Starting phenix.real_space_refine on Sun Jul 5 08:43:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y0c_72391/07_2026/9y0c_72391.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y0c_72391/07_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_72391/07_2026/9y0c_72391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y0c_72391/07_2026/9y0c_72391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y0c_72391/07_2026/9y0c_72391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y0c_72391/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 5.17, per 1000 atoms: 0.20 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: 1.87 Conformation dependent library (CDL) restraints added in 956.1 milliseconds 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: 0.53 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: 4.46 Time building geometry restraints manager: 2.53 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=" O3B AGS D 902 " pdb=" PB AGS D 902 " ideal model delta sigma weight residual 1.673 1.579 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" O3B AGS B 901 " pdb=" PB AGS B 901 " ideal model delta sigma weight residual 1.673 1.579 0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" O3B AGS C 901 " pdb=" PB AGS C 901 " ideal model delta sigma weight residual 1.673 1.580 0.093 2.00e-02 2.50e+03 2.19e+01 bond pdb=" O3B AGS E 902 " pdb=" PB AGS E 902 " ideal model delta sigma weight residual 1.673 1.580 0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" O3B AGS C 904 " pdb=" PB AGS C 904 " ideal model delta sigma weight residual 1.673 1.580 0.093 2.00e-02 2.50e+03 2.18e+01 ... (remaining 26425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 35044 2.09 - 4.19: 537 4.19 - 6.28: 83 6.28 - 8.37: 44 8.37 - 10.47: 46 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=" PB AGS B 901 " pdb=" O3B AGS B 901 " pdb=" PG AGS B 901 " ideal model delta sigma weight residual 129.21 118.74 10.47 3.00e+00 1.11e-01 1.22e+01 angle pdb=" PB AGS F 902 " pdb=" O3B AGS F 902 " pdb=" PG AGS F 902 " ideal model delta sigma weight residual 129.21 118.84 10.37 3.00e+00 1.11e-01 1.20e+01 ... (remaining 35749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 16200 35.88 - 71.76: 279 71.76 - 107.64: 53 107.64 - 143.52: 17 143.52 - 179.40: 17 Dihedral angle restraints: 16566 sinusoidal: 7128 harmonic: 9438 Sorted by residual: dihedral pdb=" O2B AGS E 902 " pdb=" O3B AGS E 902 " pdb=" PB AGS E 902 " pdb=" PG AGS E 902 " ideal model delta sinusoidal sigma weight residual 7.37 -173.23 -179.40 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2B AGS B 901 " pdb=" O3B AGS B 901 " pdb=" PB AGS B 901 " pdb=" PG AGS B 901 " ideal model delta sinusoidal sigma weight residual 7.37 -173.44 -179.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2B AGS A 902 " pdb=" O3B AGS A 902 " pdb=" PB AGS A 902 " pdb=" PG AGS A 902 " ideal model delta sinusoidal sigma weight residual 7.37 -173.91 -178.72 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 16563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3248 0.054 - 0.109: 641 0.109 - 0.163: 92 0.163 - 0.218: 3 0.218 - 0.272: 12 Chirality restraints: 3996 Sorted by residual: chirality pdb=" C3' AGS C 904 " pdb=" C2' AGS C 904 " pdb=" C4' AGS C 904 " pdb=" O3' AGS C 904 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' AGS F 901 " pdb=" C2' AGS F 901 " pdb=" C4' AGS F 901 " pdb=" O3' AGS F 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C3' AGS B 902 " pdb=" C2' AGS B 902 " pdb=" C4' AGS B 902 " pdb=" O3' AGS B 902 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3993 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: 5.340 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.620 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.005 0.094 26430 Z= 0.220 Angle : 0.749 10.466 35754 Z= 0.342 Chirality : 0.046 0.272 3996 Planarity : 0.005 0.062 4668 Dihedral : 16.814 179.397 10446 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 0.00452 / 0.22 (26430) covalent geometry : angle 0.74920 / 0.34 (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 : 0.828 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: 0.7374 time to fit residues: 525.9946 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 : 0.907 ------------------------------------------------------------------------------- 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: 0.4980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN A 558 ASN A 603 GLN B 226 HIS B 337 GLN B 499 HIS 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 = 0.3796 r_free = 0.3796 target = 0.133376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.100026 restraints weight = 39633.632| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.04 r_work: 0.3185 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26430 Z= 0.142 Angle : 0.613 7.286 35754 Z= 0.302 Chirality : 0.044 0.149 3996 Planarity : 0.006 0.063 4668 Dihedral : 18.278 179.411 3998 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.03 % Favored : 96.79 % Rotamer: Outliers : 2.71 % Allowed : 11.03 % Favored : 86.26 % 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: 1.21 (0.15), residues: 3270 helix: 0.87 (0.13), residues: 1674 sheet: 0.65 (0.25), residues: 360 loop : 1.04 (0.20), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 465 TYR 0.014 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 0.00331 / 0.14 (26430) covalent geometry : angle 0.61284 / 0.30 (35754) hydrogen bonds : bond 0.03695 / 2.50 ( 1258) hydrogen bonds : angle 4.14162 / 2.90 ( 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 434 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 360 time to evaluate : 1.025 Fit side-chains REVERT: A 417 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7852 (OUTLIER) REVERT: A 442 MET cc_start: 0.7291 (tmm) cc_final: 0.5856 (mpp) REVERT: A 450 ASP cc_start: 0.8798 (t70) cc_final: 0.8504 (t0) REVERT: A 740 MET cc_start: 0.8846 (mmm) cc_final: 0.8556 (mmm) REVERT: B 352 SER cc_start: 0.9334 (m) cc_final: 0.9125 (p) REVERT: B 389 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8271 (tptm) REVERT: B 397 GLU cc_start: 0.8652 (tp30) cc_final: 0.8135 (tp30) REVERT: B 442 MET cc_start: 0.6978 (tmm) cc_final: 0.6030 (mpp) REVERT: B 498 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8249 (mm-30) REVERT: B 603 GLN cc_start: 0.8518 (tp40) cc_final: 0.7952 (tt0) REVERT: B 677 