 (tptm) REVERT: B 397 GLU cc_start: 0.8636 (tp30) cc_final: 0.8113 (tp30) REVERT: B 442 MET cc_start: 0.7432 (tmm) cc_final: 0.6380 (mpp) REVERT: B 450 ASP cc_start: 0.8868 (t70) cc_final: 0.8483 (t0) REVERT: B 465 ARG cc_start: 0.6506 (ttm110) cc_final: 0.6190 (mpt-90) REVERT: B 584 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7781 (mtpt) REVERT: B 603 GLN cc_start: 0.8561 (tp40) cc_final: 0.7989 (tt0) REVERT: B 678 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7893 (ptt) REVERT: B 689 GLU cc_start: 0.8486 (tt0) cc_final: 0.8280 (tp30) REVERT: C 389 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8336 (tmtm) REVERT: C 442 MET cc_start: 0.7249 (tmm) cc_final: 0.6386 (mpp) REVERT: C 450 ASP cc_start: 0.8767 (t70) cc_final: 0.8361 (t0) REVERT: C 508 MET cc_start: 0.8596 (ttt) cc_final: 0.8268 (ttt) REVERT: C 584 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7755 (mtpp) REVERT: C 603 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8479 (mt0) REVERT: C 689 GLU cc_start: 0.8633 (tt0) cc_final: 0.8317 (tp30) REVERT: D 417 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8142 (tp30) REVERT: D 442 MET cc_start: 0.7289 (tmm) cc_final: 0.6063 (mpp) REVERT: D 450 ASP cc_start: 0.8859 (t70) cc_final: 0.8525 (t0) REVERT: D 465 ARG cc_start: 0.6351 (ttm110) cc_final: 0.6079 (mtt-85) REVERT: D 470 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8256 (mt-10) REVERT: D 689 GLU cc_start: 0.8588 (tt0) cc_final: 0.8291 (tp30) REVERT: D 744 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7781 (ptp-110) REVERT: E 352 SER cc_start: 0.9328 (m) cc_final: 0.9118 (p) REVERT: E 397 GLU cc_start: 0.8744 (tt0) cc_final: 0.8375 (tm-30) REVERT: E 442 MET cc_start: 0.7386 (tmm) cc_final: 0.6289 (mpp) REVERT: E 450 ASP cc_start: 0.8850 (t70) cc_final: 0.8464 (t0) REVERT: E 465 ARG cc_start: 0.6522 (ttm110) cc_final: 0.6221 (mpt-90) REVERT: E 584 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7765 (mtpt) REVERT: E 603 GLN cc_start: 0.8564 (tp40) cc_final: 0.8014 (tt0) REVERT: E 674 PHE cc_start: 0.8329 (t80) cc_final: 0.7854 (t80) REVERT: F 442 MET cc_start: 0.6600 (tmm) cc_final: 0.6178 (mpp) REVERT: F 450 ASP cc_start: 0.8878 (t70) cc_final: 0.8503 (t0) REVERT: F 508 MET cc_start: 0.8611 (ttt) cc_final: 0.8284 (ttt) REVERT: F 560 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7503 (mmt180) REVERT: F 584 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7810 (mtpp) REVERT: F 689 GLU cc_start: 0.8595 (tt0) cc_final: 0.8262 (tp30) REVERT: F 745 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.6635 (ttp80) REVERT: F 764 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.6946 (mt0) outliers start: 66 outliers final: 30 residues processed: 374 average time/residue: 0.7230 time to fit residues: 308.9183 Evaluate side-chains 352 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 313 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 658 LYS Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 603 GLN Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 745 ARG Chi-restraints excluded: chain F residue 764 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 169 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 262 optimal weight: 0.0170 chunk 32 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN D 764 GLN ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 ASN F 226 HIS ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.129087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.096245 restraints weight = 39666.867| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.99 r_work: 0.3115 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26430 