Starting phenix.real_space_refine on Sun Jul 5 08:40:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y09_72389/07_2026/9y09_72389.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y09_72389/07_2026/9y09_72389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y09_72389/07_2026/9y09_72389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y09_72389/07_2026/9y09_72389.map" model { file = "/net/cci-nas-00/data/ceres_data/9y09_72389/07_2026/9y09_72389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y09_72389/07_2026/9y09_72389.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.020 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 5 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: 6.14, per 1000 atoms: 0.24 Number of scatterers: 25998 At special positions: 0 Unit cell: (138, 145, 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.2 seconds 6540 Ramachandran restraints generated. 3270 Oldfield, 0 Emsley, 3270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6120 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 12 sheets defined 57.8% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 210 through 226 removed outlier: 4.293A 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: 4.308A 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 277 removed outlier: 3.576A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.624A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.053A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.828A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) 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: 3.664A 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 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: 4.207A 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: 3.808A 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 removed outlier: 3.527A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 569 Processing helix chain 'A' and resid 578 through 584 removed outlier: 4.086A pdb=" N ILE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 610 removed outlier: 4.354A 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 removed outlier: 3.559A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 683 through 707 removed outlier: 3.590A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 743 removed outlier: 3.773A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.694A 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: 4.237A 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: 4.321A 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 277 removed outlier: 3.557A pdb=" N LYS B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.709A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.123A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.809A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) 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: 4.053A pdb=" N ARG B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 359' Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.500A pdb=" N LYS B 425 " --> pdb=" O GLN B 421 " (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: 4.287A 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 506 removed outlier: 3.838A 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: 4.627A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 584 removed outlier: 4.133A pdb=" N ILE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 610 removed outlier: 4.102A 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 removed outlier: 3.505A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 678 removed outlier: 3.933A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 707 removed outlier: 3.583A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE B 707 " --> pdb=" O ILE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.970A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.621A 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: 4.222A 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: 4.227A 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 277 removed outlier: 3.600A pdb=" N LYS C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.665A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.020A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.676A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.658A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 425 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: 4.197A 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: 3.912A 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 557 through 569 Processing helix chain 'C' and resid 578 through 584 removed outlier: 4.075A pdb=" N ILE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 610 removed outlier: 4.322A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 649 through 661 removed outlier: 3.545A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 678 removed outlier: 3.930A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 707 removed outlier: 3.507A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE C 707 " --> pdb=" O ILE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.818A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 3.612A 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: 4.285A 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: 4.310A 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 277 removed outlier: 3.541A pdb=" N LYS D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.730A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.058A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 removed outlier: 3.822A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) 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: 3.668A 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 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: 4.199A 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 506 removed outlier: 3.827A 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 543 through 550 removed outlier: 3.538A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 569 Processing helix chain 'D' and resid 578 through 584 removed outlier: 4.086A pdb=" N ILE D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 610 removed outlier: 4.350A 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 removed outlier: 3.568A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 683 through 707 removed outlier: 3.574A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE D 707 " --> pdb=" O ILE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.765A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 3.692A 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: 4.234A 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: 4.317A 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 277 removed outlier: 