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8176 (ttmm) REVERT: B 689 GLU cc_start: 0.8481 (tt0) cc_final: 0.8160 (tp30) REVERT: C 389 LYS cc_start: 0.8595 (ttmt) cc_final: 0.8262 (tptm) REVERT: C 508 MET cc_start: 0.8467 (ttt) cc_final: 0.8027 (ttt) REVERT: C 548 LEU cc_start: 0.9083 (mt) cc_final: 0.8781 (mt) REVERT: C 584 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7740 (mtpp) REVERT: C 689 GLU cc_start: 0.8551 (tt0) cc_final: 0.8222 (tp30) REVERT: D 417 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7958 (OUTLIER) REVERT: D 442 MET cc_start: 0.7171 (tmm) cc_final: 0.5747 (mpp) REVERT: D 450 ASP cc_start: 0.8833 (t70) cc_final: 0.8529 (t0) REVERT: D 689 GLU cc_start: 0.8524 (tt0) cc_final: 0.8237 (tp30) REVERT: E 352 SER cc_start: 0.9310 (m) cc_final: 0.9101 (p) REVERT: E 603 GLN cc_start: 0.8548 (tp40) cc_final: 0.8005 (tt0) REVERT: E 689 GLU cc_start: 0.8503 (tt0) cc_final: 0.8265 (tp30) REVERT: F 389 LYS cc_start: 0.8504 (ttmt) cc_final: 0.8201 (tptm) REVERT: F 508 MET cc_start: 0.8480 (ttt) cc_final: 0.8034 (ttt) REVERT: F 548 LEU cc_start: 0.9049 (mt) cc_final: 0.8756 (mt) REVERT: F 560 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7276 (mmt180) REVERT: F 584 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7728 (mtpp) REVERT: F 689 GLU cc_start: 0.8602 (tt0) cc_final: 0.8283 (tp30) REVERT: F 740 MET cc_start: 0.8620 (mmm) cc_final: 0.8273 (mmm) REVERT: F 745 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.6826 (ttp80) outliers start: 74 outliers final: 30 residues processed: 407 average time/residue: 0.5953 time to fit residues: 280.0802 Evaluate side-chains 361 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 329 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 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 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 301 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 423 ILE 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 562 ILE 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: 0.9980 chunk 68 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 307 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 168 optimal weight: 0.0570 chunk 85 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 250 optimal weight: 0.0970 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS A 603 GLN 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 735 HIS C 764 GLN D 226 HIS ** 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** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.132316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.099084 restraints weight = 39751.040| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.04 r_work: 0.3178 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26430 Z= 0.128 Angle : 0.570 7.272 35754 Z= 0.279 Chirality : 0.044 0.147 3996 Planarity : 0.005 0.063 4668 Dihedral : 17.419 179.943 3996 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.42 % Favored : 97.40 % Rotamer: Outliers : 3.00 % Allowed : 11.54 % Favored : 85.46 % 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: 1.27 (0.15), residues: 3270 helix: 1.05 (0.13), residues: 1644 sheet: 0.29 (0.25), residues: 378 loop : 1.01 (0.20), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 359 TYR 0.011 0.001 TYR B 244 PHE 0.010 0.001 PHE A 742 TRP 0.014 0.002 TRP E 551 HIS 0.010 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (26430) covalent geometry : angle 0.56963 / 0.28 (35754) hydrogen bonds : bond 0.03456 / 2.34 ( 1258) hydrogen bonds : angle 3.98603 / 2.80 ( 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 416 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 334 time to evaluate : 0.678 Fit side-chains REVERT: A 344 MET cc_start: 0.9319 (mtp) cc_final: 0.9082 (mtt) REVERT: A 417 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7982 (tp30) REVERT: A 442 MET cc_start: 0.7317 (tmm) cc_final: 0.5810 (mpp) REVERT: A 450 ASP cc_start: 0.8854 (t70) cc_final: 0.8494 (t0) REVERT: B 352 SER cc_start: 0.9316 (m) cc_final: 0.9107 (p) REVERT: B 389 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8304 (tptm) REVERT: B 397 GLU cc_start: 0.8656 (tp30) cc_final: 0.8135 (tp30) REVERT: B 442 MET cc_start: 0.7057 (tmm) cc_final: 0.5969 (mpp) REVERT: B 603 GLN cc_start: 0.8509 (tp40) cc_final: 0.7967 (tt0) REVERT: B 678 MET cc_start: 0.8199 (ptm) cc_final: 0.7213 (ppp) REVERT: B 689 GLU cc_start: 0.8460 (tt0) cc_final: 0.8213 (tp30) REVERT: C 389 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8364 (tmtm) REVERT: C 442 MET cc_start: 0.7039 (tmm) cc_final: 0.6263 (mpp) REVERT: C 450 ASP cc_start: 0.8783 (t70) cc_final: 0.8435 (t0) REVERT: C 508 MET cc_start: 0.8568 (ttt) cc_final: 0.8108 (ttt) REVERT: C 584 LYS cc_start: 0.8110 (ttmt) cc_final: 0.7752 (mtpp) REVERT: C 689 GLU cc_start: 0.8560 (tt0) cc_final: 0.8237 (tp30) REVERT: D 417 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8097 (tp30) REVERT: D 442 MET cc_start: 0.7210 (tmm) cc_final: 0.5763 (mpp) REVERT: D 450 ASP cc_start: 0.8889 (t70) cc_final: 0.8578 (t0) REVERT: D 689 GLU cc_start: 0.8549 (tt0) cc_final: 0.8253 (tp30) REVERT: E 352 SER cc_start: 0.9308 (m) cc_final: 0.9104 (p) REVERT: E 442 MET cc_start: 0.6988 (tmm) cc_final: 0.5799 (pmm) REVERT: E 584 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7751 (mtpp) REVERT: E 603 GLN cc_start: 0.8539 (tp40) cc_final: 0.8009 (tt0) REVERT: F 389 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8260 (tptm) REVERT: F 450 ASP cc_start: 0.8784 (t70) cc_final: 0.8461 (t0) REVERT: F 508 MET cc_start: 0.8586 (ttt) cc_final: 0.8132 (ttt) REVERT: F 560 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7352 (mmt180) REVERT: F 584 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7775 (mtpp) REVERT: F 689 GLU cc_start: 0.8598 (tt0) cc_final: 0.8273 (tp30) REVERT: F 740 MET cc_start: 0.8748 (mmm) cc_final: 0.8431 (mmm) REVERT: F 745 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.6769 (ttp80) outliers start: 82 outliers final: 31 residues processed: 385 average time/residue: 0.5775 time to fit residues: 257.3261 Evaluate side-chains 344 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 310 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 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 633 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 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 301 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: 