Z= 0.154 Angle : 0.549 8.874 35754 Z= 0.273 Chirality : 0.043 0.172 4020 Planarity : 0.005 0.061 4668 Dihedral : 8.339 59.874 3780 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.57 % Favored : 97.25 % Rotamer: Outliers : 2.67 % Allowed : 14.18 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.28 (0.16), residues: 3270 helix: 1.22 (0.13), residues: 1680 sheet: -0.08 (0.24), residues: 396 loop : 0.92 (0.21), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 744 TYR 0.010 0.001 TYR E 244 PHE 0.018 0.001 PHE F 674 TRP 0.014 0.002 TRP D 551 HIS 0.009 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (26430) covalent geometry : angle 0.54898 / 0.27 (35754) hydrogen bonds : bond 0.03308 / 2.26 ( 1258) hydrogen bonds : angle 3.83937 / 2.70 ( 3522) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 319 time to evaluate : 1.014 Fit side-chains REVERT: A 239 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6611 (ptt180) REVERT: A 344 MET cc_start: 0.9386 (mtp) cc_final: 0.9106 (mtt) REVERT: A 417 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8128 (tp30) REVERT: A 442 MET cc_start: 0.7294 (tmm) cc_final: 0.6041 (mpp) REVERT: A 449 MET cc_start: 0.8554 (tpt) cc_final: 0.8354 (tpp) REVERT: A 450 ASP cc_start: 0.8878 (t70) cc_final: 0.8551 (t0) REVERT: A 465 ARG cc_start: 0.6475 (ttm110) cc_final: 0.6180 (mtt-85) REVERT: A 470 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8339 (mt-10) REVERT: A 475 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8115 (p) REVERT: A 558 ASN cc_start: 0.7772 (m-40) cc_final: 0.7461 (m-40) REVERT: A 744 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7794 (ptp-110) REVERT: B 309 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8830 (pt) REVERT: B 352 SER cc_start: 0.9335 (m) cc_final: 0.9123 (p) REVERT: B 389 LYS cc_start: 0.8537 (ttmt) cc_final: 0.8317 (tptm) REVERT: B 397 GLU cc_start: 0.8664 (tp30) cc_final: 0.8140 (tp30) REVERT: B 442 MET cc_start: 0.7436 (tmm) cc_final: 0.6446 (mpp) REVERT: B 450 ASP cc_start: 0.8850 (t70) cc_final: 0.8492 (t0) REVERT: B 465 ARG cc_start: 0.6539 (ttm110) cc_final: 0.6175 (mpt-90) REVERT: B 584 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7814 (mtpt) REVERT: B 603 GLN cc_start: 0.8580 (tp40) cc_final: 0.7996 (tt0) REVERT: B 689 GLU cc_start: 0.8514 (tt0) cc_final: 0.8294 (tp30) REVERT: C 442 MET cc_start: 0.7286 (tmm) cc_final: 0.6443 (mpp) REVERT: C 450 ASP cc_start: 0.8849 (t70) cc_final: 0.8436 (t0) REVERT: C 508 MET cc_start: 0.8578 (ttt) cc_final: 0.8251 (ttt) REVERT: C 584 LYS cc_start: 0.8176 (mtmt) cc_final: 0.7817 (mtpp) REVERT: C 603 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8505 (mt0) REVERT: C 689 GLU cc_start: 0.8618 (tt0) cc_final: 0.8320 (tp30) REVERT: D 239 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6822 (ptt180) REVERT: D 417 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8181 (tp30) REVERT: D 442 MET cc_start: 0.7375 (tmm) cc_final: 0.6152 (mpp) REVERT: D 450 ASP cc_start: 0.8866 (t70) cc_final: 0.8533 (t0) REVERT: D 465 ARG cc_start: 0.6380 (ttm110) cc_final: 0.6056 (mpt-90) REVERT: D 470 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8331 (mt-10) REVERT: D 475 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8111 (p) REVERT: D 689 GLU cc_start: 0.8550 (tt0) cc_final: 0.8271 (tp30) REVERT: D 744 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7888 (ptp-110) REVERT: E 352 SER cc_start: 0.9325 (m) cc_final: 0.9116 (p) REVERT: E 442 MET cc_start: 0.7433 (tmm) cc_final: 0.6319 (mpp) REVERT: E 450 ASP cc_start: 0.8822 (t70) cc_final: 0.8459 (t0) REVERT: E 465 ARG cc_start: 0.6539 (ttm110) cc_final: 0.6255 (mpt-90) REVERT: E 584 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7822 (mtpt) REVERT: E 603 GLN cc_start: 0.8594 (tp40) cc_final: 0.8027 (tt0) REVERT: E 674 PHE cc_start: 0.8348 (t80) cc_final: 0.7929 (t80) REVERT: F 442 MET cc_start: 0.6724 (tmm) cc_final: 0.6311 (mpp) REVERT: F 450 ASP cc_start: 0.8869 (t70) cc_final: 0.8505 (t0) REVERT: F 508 MET cc_start: 0.8607 (ttt) cc_final: 0.8287 (ttt) REVERT: F 560 ARG cc_start: 0.8140 (mmm-85) cc_final: 0.7515 (mmt180) REVERT: F 584 LYS cc_start: 0.8230 (mtmt) cc_final: 0.7853 (mtpp) REVERT: F 689 GLU cc_start: 0.8653 (tt0) cc_final: 0.8386 (tp30) REVERT: F 745 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.6713 (ttp80) outliers start: 73 outliers final: 41 residues processed: 369 average time/residue: 0.7188 time to fit residues: 302.9871 Evaluate side-chains 357 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 305 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 658 LYS Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 603 GLN Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 745 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 269 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN C 226 HIS ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 ASN F 226 HIS ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.128447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095403 restraints weight = 39791.758| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.02 r_work: 0.3112 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26430 Z= 0.150 Angle : 0.553 8.022 35754 Z= 0.275 Chirality : 0.043 0.211 4020 Planarity : 0.005 0.061 4668 Dihedral : 8.366 59.998 3780 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.72 % Favored : 97.09 % Rotamer: Outliers : 2.60 % Allowed : 14.58 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.28 (0.16), residues: 3270 helix: 1.21 (0.13), residues: 1680 sheet: -0.09 (0.24), residues: 396 loop : 0.92 (0.21), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 744 TYR 0.011 0.001 TYR E 244 PHE 0.012 0.001 PHE C 674 TRP 0.013 0.002 TRP F 551 HIS 0.018 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (26430) covalent geometry : angle 0.55250 / 0.28 (35754) hydrogen bonds : bond 0.03296 / 2.25 ( 1258) hydrogen bonds : angle 3.85659 / 2.71 ( 3522) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 318 time to evaluate : 1.013 Fit side-chains REVERT: A 239 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6633 (ptt180) REVERT: A 344 MET cc_start: 0.9387 (mtp) cc_final: 0.9082 (mtm) REVERT: A 417 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8147 (tp30) REVERT: A 442 MET cc_start: 0.7288 (tmm) cc_final: 0.6054 (mpp) REVERT: A 450 ASP cc_start: 0.8877 (t70) cc_final: 0.8540 (t0) REVERT: A 465 ARG cc_start: 0.6471 (ttm110) cc_final: 0.6186 (mtt-85) REVERT: A 470 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8326 (mt-10) REVERT: A 475 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8103 (p) REVERT: A 558 ASN cc_start: 0.7772 (m-40) cc_final: 0.7447 (m-40) REVERT: A 744 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7795 (ptp-110) REVERT: B 239 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6990 (ptt180) REVERT: B 352 SER cc_start: 0.9325 (m) cc_final: 0.9110 (p) REVERT: B 389 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8315 (tptm) REVERT: B 397 GLU cc_start: 0.8663 (tp30) cc_final: 0.8161 (tp30) REVERT: B 442 MET cc_start: 0.7471 (tmm) cc_final: 0.6486 (mpp) REVERT: B 450 ASP cc_start: 0.8844 (t70) cc_final: 0.8475 (t0) REVERT: B 465 ARG cc_start: 0.6589 (ttm110) cc_final: 