3.569A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.721A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.131A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 334 removed outlier: 3.822A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.666A 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: 3.511A pdb=" N LYS E 425 " --> pdb=" O GLN E 421 " (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: 4.279A 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 506 removed outlier: 3.852A 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: 4.621A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 584 removed outlier: 4.128A pdb=" N ILE E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 610 removed outlier: 4.151A 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: 3.555A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 678 removed outlier: 4.044A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA E 676 " --> pdb=" O LEU E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 707 removed outlier: 3.606A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE E 707 " --> pdb=" O ILE E 703 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 743 removed outlier: 3.921A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 3.626A 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: 4.241A 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: 4.225A 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 277 removed outlier: 3.578A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.598A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.024A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 334 removed outlier: 3.662A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) 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: 3.653A 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 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: 4.193A 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: 3.907A 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: 4.585A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 584 removed outlier: 4.070A pdb=" N ILE F 582 " --> pdb=" O GLU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 610 removed outlier: 4.306A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.527A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 678 removed outlier: 3.942A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 707 removed outlier: 3.522A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE F 707 " --> pdb=" O ILE F 703 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.844A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.180A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.539A pdb=" N GLU A 470 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.186A 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: 6.183A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 469 through 470 removed outlier: 3.540A pdb=" N GLU B 470 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.180A 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: 6.289A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.367A 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: 6.604A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.169A 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: 6.191A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 469 through 470 removed outlier: 3.535A pdb=" N GLU D 470 " --> pdb=" O PHE D 539 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.170A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 469 through 470 removed outlier: 3.536A pdb=" N GLU E 470 " --> pdb=" O PHE E 539 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.184A 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: 6.291A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 469 through 470 removed outlier: 6.599A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1235 hydrogen bonds defined for protein. 3480 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: 4.55 Time building geometry restraints manager: 2.83 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: 7417 1.52 - 1.66: 9780 1.66 - 1.80: 184 1.80 - 1.95: 50 Bond restraints: 26430 Sorted by residual: bond pdb=" O3B AGS E 902 " pdb=" PB AGS E 902 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" O3B AGS B 902 " pdb=" PB AGS B 902 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" O3B AGS D 902 " pdb=" PB AGS D 902 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" O3B AGS F 902 " pdb=" PB AGS F 902 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" O3B AGS A 901 " pdb=" PB AGS A 901 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.01e+01 ... (remaining 26425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 35005 2.01 - 4.02: 552 4.02 - 6.03: 107 6.03 - 8.04: 51 8.04 - 10.05: 39 Bond angle restraints: 35754 Sorted by residual: angle pdb=" C ARG D 599 " pdb=" CA ARG D 599 " pdb=" CB ARG D 599 " ideal model delta sigma weight residual 117.23 109.68 7.55 1.36e+00 5.41e-01 3.09e+01 angle pdb=" C ARG A 599 " pdb=" CA ARG A 599 " pdb=" CB ARG A 599 " ideal model delta sigma weight residual 117.23 109.74 7.49 1.36e+00 5.41e-01 3.03e+01 angle pdb=" C ARG B 599 " pdb=" CA ARG B 599 " pdb=" CB ARG B 599 " ideal model delta sigma weight residual 117.23 109.97 7.26 1.36e+00 5.41e-01 2.85e+01 angle pdb=" N VAL C 441 " pdb=" CA VAL C 441 " pdb=" C VAL C 441 " ideal model delta sigma weight residual 113.22 107.70 5.52 1.23e+00 6.61e-01 2.01e+01 angle pdb=" N VAL F 441 " pdb=" CA VAL F 441 " pdb=" C VAL F 441 " ideal model delta sigma weight residual 113.22 107.78 5.44 1.23e+00 6.61e-01 1.95e+01 ... (remaining 35749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 16202 35.00 - 70.00: 266 70.00 - 104.99: 56 104.99 - 139.99: 36 139.99 - 174.99: 6 Dihedral angle restraints: 16566 sinusoidal: 7128 harmonic: 9438 Sorted by residual: 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 -177.64 -174.99 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2B AGS E 901 " pdb=" O3B AGS E 901 " pdb=" PB AGS E 901 " pdb=" PG AGS E 901 " ideal model delta sinusoidal sigma weight residual 7.37 -177.71 -174.92 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2B AGS F 901 " pdb=" O3B AGS F 901 " pdb=" PB AGS F 901 " pdb=" PG AGS F 901 " ideal model delta sinusoidal sigma weight residual 7.37 178.07 -170.70 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 16563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3234 0.052 - 0.105: 637 0.105 - 0.157: 113 0.157 - 0.210: 0 0.210 - 0.262: 12 Chirality restraints: 3996 Sorted by residual: chirality pdb=" C3' AGS D 902 " pdb=" C2' AGS D 902 " pdb=" C4' AGS D 902 " pdb=" O3' AGS D 902 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C3' AGS E 902 " pdb=" C2' AGS E 902 " pdb=" C4' AGS E 902 " pdb=" O3' AGS E 902 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C3' AGS A 901 " pdb=" C2' AGS A 901 " pdb=" C4' AGS A 901 " pdb=" O3' AGS A 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 3993 not shown) Planarity restraints: 4668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 460 " -0.044 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO F 461 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO F 461 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 461 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 460 " 0.044 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO C 461 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 461 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 461 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 460 " -0.043 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO D 461 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 461 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 461 " -0.036 5.00e-02 4.00e+02 ... (remaining 4665 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 199 2.54 - 3.13: 20373 3.13 - 3.72: 43274 3.72 - 4.31: 60437 4.31 - 4.90: 95082 Nonbonded interactions: 219365 Sorted by model distance: nonbonded pdb=" OG1 THR F 252 " pdb="MG MG F 903 " model vdw 1.954 2.170 nonbonded pdb=" OG1 THR C 252 " pdb="MG MG C 903 " model vdw 1.954 2.170 nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 903 " model vdw 1.962 2.170 nonbonded pdb=" OG1 THR A 252 " pdb="MG MG A 902 " model vdw 1.962 2.170 nonbonded pdb=" OG1 THR E 252 " pdb="MG MG E 903 " model vdw 1.966 2.170 ... (remaining 219360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' 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: 6.050 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.990 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.040 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:5.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 : 0.004 0.091 26436 Z= 0.211 Angle : 0.726 10.051 35754 Z= 0.335 Chirality : 0.044 0.262 3996 Planarity : 0.005 0.067 4668 Dihedral : 16.574 174.988 10446 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.21 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.57 (0.15), residues: 3270 helix: 0.44 (0.13), residues: 1698 sheet: 0.10 (0.26), residues: 378 loop : 0.70 (0.20), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 256 TYR 0.011 0.001 TYR D 244 PHE 0.008 0.001 PHE A 506 TRP 0.036 0.004 TRP D 551 HIS 0.012 0.001 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 (26430) covalent geometry : angle 0.72643 / 0.34 (35754) hydrogen bonds : bond 0.20656 / 13.89 ( 1235) hydrogen bonds : angle 6.02258 / 4.38 ( 3480) Misc. bond : bond 0.00072 / 0.04 ( 6) *********************** 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 614 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 614 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 389 LYS cc_start: 0.9152 (ttmt) cc_final: 0.8918 (ttmt) REVERT: A 397 GLU cc_start: 0.8660 (tt0) cc_final: 0.8319 (tp30) REVERT: A 398 GLN cc_start: 0.9025 (tp-100) cc_final: 0.8628 (tp-100) REVERT: B 305 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8667 (mt-10) REVERT: B 340 HIS cc_start: 0.8410 (m-70) cc_final: 0.8170 (m90) REVERT: B 352 SER cc_start: 0.9231 (m) cc_final: 0.9019 (p) REVERT: B 389 LYS cc_start: 0.9115 (ttmt) cc_final: 0.8889 (ttmt) REVERT: B 689 GLU cc_start: 0.8529 (tp30) cc_final: 0.8308 (tp30) REVERT: C 352 SER cc_start: 0.9326 (m) cc_final: 0.9023 (t) REVERT: C 426 LYS cc_start: 0.8264 (mmmt) cc_final: 0.8022 (mmtm) REVERT: C 470 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8036 (pt0) REVERT: C 564 ASP cc_start: 0.8628 (m-30) cc_final: 0.8252 (m-30) REVERT: C 651 LYS cc_start: 0.8856 (tttp) cc_final: 0.8596 (mppt) REVERT: D 397 GLU cc_start: 0.8646 (tt0) cc_final: 0.8362 (tp30) REVERT: D 398 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8665 (tp-100) REVERT: E 239 ARG cc_start: 0.7273 (ptt180) cc_final: 0.6958 (pmm-80) REVERT: E 305 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8716 (mt-10) REVERT: E 340 HIS cc_start: 0.8423 (m-70) cc_final: 0.8152 (m90) REVERT: E 352 SER cc_start: 0.9245 (m) cc_final: 0.9033 (p) REVERT: E 389 LYS cc_start: 0.9104 (ttmt) cc_final: 0.8882 (ttmt) REVERT: E 397 GLU cc_start: 0.8684 (tt0) cc_final: 0.8347 (tp30) REVERT: E 689 GLU cc_start: 0.8497 (tp30) cc_final: 0.8269 (tp30) REVERT: F 352 SER cc_start: 0.9327 (m) cc_final: 0.9042 (t) REVERT: F 397 GLU cc_start: 0.8613 (tt0) cc_final: 0.8306 (tp30) REVERT: F 426 LYS cc_start: 0.8340 (mmmt) cc_final: 0.8073 (mmtm) REVERT: F 470 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8131 (pt0) REVERT: F 564 ASP cc_start: 0.8713 (m-30) cc_final: 0.8444 (m-30) REVERT: F 651 LYS cc_start: 0.8856 (tttp) cc_final: 0.8592 (mppt) outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 0.7264 time to fit residues: 501.0065 Evaluate side-chains 315 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.0670 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 GLN A 568 GLN B 226 HIS B 337 GLN B 460 ASN B 568 GLN B 603 GLN B 660 ASN B 692 GLN C 226 HIS C 285 ASN C 337 GLN C 494 GLN C 568 GLN D 337 GLN D 568 GLN E 226 HIS ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 GLN E 603 GLN E 660 ASN E 692 GLN F 226 HIS F 285 ASN F 337 GLN F 494 GLN F 499 HIS F 568 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.128825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.094128 restraints weight = 36450.417| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.68 r_work: 0.3015 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26436 Z= 0.154 Angle : 0.630 10.197 35754 Z= 0.315 Chirality : 0.045 0.187 3996 Planarity : 0.005 0.068 4668 Dihedral : 17.913 173.229 3996 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.76 % Favored : 95.87 % Rotamer: Outliers : 2.93 % Allowed : 10.81 % 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: 0.86 (0.15), residues: 3270 helix: 0.72 (0.13), residues: 1698 sheet: 0.06 (0.25), residues: 378 loop : 0.83 (0.20), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 256 TYR 0.016 0.002 TYR B 203 PHE 0.018 0.001 PHE C 742 TRP 0.025 0.003 TRP A 551 HIS 0.008 0.001 HIS C 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (26430) covalent geometry : angle 0.63049 / 0.31 (35754) hydrogen bonds : bond 0.04122 / 2.75 ( 1235) hydrogen bonds : angle 4.23144 / 3.04 ( 3480) Misc. bond : bond 0.00143 / 0.07 ( 6) *********************** 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 427 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 347 time to evaluate : 0.631 Fit side-chains REVERT: A 389 LYS cc_start: 0.9153 (ttmt) cc_final: 0.8871 (ttmt) REVERT: A 397 GLU cc_start: 0.8704 (tt0) cc_final: 0.8289 (tp30) REVERT: A 704 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: B 203 TYR cc_start: 0.8253 (m-10) cc_final: 0.8010 (m-80) REVERT: B 340 HIS cc_start: 0.8397 (m-70) cc_final: 0.8184 (m90) REVERT: B 389 