0.9980 chunk 93 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 297 optimal weight: 0.2980 chunk 244 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 114 optimal weight: 0.0020 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS 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** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 735 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.131610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.098554 restraints weight = 39487.771| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.03 r_work: 0.3167 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26430 Z= 0.126 Angle : 0.547 7.128 35754 Z= 0.270 Chirality : 0.043 0.136 3996 Planarity : 0.005 0.062 4668 Dihedral : 17.006 179.711 3996 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.66 % Favored : 97.16 % Rotamer: Outliers : 2.53 % Allowed : 12.93 % Favored : 84.54 % 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: 1.36 (0.15), residues: 3270 helix: 1.16 (0.13), residues: 1644 sheet: 0.41 (0.26), residues: 360 loop : 0.97 (0.20), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 745 TYR 0.007 0.001 TYR A 495 PHE 0.011 0.001 PHE C 674 TRP 0.014 0.002 TRP E 551 HIS 0.008 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (26430) covalent geometry : angle 0.54715 / 0.27 (35754) hydrogen bonds : bond 0.03264 / 2.22 ( 1258) hydrogen bonds : angle 3.91742 / 2.75 ( 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 396 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 327 time to evaluate : 0.855 Fit side-chains REVERT: A 344 MET cc_start: 0.9347 (mtp) cc_final: 0.9123 (mtp) REVERT: A 417 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8045 (tp30) REVERT: A 442 MET cc_start: 0.7227 (tmm) cc_final: 0.5801 (mpp) REVERT: A 450 ASP cc_start: 0.8859 (t70) cc_final: 0.8517 (t0) REVERT: A 475 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8216 (p) REVERT: A 558 ASN cc_start: 0.7675 (m-40) cc_final: 0.7406 (m-40) REVERT: A 677 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8681 (ttmm) REVERT: A 744 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7650 (ptp-170) REVERT: B 352 SER cc_start: 0.9328 (m) cc_final: 0.9115 (p) REVERT: B 389 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8317 (tptm) REVERT: B 397 GLU cc_start: 0.8666 (tp30) cc_final: 0.8156 (tp30) REVERT: B 442 MET cc_start: 0.7260 (tmm) cc_final: 0.6177 (mpp) REVERT: B 584 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7749 (mtpp) REVERT: B 603 GLN cc_start: 0.8543 (tp40) cc_final: 0.7992 (tt0) REVERT: B 689 GLU cc_start: 0.8497 (tt0) cc_final: 0.8292 (tp30) REVERT: B 740 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8222 (ttp) REVERT: C 389 LYS cc_start: 0.8641 (ttmt) cc_final: 0.8333 (tptm) REVERT: C 442 MET cc_start: 0.6959 (tmm) cc_final: 0.6188 (mpp) REVERT: C 450 ASP cc_start: 0.8785 (t70) cc_final: 0.8409 (t0) REVERT: C 508 MET cc_start: 0.8652 (ttt) cc_final: 0.8212 (ttt) REVERT: C 584 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7795 (mtpp) REVERT: C 689 GLU cc_start: 0.8587 (tt0) cc_final: 0.8247 (tp30) REVERT: D 417 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8139 (tp30) REVERT: D 442 MET cc_start: 0.7227 (tmm) cc_final: 0.5776 (mpp) REVERT: D 450 ASP cc_start: 0.8880 (t70) cc_final: 0.8560 (t0) REVERT: D 677 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8688 (ttmm) REVERT: D 689 GLU cc_start: 0.8584 (tt0) cc_final: 0.8283 (tp30) REVERT: E 352 SER cc_start: 0.9315 (m) cc_final: 0.9111 (p) REVERT: E 442 MET cc_start: 0.7146 (tmm) cc_final: 0.5929 (pmm) REVERT: E 465 ARG cc_start: 0.6520 (ttm110) cc_final: 0.6173 (mpt-90) REVERT: E 584 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7725 (mtpt) REVERT: E 603 GLN cc_start: 0.8531 (tp40) cc_final: 0.7976 (tt0) REVERT: E 674 PHE cc_start: 0.8513 (t80) cc_final: 0.8234 (t80) REVERT: F 389 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8332 (tmtm) REVERT: F 442 MET cc_start: 0.6686 (tmm) cc_final: 0.6180 (mpp) REVERT: F 450 ASP cc_start: 0.8800 (t70) cc_final: 0.8441 (t0) REVERT: F 508 MET cc_start: 0.8661 (ttt) cc_final: 0.8222 (ttt) REVERT: F 560 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7451 (mmt180) REVERT: F 584 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7831 (mtpp) REVERT: F 689 GLU cc_start: 0.8580 (tt0) cc_final: 0.8268 (tp30) REVERT: F 740 MET cc_start: 0.8762 (mmm) cc_final: 0.8508 (mmm) REVERT: F 745 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.6622 (ttp80) REVERT: F 764 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7065 (mt0) outliers start: 69 outliers final: 28 residues processed: 372 average time/residue: 0.5815 time to fit residues: 251.0261 Evaluate side-chains 349 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 312 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 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 423 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 702 SER 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 499 HIS Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain E residue 301 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 562 ILE Chi-restraints excluded: chain F residue 633 ILE 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: 0.8980 chunk 134 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 217 optimal weight: 0.0770 chunk 168 optimal weight: 0.0020 chunk 292 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 227 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 overall best weight: 0.5746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.131597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.098557 restraints weight = 39495.457| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.02 r_work: 0.3170 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26430 Z= 0.122 Angle : 0.526 6.881 35754 Z= 0.260 Chirality : 0.043 0.136 3996 Planarity : 0.005 0.061 4668 Dihedral : 16.879 179.698 3996 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.42 % Favored : 97.40 % Rotamer: Outliers : 2.67 % Allowed : 13.19 % Favored : 84.14 % 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: 1.37 (0.16), residues: 3270 helix: 1.29 (0.13), residues: 1614 sheet: 0.22 (0.25), residues: 378 loop : 0.87 (0.20), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 744 TYR 0.010 0.001 TYR E 244 PHE 0.008 0.001 PHE E 758 TRP 0.014 0.001 TRP E 551 HIS 0.009 