0.6186 (mpt-90) REVERT: B 584 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7781 (mtpt) REVERT: B 603 GLN cc_start: 0.8582 (tp40) cc_final: 0.8014 (tt0) REVERT: B 689 GLU cc_start: 0.8515 (tt0) cc_final: 0.8300 (tp30) REVERT: C 442 MET cc_start: 0.7338 (tmm) cc_final: 0.6499 (mpp) REVERT: C 450 ASP cc_start: 0.8896 (t70) cc_final: 0.8494 (t0) REVERT: C 508 MET cc_start: 0.8584 (ttt) cc_final: 0.8281 (ttt) REVERT: C 584 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7840 (mtpp) REVERT: C 603 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: C 674 PHE cc_start: 0.8250 (t80) cc_final: 0.7906 (t80) REVERT: C 689 GLU cc_start: 0.8613 (tt0) cc_final: 0.8323 (tp30) REVERT: D 239 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6802 (ptt180) REVERT: D 417 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8178 (tp30) REVERT: D 442 MET cc_start: 0.7387 (tmm) cc_final: 0.6169 (mpp) REVERT: D 450 ASP cc_start: 0.8856 (t70) cc_final: 0.8513 (t0) REVERT: D 465 ARG cc_start: 0.6386 (ttm110) cc_final: 0.6029 (mpt-90) REVERT: D 470 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8311 (mt-10) REVERT: D 475 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8095 (p) REVERT: D 689 GLU cc_start: 0.8558 (tt0) cc_final: 0.8284 (tp30) REVERT: D 744 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7883 (ptp-110) REVERT: E 239 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7007 (ptt180) REVERT: E 352 SER cc_start: 0.9322 (m) cc_final: 0.9107 (p) REVERT: E 397 GLU cc_start: 0.8725 (tt0) cc_final: 0.8385 (tm-30) REVERT: E 442 MET cc_start: 0.7450 (tmm) cc_final: 0.6313 (mpp) REVERT: E 450 ASP cc_start: 0.8832 (t70) cc_final: 0.8460 (t0) REVERT: E 465 ARG cc_start: 0.6514 (ttm110) cc_final: 0.6283 (mtt-85) REVERT: E 584 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7745 (mtpt) REVERT: E 603 GLN cc_start: 0.8601 (tp40) cc_final: 0.8020 (tt0) REVERT: E 674 PHE cc_start: 0.8342 (t80) cc_final: 0.7951 (t80) REVERT: F 442 MET cc_start: 0.6770 (tmm) cc_final: 0.6321 (mpp) REVERT: F 450 ASP cc_start: 0.8859 (t70) cc_final: 0.8481 (t0) REVERT: F 508 MET cc_start: 0.8596 (ttt) cc_final: 0.8297 (ttt) REVERT: F 560 ARG cc_start: 0.8158 (mmm-85) cc_final: 0.7526 (mmt180) REVERT: F 584 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7860 (mtpp) REVERT: F 689 GLU cc_start: 0.8667 (tt0) cc_final: 0.8393 (tp30) REVERT: F 745 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.6692 (ttp80) outliers start: 71 outliers final: 40 residues processed: 366 average time/residue: 0.6926 time to fit residues: 290.0162 Evaluate side-chains 361 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 309 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 658 LYS Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 603 GLN Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 239 ARG Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 386 LYS Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 745 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 144 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 303 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 192 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 196 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 ASN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 HIS C 226 HIS ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN F 603 GLN F 764 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.130886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.098108 restraints weight = 39611.769| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.99 r_work: 0.3138 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26430 