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8896 (ttmt) REVERT: B 689 GLU cc_start: 0.8427 (tp30) cc_final: 0.8214 (tp30) REVERT: B 701 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8274 (mt-10) REVERT: B 764 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.6862 (mt0) REVERT: C 352 SER cc_start: 0.9305 (m) cc_final: 0.9054 (t) REVERT: C 402 GLU cc_start: 0.8633 (tt0) cc_final: 0.8390 (mt-10) REVERT: C 426 LYS cc_start: 0.8313 (mmmt) cc_final: 0.7825 (mtpt) REVERT: C 470 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8097 (pt0) REVERT: C 564 ASP cc_start: 0.8723 (m-30) cc_final: 0.8475 (m-30) REVERT: C 704 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: D 309 ILE cc_start: 0.8976 (pt) cc_final: 0.8758 (pt) REVERT: D 319 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: D 397 GLU cc_start: 0.8601 (tt0) cc_final: 0.8251 (tp30) REVERT: D 701 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8148 (mt-10) REVERT: D 764 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7587 (mp10) REVERT: E 340 HIS cc_start: 0.8359 (m-70) cc_final: 0.8089 (m90) REVERT: E 389 LYS cc_start: 0.9165 (ttmt) cc_final: 0.8919 (ttmt) REVERT: E 397 GLU cc_start: 0.8506 (tt0) cc_final: 0.8211 (tp30) REVERT: E 689 GLU cc_start: 0.8417 (tp30) cc_final: 0.8207 (tp30) REVERT: E 701 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8272 (mt-10) REVERT: E 764 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.6890 (mt0) REVERT: F 321 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8272 (mt-10) REVERT: F 352 SER cc_start: 0.9311 (m) cc_final: 0.9064 (t) REVERT: F 402 GLU cc_start: 0.8610 (tt0) cc_final: 0.8358 (mt-10) REVERT: F 426 LYS cc_start: 0.8290 (mmmt) cc_final: 0.7845 (mtpt) outliers start: 80 outliers final: 40 residues processed: 406 average time/residue: 0.6111 time to fit residues: 284.6597 Evaluate side-chains 343 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 297 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 764 GLN Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 693 ARG Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 693 ARG Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 764 GLN Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 693 ARG Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 764 GLN Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 693 ARG Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 265 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 292 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 307 optimal weight: 1.9990 chunk 165 optimal weight: 0.2980 chunk 168 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN A 494 GLN B 226 HIS B 327 GLN B 398 GLN C 226 HIS C 327 GLN D 285 ASN D 327 GLN D 494 GLN E 226 HIS E 327 GLN E 398 GLN F 226 HIS F 327 GLN F 337 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.124875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.089687 restraints weight = 36305.169| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.69 r_work: 0.2946 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26436 Z= 0.187 Angle : 0.625 9.503 35754 Z= 0.310 Chirality : 0.045 0.164 3996 Planarity : 0.005 0.068 4668 Dihedral : 16.866 165.908 3996 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.82 % Favored : 95.84 % Rotamer: Outliers : 2.93 % Allowed : 12.78 % Favored : 84.29 % 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: 0.93 (0.15), residues: 3270 helix: 0.84 (0.13), residues: 1746 sheet: -0.25 (0.24), residues: 396 loop : 0.92 (0.21), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 256 TYR 0.013 0.002 TYR C 244 PHE 0.011 0.001 PHE F 267 TRP 0.019 0.002 TRP A 551 HIS 0.006 0.001 HIS C 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (26430) covalent geometry : angle 0.62491 / 0.31 (35754) hydrogen bonds : bond 0.04189 / 2.82 ( 1235) hydrogen bonds : angle 3.97942 / 2.84 ( 3480) Misc. bond : bond 0.00281 / 0.15 ( 6) *********************** 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 375 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 295 time to evaluate : 0.986 Fit side-chains REVERT: A 389 LYS cc_start: 0.9161 (ttmt) cc_final: 0.8867 (ttmt) REVERT: A 397 GLU cc_start: 0.8595 (tt0) cc_final: 0.8139 (tp30) REVERT: B 389 LYS cc_start: 0.9198 (ttmt) cc_final: 0.8926 (ttmt) REVERT: B 561 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8378 (mt-10) REVERT: B 689 GLU cc_start: 0.8407 (tp30) cc_final: 0.8184 (tp30) REVERT: B 764 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7010 (mt0) REVERT: C 352 SER cc_start: 0.9307 (m) cc_final: 0.9036 (t) REVERT: C 402 GLU cc_start: 0.8631 (tt0) cc_final: 0.8411 (mt-10) REVERT: C 470 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8141 (pt0) REVERT: D 309 ILE cc_start: 0.8981 (pt) cc_final: 0.8736 (pt) REVERT: D 332 MET cc_start: 0.9211 (mtp) cc_final: 0.9002 (mmm) REVERT: D 397 GLU cc_start: 0.8612 (tt0) cc_final: 0.8180 (tp30) REVERT: D 701 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8100 (mt-10) REVERT: D 764 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7593 (mp10) REVERT: E 389 LYS cc_start: 0.9209 (ttmt) cc_final: 0.8946 (ttmt) REVERT: E 397 GLU cc_start: 0.8528 (tt0) cc_final: 0.8181 (tp30) REVERT: E 561 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8389 (mt-10) REVERT: E 689 GLU cc_start: 0.8389 (tp30) cc_final: 0.8172 (tp30) REVERT: E 764 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7006 (mt0) REVERT: F 352 SER cc_start: 0.9306 (m) cc_final: 0.9038 (t) REVERT: F 402 GLU cc_start: 0.8656 (tt0) cc_final: 0.8429 (mt-10) REVERT: F 426 LYS cc_start: 0.8370 (mmmt) cc_final: 0.7934 (mtpt) REVERT: F 704 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7895 (mp0) outliers start: 80 outliers final: 47 residues processed: 355 average time/residue: 0.7207 time to fit residues: 289.7687 Evaluate side-chains 309 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 764 GLN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 693 ARG Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 764 GLN Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 764 GLN Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 704 GLU Chi-restraints excluded: chain F residue 744 ARG Chi-restraints excluded: chain F residue 757 MET 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: 0.6980 chunk 93 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 297 optimal weight: 0.1980 chunk 244 optimal weight: 0.0980 chunk 266 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 285 ASN E 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.126326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.091665 restraints weight = 36099.579| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.67 r_work: 0.2980 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26436 Z= 0.127 Angle : 0.572 9.503 35754 Z= 0.283 Chirality : 0.043 0.154 3996 Planarity : 