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (26430) covalent geometry : angle 0.52575 / 0.26 (35754) hydrogen bonds : bond 0.03206 / 2.18 ( 1258) hydrogen bonds : angle 3.89213 / 2.73 ( 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 393 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 320 time to evaluate : 0.688 Fit side-chains REVERT: A 344 MET cc_start: 0.9371 (mtp) cc_final: 0.9101 (mtt) REVERT: A 417 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8092 (tp30) REVERT: A 442 MET cc_start: 0.7195 (tmm) cc_final: 0.5875 (mpp) REVERT: A 450 ASP cc_start: 0.8835 (t70) cc_final: 0.8499 (t0) REVERT: A 475 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8233 (p) REVERT: A 558 ASN cc_start: 0.7767 (m-40) cc_final: 0.7433 (m-40) REVERT: A 677 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8721 (ttmm) REVERT: A 744 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7676 (ptp-110) REVERT: B 389 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8325 (tmtm) REVERT: B 397 GLU cc_start: 0.8671 (tp30) cc_final: 0.8136 (tp30) REVERT: B 442 MET cc_start: 0.7283 (tmm) cc_final: 0.6231 (mpp) REVERT: B 450 ASP cc_start: 0.8869 (t70) cc_final: 0.8485 (t0) REVERT: B 584 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7785 (mtpp) REVERT: B 603 GLN cc_start: 0.8562 (tp40) cc_final: 0.8009 (tt0) REVERT: C 389 LYS cc_start: 0.8637 (ttmt) cc_final: 0.8370 (tptm) REVERT: C 442 MET cc_start: 0.6936 (tmm) cc_final: 0.6228 (mpp) REVERT: C 450 ASP cc_start: 0.8782 (t70) cc_final: 0.8413 (t0) REVERT: C 508 MET cc_start: 0.8565 (ttt) cc_final: 0.8198 (ttt) REVERT: C 584 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7893 (mtpp) REVERT: C 603 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8571 (mt0) REVERT: C 689 GLU cc_start: 0.8572 (tt0) cc_final: 0.8251 (tp30) REVERT: D 417 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8131 (tp30) REVERT: D 442 MET cc_start: 0.7272 (tmm) cc_final: 0.5949 (mpp) REVERT: D 450 ASP cc_start: 0.8857 (t70) cc_final: 0.8531 (t0) REVERT: D 475 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8241 (p) REVERT: D 677 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8724 (ttmm) REVERT: D 689 GLU cc_start: 0.8599 (tt0) cc_final: 0.8315 (tp30) REVERT: D 744 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7725 (ptp-170) REVERT: E 442 MET cc_start: 0.7148 (tmm) cc_final: 0.6086 (mpp) REVERT: E 450 ASP cc_start: 0.8848 (t70) cc_final: 0.8465 (t0) REVERT: E 465 ARG cc_start: 0.6511 (ttm110) cc_final: 0.6177 (mpt-90) REVERT: E 584 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7847 (mtpp) REVERT: E 603 GLN cc_start: 0.8578 (tp40) cc_final: 0.8009 (tt0) REVERT: E 674 PHE cc_start: 0.8487 (t80) cc_final: 0.8083 (t80) REVERT: F 442 MET cc_start: 0.6635 (tmm) cc_final: 0.6180 (mpp) REVERT: F 450 ASP cc_start: 0.8796 (t70) cc_final: 0.8451 (t0) REVERT: F 508 MET cc_start: 0.8553 (ttt) cc_final: 0.8181 (ttt) REVERT: F 560 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7509 (mmt180) REVERT: F 584 LYS cc_start: 0.8263 (ttmt) cc_final: 0.7900 (mtpp) REVERT: F 689 GLU cc_start: 0.8575 (tt0) cc_final: 0.8282 (tp30) REVERT: F 745 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.6580 (ttp80) REVERT: F 764 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.6939 (mt0) outliers start: 73 outliers final: 34 residues processed: 369 average time/residue: 0.6154 time to fit residues: 262.0349 Evaluate side-chains 349 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 304 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 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 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 603 GLN Chi-restraints excluded: chain C residue 633 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 475 THR Chi-restraints excluded: chain D residue 677 LYS 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 474 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 601 ILE 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 633 ILE Chi-restraints excluded: chain F residue 745 ARG Chi-restraints excluded: chain F residue 764 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 50 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 110 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS ** 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** B 558 ASN C 226 HIS ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 603 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.131905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.098924 restraints weight = 39425.838| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.01 r_work: 0.3144 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2576 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= 0.125 Angle : 0.526 8.346 35754 Z= 0.260 Chirality : 0.042 0.136 3996 Planarity : 0.005 0.061 4668 Dihedral : 16.840 179.575 3996 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.60 % Favored : 97.22 % Rotamer: Outliers : 2.60 % Allowed : 14.10 % Favored : 83.30 % 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: 1.39 (0.16), residues: 3270 helix: 1.29 (0.13), residues: 1644 sheet: 0.42 (0.26), residues: 360 loop : 0.81 (0.20), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 744 TYR 0.010 0.001 TYR B 244 PHE 0.022 0.001 PHE C 674 TRP 0.011 0.001 TRP E 551 HIS 0.009 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (26430) covalent geometry : angle 0.52564 / 0.26 (35754) hydrogen bonds : bond 0.03179 / 2.17 ( 1258) hydrogen bonds : angle 3.85933 / 2.71 ( 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 392 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 321 time to evaluate : 0.767 Fit side-chains REVERT: A 344 MET cc_start: 0.9382 (mtp) cc_final: 0.9077 (mtt) REVERT: A 417 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8088 (tp30) REVERT: A 442 MET cc_start: 0.7309 (tmm) cc_final: 0.6037 (mpp) REVERT: A 450 ASP cc_start: 0.8867 (t70) cc_final: 0.8526 (t0) REVERT: A 470 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8342 (mt-10) REVERT: A 475 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8161 (p) REVERT: A 558 ASN cc_start: 0.7738 (m-40) cc_final: 0.7430 (m-40) REVERT: A 744 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7690 (ptp-110) REVERT: B 389 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8240 (tmtm) REVERT: B 397 GLU cc_start: 0.8661 (tp30) cc_final: 0.8125 (tp30) REVERT: B 442 MET cc_start: 0.7371 (tmm) cc_final: 0.6327 (mpp) REVERT: B 450 ASP cc_start: 0.8865 (t70) cc_final: 0.8461 (t0) REVERT: B 465 ARG cc_start: 0.6377 (ttm110) cc_final: 0.6088 (mpt-90) REVERT: B 584 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7758 (mtpt) REVERT: B 603 GLN cc_start: 0.8553 (tp40) cc_final: 0.7984 (tt0) REVERT: C 389 LYS cc_start: 0.8636 (ttmt) cc_final: 0.8398 (tmtm) REVERT: C 442 MET cc_start: 0.7111 (tmm) cc_final: 0.6342 (mpp) REVERT: C 450 ASP cc_start: 0.8801 (t70) cc_final: 0.8413 (t0) REVERT: C 508 MET cc_start: 0.8554 (ttt) cc_final: 0.8202 (ttt) REVERT: C 584 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7875 (mtpp) REVERT: C 689 GLU cc_start: 0.8597 (tt0) cc_final: 0.8247 (tp30) REVERT: D 417 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8134 (tp30) REVERT: D 442 MET cc_start: 0.7250 (tmm) cc_final: 0.5998 (mpp) REVERT: D 450 ASP cc_start: 0.8867 (t70) cc_final: 0.8544 (t0) REVERT: D 475 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8204 (p) REVERT: D 558 ASN cc_start: 0.7787 (m-40) cc_final: 0.7403 (m110) REVERT: D 677 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8692 (ttmm) REVERT: D 689 GLU cc_start: 0.8583 (tt0) cc_final: 0.8294 (tp30) REVERT: D 744 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7762 (ptp-110) REVERT: E 442 MET cc_start: 0.7292 (tmm) cc_final: 0.6188 (mpp) REVERT: E 450 ASP cc_start: 0.8858 (t70) cc_final: 0.8452 (t0) REVERT: E 465 ARG cc_start: 0.6501 (ttm110) cc_final: 0.6199 (mpt-90) REVERT: E 584 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7769 (mtpt) REVERT: E 603 GLN cc_start: 0.8567 (tp40) cc_final: 0.7983 (tt0) REVERT: E 674 PHE cc_start: 0.8471 (t80) cc_final: 0.8247 (t80) REVERT: F 442 MET cc_start: 0.6722 (tmm) cc_final: 0.6269 (mpp) REVERT: F 450 ASP cc_start: 0.8891 (t70) cc_final: 0.8520 (t0) REVERT: F 508 MET cc_start: 0.8556 (ttt) cc_final: 0.8205 (ttt) REVERT: F 560 ARG cc_start: 0.8023 (mmm-85) cc_final: 0.7524 (mmt180) REVERT: F 584 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7889 (mtpp) REVERT: F 689 GLU cc_start: 0.8584 (tt0) cc_final: 0.8262 (tp30) REVERT: F 745 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.6482 (ttp80) outliers start: 71 outliers final: 34 residues processed: 369 average time/residue: 0.6209 time to fit residues: 264.2793 Evaluate side-chains 345 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 303 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 633 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 475 THR Chi-restraints excluded: chain D residue 677 LYS 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 474 VAL Chi-restraints excluded: chain E residue 561 GLU 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 562 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 745 ARG 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: 0.9990 chunk 275 optimal weight: 0.8980 chunk 248 optimal weight: 0.1980 chunk 26 optimal weight: 0.0040 chunk 12 optimal weight: 0.6980 chunk 195 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 262 optimal weight: 0.5980 chunk 32 optimal weight: 0.0170 chunk 44 optimal weight: 0.4980 overall best weight: 0.2630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN B 735 HIS C 226 HIS ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN D 327 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 764 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.133611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.100796 restraints weight = 39403.425| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.00 r_work: 0.3197 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26430 Z= 0.103 Angle : 0.526 9.153 35754 Z= 0.259 Chirality : 0.042 0.159 3996 Planarity : 0.005 0.060 4668 Dihedral : 16.858 179.067 3996 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.17 % Favored : 97.65 % Rotamer: Outliers : 2.34 % Allowed : 14.69 % Favored : 82.97 % 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: 1.47 (0.16), residues: 3270 helix: 1.36 (0.13), residues: 1644 sheet: 0.45 (0.26), residues: 360 loop : 0.84 (0.20), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 744 TYR 0.010 0.001 TYR E 244 PHE 0.012 0.001 PHE C 674 TRP 0.008 0.001 TRP F 551 HIS 0.010 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (26430) covalent geometry : angle 0.52611 / 0.26 (35754) hydrogen bonds : bond 0.02966 / 2.01 ( 1258) hydrogen bonds : angle 3.83199 / 2.69 ( 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 389 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 325 time to evaluate : 0.716 Fit side-chains REVERT: A 344 MET cc_start: 0.9385 (mtp) cc_final: 0.9105 (mtm) REVERT: A 417 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8114 (tp30) REVERT: A 442 MET cc_start: 0.7297 (tmm) cc_final: 0.6041 (mpp) REVERT: A 450 ASP cc_start: 0.8819 (t70) cc_final: 0.8482 (t0) REVERT: A 470 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8258 (mt-10) REVERT: A 475 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8159 (p) REVERT: A 558 ASN cc_start: 0.7778 (m-40) cc_final: 0.7532 (m-40) REVERT: A 618 PHE cc_start: 0.8721 (t80) cc_final: 0.8384 (t80) REVERT: A 744 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7696 (ptp-110) REVERT: B 389 LYS cc_start: 0.8576 (ttmt) cc_final: 0.8347 (tptm) REVERT: B 397 GLU cc_start: 0.8641 (tp30) cc_final: 0.8133 (tp30) REVERT: B 442 MET cc_start: 0.7371 (tmm) cc_final: 0.6397 (mpp) REVERT: B 450 ASP cc_start: 0.8845 (t70) cc_final: 0.8476 (t0) REVERT: B 465 ARG cc_start: 0.6379 (ttm110) cc_final: 0.6020 (mpt-90) REVERT: B 584 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7743 (mtpt) REVERT: B 603 GLN cc_start: 0.8581 (tp40) cc_final: 0.8015 (tt0) REVERT: C 389 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8419 (tmtm) REVERT: C 442 MET cc_start: 0.7058 (tmm) cc_final: 0.6338 (mpp) REVERT: C 450 ASP cc_start: 0.8782 (t70) cc_final: 0.8373 (t0) REVERT: C 508 MET cc_start: 0.8571 (ttt) cc_final: 0.8226 (ttt) REVERT: C 584 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7902 (mtpp) REVERT: C 674 PHE cc_start: 0.8139 (t80) cc_final: 0.7822 (t80) REVERT: C 689 GLU cc_start: 0.8580 (tt0) cc_final: 0.8273 (tp30) REVERT: D 239 ARG cc_start: 0.7243 (ptt180) cc_final: 0.7029 (ptt180) REVERT: D 417 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8149 (tp30) REVERT: D 442 MET cc_start: 0.7248 (tmm) cc_final: 0.6032 (mpp) REVERT: D 450 ASP cc_start: 0.8847 (t70) cc_final: 0.8501 (t0) REVERT: D 470 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8300 (mt-10) REVERT: D 475 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8140 (p) REVERT: D 558 ASN cc_start: 0.7820 (m-40) cc_final: 0.7467 (m110) REVERT: D 677 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8758 (ttmm) REVERT: D 689 GLU cc_start: 0.8561 (tt0) cc_final: 0.8305 (tp30) REVERT: D 744 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7746 (ptp-110) REVERT: E 442 MET cc_start: 0.7302 (tmm) cc_final: 0.6197 (mpp) REVERT: E 450 ASP cc_start: 0.8806 (t70) cc_final: 0.8441 (t0) REVERT: E 465 ARG cc_start: 0.6425 (ttm110) cc_final: 0.6139 (mpt-90) REVERT: E 584 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7783 (mtpt) REVERT: E 603 GLN cc_start: 0.8596 (tp40) cc_final: 0.8026 (tt0) REVERT: E 674 PHE cc_start: 0.8484 (t80) cc_final: 0.8160 (t80) REVERT: F 442 MET cc_start: 0.6698 (tmm) cc_final: 0.6253 (mpp) REVERT: F 450 ASP cc_start: 0.8862 (t70) cc_final: 0.8503 (t0) REVERT: F 508 MET cc_start: 0.8569 (ttt) cc_final: 0.8217 (ttt) REVERT: F 560 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7530 (mmt180) REVERT: F 584 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7920 (mtpp) REVERT: F 689 GLU cc_start: 0.8544 (tt0) cc_final: 0.8270 (tp30) REVERT: F 745 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.6525 (ttp80) REVERT: F 764 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.6912 (mt0) outliers start: 64 outliers final: 31 residues processed: 370 average time/residue: 0.6088 time to fit residues: 260.9464 Evaluate side-chains 343 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 303 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 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 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 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 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 468 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 677 LYS 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 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 745 ARG Chi-restraints excluded: chain F residue 764 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 269 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 109 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS ** 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** C 558 ASN C 603 GLN ** 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** F 764 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.131706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.098759 restraints weight = 39591.994| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.00 r_work: 0.3160 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2730 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= 0.141 Angle : 0.549 9.539 35754 Z= 0.271 Chirality : 0.043 0.193 3996 Planarity : 0.005 0.060 4668 Dihedral : 16.815 179.965 3996 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.63 % Favored : 97.19 % Rotamer: Outliers : 2.23 % Allowed : 14.95 % 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: 1.38 (0.16), residues: 3270 helix: 1.32 (0.13), residues: 1644 sheet: 0.06 (0.25), residues: 396 loop : 0.89 (0.21), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 359 TYR 0.010 0.001 TYR E 244 PHE 0.020 0.001 PHE F 674 TRP 0.013 0.002 TRP C 551 HIS 0.009 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (26430) covalent geometry : angle 0.54923 / 0.27 (35754) hydrogen bonds : bond 0.03167 / 2.16 ( 1258) hydrogen bonds : angle 3.87118 / 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 365 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 304 time to evaluate : 0.955 Fit side-chains REVERT: A 344 MET cc_start: 0.9386 (mtp) cc_final: 0.9110 (mtm) REVERT: A 417 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8160 (tp30) REVERT: A 442 MET cc_start: 0.7304 (tmm) cc_final: 0.6032 (mpp) REVERT: A 450 ASP cc_start: 0.8831 (t70) cc_final: 0.8502 (t0) REVERT: A 470 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8307 (mt-10) REVERT: A 475 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8147 (p) REVERT: A 558 ASN cc_start: 0.7816 (m-40) cc_final: 0.7500 (m-40) REVERT: A 744 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7664 (ptp-110) REVERT: B 389 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8336 (tptm) REVERT: B 397 GLU cc_start: 0.8679 (tp30) cc_final: 0.8167 (tp30) REVERT: B 442 MET cc_start: 0.7401 (tmm) cc_final: 0.6415 (mpp) REVERT: B 450 ASP cc_start: 0.8854 (t70) cc_final: 0.8483 (t0) REVERT: B 465 ARG cc_start: 0.6519 (ttm110) cc_final: 0.6138 (mpt-90) REVERT: B 584 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7738 (mtpt) REVERT: B 603 GLN cc_start: 0.8570 (tp40) cc_final: 0.7984 (tt0) REVERT: C 389 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8444 (tmtm) REVERT: C 442 MET cc_start: 0.7172 (tmm) cc_final: 0.6456 (mpp) REVERT: C 450 ASP cc_start: 0.8828 (t70) cc_final: 0.8418 (t0) REVERT: C 470 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8244 (mt-10) REVERT: C 508 MET cc_start: 0.8589 (ttt) cc_final: 0.8252 (ttt) REVERT: C 584 LYS cc_start: 0.8289 (ttmt) cc_final: 0.7921 (mtpp) REVERT: C 674 PHE cc_start: 0.8246 (t80) cc_final: 0.7962 (t80) REVERT: C 689 GLU cc_start: 0.8606 (tt0) cc_final: 0.8306 (tp30) REVERT: D 239 ARG cc_start: 0.7372 (ptt180) cc_final: 0.7131 (ptt180) REVERT: D 417 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8194 (tp30) REVERT: D 442 MET cc_start: 0.7281 (tmm) cc_final: 0.6088 (mpp) REVERT: D 450 ASP cc_start: 0.8872 (t70) cc_final: 0.8531 (t0) REVERT: D 470 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8268 (mt-10) REVERT: D 475 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8154 (p) REVERT: D 558 ASN cc_start: 0.7869 (m-40) cc_final: 0.7497 (m110) REVERT: D 677 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8743 (ttmm) REVERT: D 689 GLU cc_start: 0.8563 (tt0) cc_final: 0.8296 (tp30) REVERT: D 744 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7774 (ptp-110) REVERT: E 442 MET cc_start: 0.7335 (tmm) cc_final: 0.6213 (mpp) REVERT: E 450 ASP cc_start: 0.8816 (t70) cc_final: 0.8444 (t0) REVERT: E 465 ARG cc_start: 0.6447 (ttm110) cc_final: 0.6211 (mpt-90) REVERT: E 584 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7794 (mtpt) REVERT: E 603 GLN cc_start: 0.8578 (tp40) cc_final: 0.7975 (tt0) REVERT: E 674 PHE cc_start: 0.8529 (t80) cc_final: 0.8222 (t80) REVERT: F 442 MET cc_start: 0.6723 (tmm) cc_final: 0.6266 (mpp) REVERT: F 450 ASP cc_start: 0.8885 (t70) cc_final: 0.8511 (t0) REVERT: F 508 MET cc_start: 0.8588 (ttt) cc_final: 0.8250 (ttt) REVERT: F 560 ARG cc_start: 0.8120 (mmm-85) cc_final: 0.7538 (mmt180) REVERT: F 584 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7928 (mtpp) REVERT: F 689 GLU cc_start: 0.8603 (tt0) cc_final: 0.8267 (tp30) REVERT: F 745 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.6619 (ttp80) outliers start: 61 outliers final: 40 residues processed: 351 average time/residue: 0.6247 time to fit residues: 252.6003 Evaluate side-chains 346 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 298 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 HIS 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 603 GLN 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 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 211 LYS 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 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 677 LYS 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 550 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 144 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 303 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 192 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 196 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 22 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 HIS ** 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** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.131714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.098888 restraints weight = 39529.950| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.99 r_work: 0.3161 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26430 Z= 0.136 Angle : 0.549 10.037 35754 Z= 0.271 Chirality : 0.043 0.156 3996 Planarity : 0.005 0.060 4668 Dihedral : 16.779 179.861 3996 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.35 % Favored : 97.46 % Rotamer: Outliers : 2.12 % Allowed : 15.46 % 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: 1.39 (0.16), residues: 3270 helix: 1.27 (0.13), residues: 1680 sheet: 0.05 (0.25), residues: 396 loop : 1.01 (0.21), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 744 TYR 0.011 0.001 TYR E 244 PHE 0.013 0.001 PHE F 363 TRP 0.013 0.002 TRP C 551 HIS 0.013 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (26430) covalent geometry : angle 0.54938 / 0.27 (35754) hydrogen bonds : bond 0.03168 / 2.16 ( 1258) hydrogen bonds : angle 3.82713 / 2.68 ( 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 362 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 304 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 344 MET cc_start: 0.9389 (mtp) cc_final: 0.9114 (mtm) REVERT: A 417 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8156 (tp30) REVERT: A 442 MET cc_start: 0.7309 (tmm) cc_final: 0.6052 (mpp) REVERT: A 450 ASP cc_start: 0.8848 (t70) cc_final: 0.8504 (t0) REVERT: A 470 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8295 (mt-10) REVERT: A 475 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8136 (p) REVERT: A 558 ASN cc_start: 0.7835 (m-40) cc_final: 0.7539 (m-40) REVERT: A 744 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7682 (ptp-110) REVERT: B 389 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8324 (tmtm) REVERT: B 397 GLU cc_start: 0.8659 (tp30) cc_final: 0.8156 (tp30) REVERT: B 442 MET cc_start: 0.7417 (tmm) cc_final: 0.6450 (mpp) REVERT: B 450 ASP cc_start: 0.8849 (t70) cc_final: 0.8477 (t0) REVERT: B 465 ARG cc_start: 0.6512 (ttm110) cc_final: 0.6131 (mpt-90) REVERT: B 584 LYS cc_start: 0.8184 (ttmt) cc_final: 0.7780 (mtpt) REVERT: B 603 GLN cc_start: 0.8599 (tp40) cc_final: 0.7971 (tt0) REVERT: C 442 MET cc_start: 0.7219 (tmm) cc_final: 0.6510 (mpp) REVERT: C 450 ASP cc_start: 0.8820 (t70) cc_final: 0.8407 (t0) REVERT: C 470 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8231 (mt-10) REVERT: C 508 MET cc_start: 0.8597 (ttt) cc_final: 0.8261 (ttt) REVERT: C 584 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7963 (mtpp) REVERT: C 689 GLU cc_start: 0.8602 (tt0) cc_final: 0.8307 (tp30) REVERT: D 417 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8209 (tp30) REVERT: D 442 MET cc_start: 0.7296 (tmm) cc_final: 0.6100 (mpp) REVERT: D 450 ASP cc_start: 0.8872 (t70) cc_final: 0.8524 (t0) REVERT: D 470 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8265 (mt-10) REVERT: D 475 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8132 (p) REVERT: D 677 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8773 (ttmm) REVERT: D 689 GLU cc_start: 0.8585 (tt0) cc_final: 0.8302 (tp30) REVERT: D 744 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7884 (ptp-110) REVERT: E 442 MET cc_start: 0.7404 (tmm) cc_final: 0.6267 (mpp) REVERT: E 450 ASP cc_start: 0.8837 (t70) cc_final: 0.8474 (t0) REVERT: E 465 ARG cc_start: 0.6420 (ttm110) cc_final: 0.6211 (mpt-90) REVERT: E 584 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7828 (mtpt) REVERT: E 603 GLN cc_start: 0.8592 (tp40) cc_final: 0.7982 (tt0) REVERT: E 674 PHE cc_start: 0.8555 (t80) cc_final: 0.8243 (t80) REVERT: F 442 MET cc_start: 0.6748 (tmm) cc_final: 0.6298 (mpp) REVERT: F 450 ASP cc_start: 0.8875 (t70) cc_final: 0.8490 (t0) REVERT: F 470 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8226 (mt-10) REVERT: F 508 MET cc_start: 0.8578 (ttt) cc_final: 0.8243 (ttt) REVERT: F 560 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7583 (mmt180) REVERT: F 689 GLU cc_start: 0.8601 (tt0) cc_final: 0.8273 (tp30) REVERT: F 745 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.6641 (ttp80) outliers start: 58 outliers final: 41 residues processed: 346 average time/residue: 0.5907 time to fit residues: 235.7120 Evaluate side-chains 347 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 298 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 348 ASN 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 603 GLN 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 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 474 VAL Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 740 MET 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 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 677 LYS 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 550 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 194 optimal weight: 