Z= 0.119 Angle : 0.537 8.419 35754 Z= 0.268 Chirality : 0.043 0.176 4020 Planarity : 0.005 0.061 4668 Dihedral : 8.283 59.901 3780 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.45 % Favored : 97.37 % Rotamer: Outliers : 2.31 % Allowed : 15.02 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.33 (0.16), residues: 3270 helix: 1.23 (0.13), residues: 1680 sheet: 0.10 (0.25), residues: 378 loop : 0.90 (0.21), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 744 TYR 0.011 0.001 TYR E 244 PHE 0.029 0.001 PHE F 674 TRP 0.016 0.002 TRP F 551 HIS 0.009 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (26430) covalent geometry : angle 0.53744 / 0.27 (35754) hydrogen bonds : bond 0.03129 / 2.14 ( 1258) hydrogen bonds : angle 3.85778 / 2.71 ( 3522) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 307 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 344 MET cc_start: 0.9378 (mtp) cc_final: 0.9072 (mtm) REVERT: A 417 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8172 (tp30) REVERT: A 442 MET cc_start: 0.7348 (tmm) cc_final: 0.6186 (mpp) REVERT: A 450 ASP cc_start: 0.8854 (t70) cc_final: 0.8484 (t0) REVERT: A 470 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8298 (mt-10) REVERT: A 475 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8051 (p) REVERT: A 744 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7836 (ptp-110) REVERT: B 239 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6911 (ptt180) REVERT: B 352 SER cc_start: 0.9326 (m) cc_final: 0.9110 (p) REVERT: B 397 GLU cc_start: 0.8657 (tp30) cc_final: 0.8162 (tp30) REVERT: B 442 MET cc_start: 0.7457 (tmm) cc_final: 0.6502 (mpp) REVERT: B 450 ASP cc_start: 0.8842 (t70) cc_final: 0.8465 (t0) REVERT: B 465 ARG cc_start: 0.6547 (ttm110) cc_final: 0.6159 (mpt-90) REVERT: B 584 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7755 (mtpt) REVERT: B 603 GLN cc_start: 0.8568 (tp40) cc_final: 0.7973 (tt0) REVERT: B 689 GLU cc_start: 0.8525 (tt0) cc_final: 0.8297 (tp30) REVERT: C 442 MET cc_start: 0.7393 (tmm) cc_final: 0.6546 (mpp) REVERT: C 450 ASP cc_start: 0.8859 (t70) cc_final: 0.8420 (t0) REVERT: C 508 MET cc_start: 0.8564 (ttt) cc_final: 0.8269 (ttt) REVERT: C 584 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7836 (mtpp) REVERT: C 674 PHE cc_start: 0.8290 (t80) cc_final: 0.7895 (t80) REVERT: C 689 GLU cc_start: 0.8605 (tt0) cc_final: 0.8315 (tp30) REVERT: D 417 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8201 (tp30) REVERT: D 442 MET cc_start: 0.7363 (tmm) cc_final: 0.6222 (mpp) REVERT: D 450 ASP cc_start: 0.8854 (t70) cc_final: 0.8491 (t0) REVERT: D 465 ARG cc_start: 0.6367 (ttm110) cc_final: 0.6032 (mpt-90) REVERT: D 470 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8289 (mt-10) REVERT: D 475 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8066 (p) REVERT: D 689 GLU cc_start: 0.8524 (tt0) cc_final: 0.8241 (tp30) REVERT: E 352 SER cc_start: 0.9319 (m) cc_final: 0.9112 (p) REVERT: E 397 GLU cc_start: 0.8740 (tt0) cc_final: 0.8374 (tm-30) REVERT: E 442 MET cc_start: 0.7531 (tmm) cc_final: 0.6419 (mpp) REVERT: E 450 ASP cc_start: 0.8812 (t70) cc_final: 0.8424 (t0) REVERT: E 465 ARG cc_start: 0.6449 (ttm110) cc_final: 0.6239 (mtt-85) REVERT: E 584 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7717 (mtpt) REVERT: E 603 GLN cc_start: 0.8596 (tp40) cc_final: 0.8009 (tt0) REVERT: E 674 PHE cc_start: 0.8335 (t80) cc_final: 0.7899 (t80) REVERT: F 442 MET cc_start: 0.6841 (tmm) cc_final: 0.6357 (mpp) REVERT: F 450 ASP cc_start: 0.8870 (t70) cc_final: 0.8476 (t0) REVERT: F 508 MET cc_start: 0.8578 (ttt) cc_final: 0.8278 (ttt) REVERT: F 560 ARG cc_start: 0.8188 (mmm-85) cc_final: 0.7578 (mmt180) REVERT: F 584 LYS cc_start: 0.8226 (mtmt) cc_final: 0.7848 (mtpp) REVERT: F 689 GLU cc_start: 0.8662 (tt0) cc_final: 0.8378 (tp30) REVERT: F 745 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.6658 (ttp80) outliers start: 63 outliers final: 41 residues processed: 352 average time/residue: 0.7408 time to fit residues: 297.4800 Evaluate side-chains 351 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 303 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 239 ARG Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 658 LYS Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 745 ARG Chi-restraints excluded: chain F residue 764 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 194 optimal weight: 0.0870 chunk 244 optimal weight: 0.8980 chunk 230 optimal weight: 5.9990 chunk 82 optimal weight: 0.3980 chunk 43 optimal weight: 0.0870 chunk 67 optimal weight: 0.9980 chunk 302 optimal weight: 0.0270 chunk 303 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 ASN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN F 603 GLN F 764 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.131420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.098607 restraints weight = 39612.683| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.99 r_work: 0.3157 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26430 Z= 0.111 Angle : 0.545 9.901 35754 Z= 0.271 Chirality : 0.042 0.150 4020 Planarity : 0.005 0.062 4668 Dihedral : 8.202 59.916 3780 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.48 % Favored : 97.34 % Rotamer: Outliers : 1.94 % Allowed : 15.64 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.43 (0.16), residues: 3270 helix: 1.27 (0.13), residues: 1680 sheet: 0.32 (0.25), residues: 360 loop : 0.95 (0.21), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 744 TYR 0.011 0.001 TYR A 495 PHE 0.018 0.001 PHE B 674 TRP 0.019 0.002 TRP F 551 HIS 0.006 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (26430) covalent geometry : angle 0.54463 / 0.27 (35754) hydrogen bonds : bond 0.03044 / 2.08 ( 1258) hydrogen bonds : angle 3.84431 / 2.70 ( 3522) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 310 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.9390 (mtp) cc_final: 0.9090 (mtm) REVERT: A 417 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8204 (tp30) REVERT: A 442 MET cc_start: 0.7380 (tmm) cc_final: 0.6251 (mpp) REVERT: A 450 ASP cc_start: 0.8844 (t70) cc_final: 0.8488 (t0) REVERT: A 470 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8283 (mt-10) REVERT: A 475 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8053 (p) REVERT: A 744 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7840 (ptp-110) REVERT: B 352 SER cc_start: 0.9333 (m) cc_final: 0.9125 (p) REVERT: B 397 GLU cc_start: 0.8640 (tp30) cc_final: 0.8145 (tp30) REVERT: B 442 MET cc_start: 0.7489 (tmm) cc_final: 0.6558 (mpp) REVERT: B 450 ASP cc_start: 0.8830 (t70) cc_final: 0.8459 (t0) REVERT: B 465 ARG cc_start: 0.6481 (ttm110) cc_final: 0.6124 (mpt-90) REVERT: B 584 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7708 (mtpt) REVERT: B 603 GLN cc_start: 0.8583 (tp40) cc_final: 0.7979 (tt0) REVERT: B 689 GLU cc_start: 0.8534 (tt0) cc_final: 0.8297 (tp30) REVERT: C 442 MET cc_start: 0.7406 (tmm) cc_final: 0.6573 (mpp) REVERT: C 450 ASP cc_start: 0.8834 (t70) cc_final: 0.8390 (t0) REVERT: C 508 MET cc_start: 0.8562 (ttt) cc_final: 0.8266 (ttt) REVERT: C 584 LYS cc_start: 0.8170 (mtmt) cc_final: 0.7830 (mtpp) REVERT: C 674 PHE cc_start: 0.8253 (t80) cc_final: 0.7863 (t80) REVERT: C 689 GLU