0.005 0.068 4668 Dihedral : 16.772 168.532 3996 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.70 % Favored : 95.96 % Rotamer: Outliers : 2.78 % Allowed : 14.21 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.15), residues: 3270 helix: 1.06 (0.13), residues: 1746 sheet: -0.15 (0.25), residues: 378 loop : 0.97 (0.21), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 256 TYR 0.010 0.001 TYR F 244 PHE 0.009 0.001 PHE F 302 TRP 0.012 0.002 TRP D 551 HIS 0.005 0.000 HIS C 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (26430) covalent geometry : angle 0.57248 / 0.28 (35754) hydrogen bonds : bond 0.03477 / 2.33 ( 1235) hydrogen bonds : angle 3.91105 / 2.79 ( 3480) Misc. bond : bond 0.00119 / 0.06 ( 6) *********************** 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 359 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 283 time to evaluate : 1.030 Fit side-chains REVERT: A 389 LYS cc_start: 0.9177 (ttmt) cc_final: 0.8908 (ttmt) REVERT: A 397 GLU cc_start: 0.8622 (tt0) cc_final: 0.8166 (tp30) REVERT: A 668 LYS cc_start: 0.8925 (mmpt) cc_final: 0.8694 (mmpt) REVERT: B 389 LYS cc_start: 0.9216 (ttmt) cc_final: 0.8941 (ttmt) REVERT: B 561 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8370 (mt-10) REVERT: B 689 GLU cc_start: 0.8435 (tp30) cc_final: 0.8226 (tp30) REVERT: C 292 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8111 (mm-30) REVERT: C 352 SER cc_start: 0.9297 (m) cc_final: 0.9028 (t) REVERT: C 358 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8504 (mtm180) REVERT: C 402 GLU cc_start: 0.8634 (tt0) cc_final: 0.8415 (mt-10) REVERT: C 470 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8105 (pt0) REVERT: D 309 ILE cc_start: 0.8936 (pt) cc_final: 0.8712 (pt) REVERT: D 321 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8353 (mt-10) REVERT: D 397 GLU cc_start: 0.8587 (tt0) cc_final: 0.8164 (tp30) REVERT: D 668 LYS cc_start: 0.8939 (mmpt) cc_final: 0.8650 (mmpt) REVERT: D 701 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8042 (mt-10) REVERT: D 764 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: E 389 LYS cc_start: 0.9211 (ttmt) cc_final: 0.8939 (ttmt) REVERT: E 397 GLU cc_start: 0.8522 (tt0) cc_final: 0.8185 (tp30) REVERT: E 561 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8389 (mt-10) REVERT: E 668 LYS cc_start: 0.8948 (mmpt) cc_final: 0.8691 (mmpt) REVERT: E 689 GLU cc_start: 0.8418 (tp30) cc_final: 0.8213 (tp30) REVERT: E 701 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8243 (tt0) REVERT: E 764 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7662 (mp10) REVERT: F 352 SER cc_start: 0.9293 (m) cc_final: 0.9027 (t) REVERT: F 358 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8486 (mtm180) REVERT: F 402 GLU cc_start: 0.8660 (tt0) cc_final: 0.8428 (mt-10) REVERT: F 426 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8111 (mtpt) REVERT: F 764 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.6980 (mt0) outliers start: 76 outliers final: 36 residues processed: 337 average time/residue: 0.8202 time to fit residues: 311.7052 Evaluate side-chains 306 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 265 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 764 GLN Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 677 LYS Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 764 GLN Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 744 ARG Chi-restraints excluded: chain F residue 757 MET 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: 4.9990 chunk 226 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 217 optimal weight: 0.9990 chunk 168 optimal weight: 0.7980 chunk 292 optimal weight: 0.1980 chunk 179 optimal weight: 0.3980 chunk 227 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 603 GLN E 327 GLN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.125673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.090844 restraints weight = 36113.159| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.68 r_work: 0.2968 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26436 Z= 0.136 Angle : 0.572 9.259 35754 Z= 0.280 Chirality : 0.043 0.143 3996 Planarity : 0.005 0.067 4668 Dihedral : 16.708 167.094 3996 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.91 % Favored : 95.75 % Rotamer: Outliers : 3.15 % Allowed : 14.65 % Favored : 82.20 % 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: 1.29 (0.16), residues: 3270 helix: 1.17 (0.13), residues: 1746 sheet: -0.16 (0.25), residues: 378 loop : 1.00 (0.21), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 256 TYR 0.010 0.001 TYR A 244 PHE 0.009 0.001 PHE F 302 TRP 0.012 0.002 TRP D 551 HIS 0.004 0.000 HIS C 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (26430) covalent geometry : angle 0.57203 / 0.28 (35754) hydrogen bonds : bond 0.03469 / 2.32 ( 1235) hydrogen bonds : angle 3.83506 / 2.73 ( 3480) Misc. bond : bond 0.00134 / 0.07 ( 6) *********************** 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 374 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 288 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8769 (mm) REVERT: A 397 GLU cc_start: 0.8633 (tt0) cc_final: 0.8181 (tp30) REVERT: A 668 LYS cc_start: 0.8934 (mmpt) cc_final: 0.8623 (mmpt) REVERT: B 292 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8239 (mm-30) REVERT: B 332 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8955 (mmm) REVERT: B 389 LYS cc_start: 0.9217 (ttmt) cc_final: 0.8983 (ttmt) REVERT: B 561 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8394 (mt-10) REVERT: C 256 ARG cc_start: 0.7764 (mtt-85) cc_final: 0.6979 (mtp180) REVERT: C 292 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8123 (mm-30) REVERT: C 352 SER cc_start: 0.9299 (m) cc_final: 0.9026 (t) REVERT: C 358 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8515 (mtm180) REVERT: C 470 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8075 (pt0) REVERT: D 321 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8341 (mt-10) REVERT: D 397 GLU cc_start: 0.8609 (tt0) cc_final: 0.8158 (tp30) REVERT: D 668 LYS cc_start: 0.8941 (mmpt) cc_final: 0.8621 (mmpt) REVERT: D 764 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7550 (mp10) REVERT: E 288 LYS cc_start: 0.9052 (mttp) cc_final: 0.8797 (mttm) REVERT: E 332 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8928 (mmm) REVERT: E 389 LYS cc_start: 0.9215 (ttmt) cc_final: 0.8933 (ttmt) REVERT: E 397 GLU cc_start: 0.8533 (tt0) cc_final: 0.8169 (tp30) REVERT: E 561 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8399 (mt-10) REVERT: E 668 LYS cc_start: 0.8984 (mmpt) cc_final: 0.8719 (mmpt) REVERT: E 764 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7665 (mp10) REVERT: F 256 ARG cc_start: 0.7742 (mtt-85) cc_final: 0.6940 (mtp180) REVERT: F 292 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8140 (mm-30) REVERT: F 352 