0.7980 chunk 244 optimal weight: 0.4980 chunk 230 optimal weight: 5.9990 chunk 82 optimal weight: 0.2980 chunk 43 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 302 optimal weight: 0.7980 chunk 303 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.131355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.098551 restraints weight = 39543.113| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.00 r_work: 0.3163 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26430 Z= 0.125 Angle : 0.545 9.877 35754 Z= 0.269 Chirality : 0.043 0.140 3996 Planarity : 0.005 0.060 4668 Dihedral : 16.746 179.993 3996 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.54 % Favored : 97.28 % Rotamer: Outliers : 1.98 % Allowed : 16.08 % Favored : 81.94 % 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: 1.38 (0.16), residues: 3270 helix: 1.32 (0.13), residues: 1644 sheet: 0.23 (0.25), residues: 378 loop : 0.83 (0.21), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 359 TYR 0.011 0.001 TYR E 244 PHE 0.026 0.001 PHE C 674 TRP 0.014 0.002 TRP C 551 HIS 0.012 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (26430) covalent geometry : angle 0.54544 / 0.27 (35754) hydrogen bonds : bond 0.03104 / 2.12 ( 1258) hydrogen bonds : angle 3.82678 / 2.68 ( 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 356 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 302 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 344 MET cc_start: 0.9374 (mtp) cc_final: 0.9085 (mtm) REVERT: A 417 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8183 (tp30) REVERT: A 442 MET cc_start: 0.7356 (tmm) cc_final: 0.6130 (mpp) REVERT: A 450 ASP cc_start: 0.8808 (t70) cc_final: 0.8437 (t0) REVERT: A 470 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8322 (mt-10) REVERT: A 475 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8109 (p) REVERT: A 558 ASN cc_start: 0.7820 (m-40) cc_final: 0.7514 (m-40) REVERT: A 744 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7675 (ptp-110) REVERT: B 397 GLU cc_start: 0.8641 (tp30) cc_final: 0.8143 (tp30) REVERT: B 442 MET cc_start: 0.7390 (tmm) cc_final: 0.6467 (mpp) REVERT: B 450 ASP cc_start: 0.8821 (t70) cc_final: 0.8447 (t0) REVERT: B 465 ARG cc_start: 0.6531 (ttm110) cc_final: 0.6149 (mpt-90) REVERT: B 584 LYS cc_start: 0.8174 (ttmt) cc_final: 0.7773 (mtpt) REVERT: B 603 GLN cc_start: 0.8581 (tp40) cc_final: 0.7940 (tt0) REVERT: C 442 MET cc_start: 0.7224 (tmm) cc_final: 0.6526 (mpp) REVERT: C 450 ASP cc_start: 0.8876 (t70) cc_final: 0.8441 (t0) REVERT: C 470 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8215 (mt-10) REVERT: C 508 MET cc_start: 0.8581 (ttt) cc_final: 0.8255 (ttt) REVERT: C 689 GLU cc_start: 0.8592 (tt0) cc_final: 0.8310 (tp30) REVERT: D 417 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8222 (tp30) REVERT: D 442 MET cc_start: 0.7298 (tmm) cc_final: 0.6124 (mpp) REVERT: D 450 ASP cc_start: 0.8855 (t70) cc_final: 0.8493 (t0) REVERT: D 470 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8243 (mt-10) REVERT: D 475 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8116 (p) REVERT: D 677 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8796 (ttmm) REVERT: D 689 GLU cc_start: 0.8565 (tt0) cc_final: 0.8305 (tp30) REVERT: D 744 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7871 (ptp-110) REVERT: E 442 MET cc_start: 0.7479 (tmm) cc_final: 0.6356 (mpp) REVERT: E 450 ASP cc_start: 0.8831 (t70) cc_final: 0.8446 (t0) REVERT: E 465 ARG cc_start: 0.6403 (ttm110) cc_final: 0.6194 (mpt-90) REVERT: E 584 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7787 (mtpt) REVERT: E 603 GLN cc_start: 0.8590 (tp40) cc_final: 0.7965 (tt0) REVERT: E 674 PHE cc_start: 0.8589 (t80) cc_final: 0.8294 (t80) REVERT: E 744 ARG cc_start: 0.8360 (ptm160) cc_final: 0.8146 (ptp-110) REVERT: F 442 MET cc_start: 0.6811 (tmm) cc_final: 0.6355 (mpp) REVERT: F 450 ASP cc_start: 0.8825 (t70) cc_final: 0.8417 (t0) REVERT: F 470 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8206 (mt-10) REVERT: F 508 MET cc_start: 0.8578 (ttt) cc_final: 0.8245 (ttt) REVERT: F 560 ARG cc_start: 0.8164 (mmm-85) cc_final: 0.7561 (mmt180) REVERT: F 584 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7888 (mtpp) REVERT: F 689 GLU cc_start: 0.8601 (tt0) cc_final: 0.8316 (tp30) REVERT: F 745 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.6448 (ttp80) outliers start: 54 outliers final: 39 residues processed: 345 average time/residue: 0.6052 time to fit residues: 241.1676 Evaluate side-chains 346 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 299 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 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 348 ASN 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 D residue 677 LYS 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 550 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 218 optimal weight: 1.9990 chunk 307 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 240 optimal weight: 0.7980 chunk 262 optimal weight: 0.2980 chunk 234 optimal weight: 0.7980 chunk 265 optimal weight: 2.9990 chunk 319 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 558 ASN ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 GLN ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.130170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097369 restraints weight = 39577.655| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.97 r_work: 0.3137 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26430 Z= 0.167 Angle : 0.576 10.150 35754 Z= 0.283 Chirality : 0.044 0.143 3996 Planarity : 0.005 0.060 4668 Dihedral : 16.742 177.861 3996 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.42 % Favored : 97.40 % Rotamer: Outliers : 2.01 % Allowed : 15.97 % Favored : 82.01 % 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: 1.31 (0.16), residues: 3270 helix: 1.27 (0.13), residues: 1644 sheet: 0.02 (0.25), residues: 396 loop : 0.86 (0.21), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 225 TYR 0.014 0.002 TYR D 495 PHE 0.014 0.001 PHE F 674 TRP 0.016 0.002 TRP C 551 HIS 0.016 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (26430) covalent geometry : angle 0.57578 / 0.28 (35754) hydrogen bonds : bond 0.03336 / 2.28 ( 1258) hydrogen bonds : angle 3.83941 / 2.69 ( 3522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7776.95 seconds wall clock time: 149 minutes 13.55 seconds (8953.55 seconds total)