cc_start: 0.8583 (tt0) cc_final: 0.8313 (tp30) REVERT: D 417 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8204 (tp30) REVERT: D 442 MET cc_start: 0.7366 (tmm) cc_final: 0.6234 (mpp) REVERT: D 450 ASP cc_start: 0.8842 (t70) cc_final: 0.8471 (t0) REVERT: D 465 ARG cc_start: 0.6380 (ttm110) cc_final: 0.6047 (mpt-90) REVERT: D 470 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8283 (mt-10) REVERT: D 475 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8059 (p) REVERT: D 689 GLU cc_start: 0.8538 (tt0) cc_final: 0.8261 (tp30) REVERT: E 239 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6899 (ptt180) REVERT: E 352 SER cc_start: 0.9323 (m) cc_final: 0.9121 (p) REVERT: E 397 GLU cc_start: 0.8727 (tt0) cc_final: 0.8347 (tm-30) REVERT: E 442 MET cc_start: 0.7541 (tmm) cc_final: 0.6457 (mpp) REVERT: E 450 ASP cc_start: 0.8801 (t70) cc_final: 0.8419 (t0) REVERT: E 584 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7707 (mtpt) REVERT: E 603 GLN cc_start: 0.8616 (tp40) cc_final: 0.7998 (tt0) REVERT: E 674 PHE cc_start: 0.8354 (t80) cc_final: 0.7912 (t80) REVERT: F 442 MET cc_start: 0.6894 (tmm) cc_final: 0.6414 (mpp) REVERT: F 450 ASP cc_start: 0.8822 (t70) cc_final: 0.8409 (t0) REVERT: F 508 MET cc_start: 0.8574 (ttt) cc_final: 0.8275 (ttt) REVERT: F 560 ARG cc_start: 0.8170 (mmm-85) cc_final: 0.7569 (mmt180) REVERT: F 584 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7851 (mtpp) REVERT: F 689 GLU cc_start: 0.8631 (tt0) cc_final: 0.8369 (tp30) REVERT: F 745 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.6661 (ttp80) outliers start: 53 outliers final: 39 residues processed: 350 average time/residue: 0.6961 time to fit residues: 278.9391 Evaluate side-chains 347 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 301 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 658 LYS Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 603 GLN Chi-restraints excluded: chain F residue 745 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 218 optimal weight: 0.0030 chunk 307 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 240 optimal weight: 0.0470 chunk 262 optimal weight: 0.0060 chunk 234 optimal weight: 0.5980 chunk 265 optimal weight: 2.9990 chunk 319 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 overall best weight: 0.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN C 226 HIS ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 764 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.131507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098743 restraints weight = 39490.525| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.99 r_work: 0.3163 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 26430 Z= 0.166 Angle : 0.699 58.965 35754 Z= 0.398 Chirality : 0.045 0.934 4020 Planarity : 0.006 0.206 4668 Dihedral : 8.221 59.934 3780 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.51 % Favored : 97.28 % Rotamer: Outliers : 1.79 % Allowed : 15.75 % Favored : 82.45 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.43 (0.16), residues: 3270 helix: 1.27 (0.13), residues: 1680 sheet: 0.32 (0.25), residues: 360 loop : 0.95 (0.21), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 745 TYR 0.010 0.001 TYR A 495 PHE 0.018 0.001 PHE B 674 TRP 0.024 0.002 TRP C 551 HIS 0.283 0.004 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (26430) covalent geometry : angle 0.69851 / 0.40 (35754) hydrogen bonds : bond 0.03087 / 2.12 ( 1258) hydrogen bonds : angle 3.84147 / 2.70 ( 3522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8936.61 seconds wall clock time: 152 minutes 45.35 seconds (9165.35 seconds total)