SER cc_start: 0.9283 (m) cc_final: 0.9017 (t) REVERT: F 358 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8427 (mtt180) REVERT: F 426 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8212 (mtpt) REVERT: F 668 LYS cc_start: 0.9251 (mmpt) cc_final: 0.9008 (mmpt) REVERT: F 764 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7057 (mt0) outliers start: 86 outliers final: 37 residues processed: 349 average time/residue: 0.8237 time to fit residues: 324.1698 Evaluate side-chains 312 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 267 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 744 ARG Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 764 GLN Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 764 GLN Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 677 LYS Chi-restraints excluded: chain F residue 744 ARG Chi-restraints excluded: chain F residue 757 MET 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: 0.5980 chunk 222 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 125 optimal weight: 0.0170 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 327 GLN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.124783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.089874 restraints weight = 36152.388| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.71 r_work: 0.2971 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26436 Z= 0.141 Angle : 0.578 11.018 35754 Z= 0.284 Chirality : 0.043 0.144 3996 Planarity : 0.005 0.066 4668 Dihedral : 16.697 166.814 3996 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.82 % Favored : 95.84 % Rotamer: Outliers : 3.15 % Allowed : 15.53 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.16), residues: 3270 helix: 1.24 (0.13), residues: 1746 sheet: -0.17 (0.25), residues: 378 loop : 0.97 (0.21), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 256 TYR 0.009 0.001 TYR F 244 PHE 0.010 0.001 PHE F 302 TRP 0.012 0.002 TRP D 551 HIS 0.004 0.001 HIS C 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (26430) covalent geometry : angle 0.57831 / 0.28 (35754) hydrogen bonds : bond 0.03423 / 2.30 ( 1235) hydrogen bonds : angle 3.79599 / 2.70 ( 3480) Misc. bond : bond 0.00128 / 0.07 ( 6) *********************** 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 366 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 280 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 275 MET cc_start: 0.9234 (mmp) cc_final: 0.8720 (mmm) REVERT: A 389 LYS cc_start: 0.9167 (ttmt) cc_final: 0.8896 (ttmt) REVERT: A 397 GLU cc_start: 0.8586 (tt0) cc_final: 0.8164 (tp30) REVERT: A 668 LYS cc_start: 0.8999 (mmpt) cc_final: 0.8709 (mmpt) REVERT: B 292 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8252 (mm-30) REVERT: B 332 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8944 (mmm) REVERT: B 389 LYS cc_start: 0.9230 (ttmt) cc_final: 0.8984 (ttmt) REVERT: B 561 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8348 (mt-10) REVERT: C 225 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8025 (ptp-170) REVERT: C 236 LYS cc_start: 0.7794 (pptt) cc_final: 0.7592 (ptmm) REVERT: C 256 ARG cc_start: 0.7775 (mtt-85) cc_final: 0.7000 (mtp180) REVERT: C 262 THR cc_start: 0.7843 (t) cc_final: 0.7384 (p) REVERT: C 292 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8135 (mm-30) REVERT: C 352 SER cc_start: 0.9274 (m) cc_final: 0.8997 (t) REVERT: C 358 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8516 (mtm180) REVERT: D 321 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8334 (mt-10) REVERT: D 397 GLU cc_start: 0.8577 (tt0) cc_final: 0.8127 (tp30) REVERT: D 668 LYS cc_start: 0.9009 (mmpt) cc_final: 0.8723 (mmpt) REVERT: D 764 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: E 332 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8925 (mmm) REVERT: E 389 LYS cc_start: 0.9229 (ttmt) cc_final: 0.8980 (ttmt) REVERT: E 397 GLU cc_start: 0.8535 (tt0) cc_final: 0.8123 (tp30) REVERT: E 561 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8417 (mt-10) REVERT: E 668 LYS cc_start: 0.9050 (mmpt) cc_final: 0.8626 (mmpt) REVERT: F 236 LYS cc_start: 0.7726 (pptt) cc_final: 0.7500 (ptmm) REVERT: F 256 ARG cc_start: 0.7746 (mtt-85) cc_final: 0.6957 (mtp180) REVERT: F 262 THR cc_start: 0.7882 (t) cc_final: 0.7415 (p) REVERT: F 292 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8189 (mm-30) REVERT: F 352 SER cc_start: 0.9274 (m) cc_final: 0.9009 (t) REVERT: F 358 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8410 (mtt180) REVERT: F 426 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8283 (mtpt) REVERT: F 668 LYS cc_start: 0.9252 (mmpt) cc_final: 0.8916 (mmpt) REVERT: F 704 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7797 (mp0) outliers start: 86 outliers final: 38 residues processed: 343 average time/residue: 0.7805 time to fit residues: 303.0536 Evaluate side-chains 315 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 270 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 225 ARG Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 744 ARG Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 764 GLN Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 704 GLU Chi-restraints excluded: chain F residue 744 ARG Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 169 optimal weight: 0.5980 chunk 243 optimal weight: 0.0010 chunk 275 optimal weight: 1.9990 chunk 248 optimal weight: 0.0770 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 262 optimal weight: 3.9990 chunk 32 optimal weight: 0.0040 chunk 44 optimal weight: 0.1980 overall best weight: 0.1756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 764 GLN D 603 GLN D 692 GLN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 GLN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN F 764 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.127053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.092048 restraints weight = 36087.742| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.75 r_work: 0.2977 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 26436 Z= 0.104 Angle : 0.552 11.183 35754 Z= 0.270 Chirality : 0.042 0.203 3996 Planarity : 0.005 0.067 4668 Dihedral : 16.580 172.184 3996 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.94 % Favored : 95.72 % Rotamer: Outliers : 2.78 % Allowed : 16.01 % Favored : 81.21 % 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: 1.46 (0.16), residues: 3270 helix: 1.38 (0.13), residues: 1746 sheet: -0.26 (0.25), residues: 378 loop : 1.04 (0.21), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 256 TYR 0.010 0.001 TYR D 244 PHE 0.010 0.001 PHE F 302 TRP 0.009 0.001 TRP D 551 HIS 0.005 0.001 HIS C 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 (26430) covalent geometry : angle 0.55160 / 0.27 (35754) hydrogen bonds : bond 0.02996 / 2.01 ( 1235) hydrogen bonds : angle 3.79290 / 2.69 ( 3480) Misc. bond : bond 0.00056 / 0.03 ( 6) *********************** 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 368 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 292 time to evaluate : 0.762 Fit side-chains REVERT: A 321 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8339 (mt-10) REVERT: A 332 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8937 (mmm) REVERT: A 389 LYS cc_start: 0.9186 (ttmt) cc_final: 0.8894 (ttmt) REVERT: A 397 GLU cc_start: 0.8563 (tt0) cc_final: 0.8118 (tp30) REVERT: A 456 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8487 (tt) REVERT: A 564 ASP cc_start: 0.8762 (m-30) cc_final: 0.8521 (m-30) REVERT: A 668 LYS cc_start: 0.9003 (mmpt) cc_final: 0.8680 (mmpt) REVERT: B 292 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8239 (mm-30) REVERT: B 389 LYS cc_start: 0.9194 (ttmt) cc_final: 0.8956 (ttmt) REVERT: B 561 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8346 (mt-10) REVERT: B 668 LYS cc_start: 0.9017 (mmpt) cc_final: 0.8803 (mmpt) REVERT: B 764 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7777 (mm110) REVERT: C 236 LYS cc_start: 0.7767 (pptt) cc_final: 0.7499 (ptmm) REVERT: C 256 ARG cc_start: 0.7673 (mtt-85) cc_final: 0.6915 (mtp180) REVERT: C 292 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8144 (mm-30) REVERT: C 332 MET cc_start: 0.8857 (mtp) cc_final: 0.8483 (mtp) REVERT: C 352 SER cc_start: 0.9233 (m) cc_final: 0.8951 (t) REVERT: C 358 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8432 (mtm180) REVERT: D 321 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8292 (mt-10) REVERT: D 397 GLU cc_start: 0.8546 (tt0) cc_final: 0.8213 (mp0) REVERT: D 456 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8496 (tt) REVERT: D 564 ASP cc_start: 0.8804 (m-30) cc_final: 0.8578 (m-30) REVERT: D 668 LYS cc_start: 0.9048 (mmpt) cc_final: 0.8725 (mmpt) REVERT: D 764 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7257 (mp10) REVERT: E 288 LYS cc_start: 0.8957 (mttp) cc_final: 0.8651 (mttp) REVERT: E 389 LYS cc_start: 0.9221 (ttmt) cc_final: 0.8952 (ttmt) REVERT: E 397 GLU cc_start: 0.8552 (tt0) cc_final: 0.8188 (tp30) REVERT: E 508 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8008 (tmm) REVERT: E 561 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8351 (mt-10) REVERT: F 225 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.8007 (ptp-170) REVERT: F 236 LYS cc_start: 0.7682 (pptt) cc_final: 0.7379 (ptmm) REVERT: F 256 ARG cc_start: 0.7649 (mtt-85) cc_final: 0.6872 (mtp180) REVERT: F 292 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8183 (mm-30) REVERT: F 352 SER cc_start: 0.9236 (m) cc_final: 0.8960 (t) REVERT: F 358 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8421 (mtm180) REVERT: F 426 LYS cc_start: 0.8589 (mmmt) cc_final: 0.8243 (mtpt) REVERT: F 668 LYS cc_start: 0.9275 (mmpt) cc_final: 0.8894 (mmpt) outliers start: 76 outliers final: 32 residues processed: 344 average time/residue: 0.6935 time to fit residues: 271.0665 Evaluate side-chains 312 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 764 GLN Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 764 GLN Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 744 ARG Chi-restraints excluded: chain F residue 757 MET 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: 0.5980 chunk 139 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 109 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 603 GLN ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.124654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.089009 restraints weight = 36010.808| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.75 r_work: 0.2916 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26436 Z= 0.142 Angle : 0.572 10.497 35754 Z= 0.281 Chirality : 0.043 0.139 3996 Planarity : 0.005 0.064 4668 Dihedral : 16.615 172.340 3996 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.82 % Favored : 95.84 % Rotamer: Outliers : 2.45 % Allowed : 16.85 % Favored : 80.70 % 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: 1.49 (0.16), residues: 3270 helix: 1.38 (0.13), residues: 1746 sheet: -0.16 (0.25), residues: 378 loop : 1.04 (0.21), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 256 TYR 0.008 0.001 TYR F 244 PHE 0.009 0.001 PHE F 302 TRP 0.013 0.002 TRP C 551 HIS 0.004 0.001 HIS C 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (26430) covalent geometry : angle 0.57209 / 0.28 (35754) hydrogen bonds : bond 0.03298 / 2.21 ( 1235) hydrogen bonds : angle 3.74047 / 2.65 ( 3480) Misc. bond : bond 0.00139 / 0.07 ( 6) *********************** 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 348 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 281 time to evaluate : 1.097 Fit side-chains REVERT: A 275 MET cc_start: 0.9227 (mmp) cc_final: 0.8657 (mmm) REVERT: A 389 LYS cc_start: 0.9195 (ttmt) cc_final: 0.8907 (ttmt) REVERT: A 397 GLU cc_start: 0.8600 (tt0) cc_final: 0.8112 (tp30) REVERT: A 564 ASP cc_start: 0.8821 (m-30) cc_final: 0.8601 (m-30) REVERT: A 668 LYS cc_start: 0.9088 (mmpt) cc_final: 0.8763 (mmpt) REVERT: B 389 LYS cc_start: 0.9199 (ttmt) cc_final: 0.8958 (ttmt) REVERT: B 561 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8307 (mt-10) REVERT: B 668 LYS cc_start: 0.9046 (mmpt) cc_final: 0.8785 (mmpt) REVERT: C 236 LYS cc_start: 0.7741 (pptt) cc_final: 0.7452 (ptmm) REVERT: C 256 ARG cc_start: 0.7653 (mtt-85) cc_final: 0.6886 (mtp180) REVERT: C 292 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8191 (mm-30) REVERT: C 352 SER cc_start: 0.9237 (m) cc_final: 0.8936 (t) REVERT: C 358 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8484 (mtm180) REVERT: C 426 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8256 (mtpt) REVERT: C 668 LYS cc_start: 0.9344 (mmmm) cc_final: 0.9067 (mmpt) REVERT: D 275 MET cc_start: 0.9307 (mmm) cc_final: 0.8988 (mmp) REVERT: D 321 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8311 (mt-10) REVERT: D 397 GLU cc_start: 0.8551 (tt0) cc_final: 0.8244 (mp0) REVERT: D 564 ASP cc_start: 0.8830 (m-30) cc_final: 0.8603 (m-30) REVERT: D 668 LYS cc_start: 0.9096 (mmpt) cc_final: 0.8766 (mmpt) REVERT: D 764 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7374 (mp10) REVERT: E 389 LYS cc_start: 0.9207 (ttmt) cc_final: 0.8948 (ttmt) REVERT: E 397 GLU cc_start: 0.8590 (tt0) cc_final: 0.8123 (tp30) REVERT: E 508 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8053 (tmm) REVERT: E 561 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8311 (mt-10) REVERT: E 668 LYS cc_start: 0.9278 (mmmm) cc_final: 0.8912 (mmpt) REVERT: F 236 LYS cc_start: 0.7735 (pptt) cc_final: 0.7403 (ptmm) REVERT: F 256 ARG cc_start: 0.7622 (mtt-85) cc_final: 0.6835 (mtp180) REVERT: F 292 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8202 (mm-30) REVERT: F 352 SER cc_start: 0.9240 (m) cc_final: 0.8951 (t) REVERT: F 358 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8402 (mtt180) REVERT: F 426 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8295 (mtpt) REVERT: F 668 LYS cc_start: 0.9293 (mmpt) cc_final: 0.8876 (mmpt) REVERT: F 704 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7847 (mp0) outliers start: 67 outliers final: 35 residues processed: 327 average time/residue: 0.7427 time to fit residues: 275.7292 Evaluate side-chains 308 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 268 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 702 SER Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 764 GLN Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 704 GLU Chi-restraints excluded: chain F residue 744 ARG Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 144 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 303 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 196 optimal weight: 0.2980 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 GLN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 764 GLN ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.088172 restraints weight = 35879.550| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.75 r_work: 0.2903 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 26436 Z= 0.144 Angle : 0.589 10.019 35754 Z= 0.287 Chirality : 0.043 0.180 3996 Planarity : 0.005 0.065 4668 Dihedral : 16.653 174.562 3996 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.82 % Favored : 95.87 % Rotamer: Outliers : 2.20 % Allowed : 17.62 % Favored : 80.18 % 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: 1.45 (0.16), residues: 3270 helix: 1.36 (0.13), residues: 1746 sheet: -0.19 (0.25), residues: 378 loop : 1.02 (0.21), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 256 TYR 0.009 0.001 TYR D 244 PHE 0.010 0.001 PHE F 302 TRP 0.014 0.002 TRP C 551 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (26430) covalent geometry : angle 0.58914 / 0.29 (35754) hydrogen bonds : bond 0.03317 / 2.23 ( 1235) hydrogen bonds : angle 3.76057 / 2.67 ( 3480) Misc. bond : bond 0.00146 / 0.08 ( 6) *********************** 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 331 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 271 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 MET cc_start: 0.9246 (mmp) cc_final: 0.8622 (mmm) REVERT: A 389 LYS cc_start: 0.9167 (ttmt) cc_final: 0.8867 (ttmt) REVERT: A 397 GLU cc_start: 0.8562 (tt0) cc_final: 0.8044 (tp30) REVERT: A 550 MET cc_start: 0.6696 (ptp) cc_final: 0.6453 (ptm) REVERT: A 564 ASP cc_start: 0.8818 (m-30) cc_final: 0.8593 (m-30) REVERT: A 668 LYS cc_start: 0.9090 (mmpt) cc_final: 0.8765 (mmpt) REVERT: B 332 MET cc_start: 0.9147 (mtp) cc_final: 0.8925 (mmm) REVERT: B 389 LYS cc_start: 0.9196 (ttmt) cc_final: 0.8963 (ttmt) REVERT: B 561 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8290 (mt-10) REVERT: B 668 LYS cc_start: 0.9118 (mmpt) cc_final: 0.8846 (mmpt) REVERT: C 236 LYS cc_start: 0.7775 (pptt) cc_final: 0.7460 (pttm) REVERT: C 256 ARG cc_start: 0.7676 (mtt-85) cc_final: 0.6922 (mtp180) REVERT: C 292 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8225 (mm-30) REVERT: C 352 SER cc_start: 0.9237 (m) cc_final: 0.8934 (t) REVERT: C 358 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8478 (mtm180) REVERT: C 668 LYS cc_start: 0.9339 (mmmm) cc_final: 0.9058 (mmpt) REVERT: D 275 MET cc_start: 0.9327 (mmm) cc_final: 0.8867 (mmp) REVERT: D 321 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8309 (mt-10) REVERT: D 397 GLU cc_start: 0.8552 (tt0) cc_final: 0.8238 (mp0) REVERT: D 564 ASP cc_start: 0.8827 (m-30) cc_final: 0.8615 (m-30) REVERT: D 668 LYS cc_start: 0.9106 (mmpt) cc_final: 0.8775 (mmpt) REVERT: D 764 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7390 (mp10) REVERT: E 332 MET cc_start: 0.9138 (mtp) cc_final: 0.8912 (mmm) REVERT: E 389 LYS cc_start: 0.9190 (ttmt) cc_final: 0.8940 (ttmt) REVERT: E 397 GLU cc_start: 0.8601 (tt0) cc_final: 0.8115 (tp30) REVERT: E 508 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8029 (tmm) REVERT: E 561 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8302 (mt-10) REVERT: E 663 LYS cc_start: 0.9200 (mptt) cc_final: 0.8997 (mppt) REVERT: E 668 LYS cc_start: 0.9297 (mmmm) cc_final: 0.9062 (mmtm) REVERT: F 236 LYS cc_start: 0.7726 (pptt) cc_final: 0.7359 (pttm) REVERT: F 256 ARG cc_start: 0.7633 (mtt-85) cc_final: 0.6855 (mtp180) REVERT: F 292 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8204 (mm-30) REVERT: F 352 SER cc_start: 0.9239 (m) cc_final: 0.8941 (t) REVERT: F 358 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8411 (mtm180) REVERT: F 426 LYS cc_start: 0.8616 (mmmt) cc_final: 0.8386 (mttt) REVERT: F 704 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7864 (mp0) outliers start: 60 outliers final: 35 residues processed: 315 average time/residue: 0.6830 time to fit residues: 245.2000 Evaluate side-chains 304 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 702 SER Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 764 GLN Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 704 GLU Chi-restraints excluded: chain F residue 744 ARG Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 194 optimal weight: 0.4980 chunk 244 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 43 optimal weight: 0.0970 chunk 67 optimal weight: 0.7980 chunk 302 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 238 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 GLN ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.124407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.088896 restraints weight = 35913.421| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.73 r_work: 0.2916 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26436 Z= 0.129 Angle : 0.584 9.629 35754 Z= 0.285 Chirality : 0.042 0.140 3996 Planarity : 0.005 0.065 4668 Dihedral : 16.637 176.250 3996 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.73 % Favored : 95.99 % Rotamer: Outliers : 1.79 % Allowed : 18.24 % Favored : 79.96 % 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: 1.48 (0.16), residues: 3270 helix: 1.38 (0.13), residues: 1746 sheet: -0.23 (0.25), residues: 378 loop : 1.06 (0.21), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 256 TYR 0.008 0.001 TYR C 203 PHE 0.010 0.001 PHE F 302 TRP 0.012 0.001 TRP C 551 HIS 0.004 0.001 HIS C 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (26430) covalent geometry : angle 0.58422 / 0.28 (35754) hydrogen bonds : bond 0.03226 / 2.17 ( 1235) hydrogen bonds : angle 3.76801 / 2.67 ( 3480) Misc. bond : bond 0.00114 / 0.06 ( 6) ********************** 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 313 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 MET cc_start: 0.9219 (mmp) cc_final: 0.8586 (mmm) REVERT: A 389 LYS cc_start: 0.9151 (ttmt) cc_final: 0.8851 (ttmt) REVERT: A 397 GLU cc_start: 0.8549 (tt0) cc_final: 0.8040 (tp30) REVERT: A 550 MET cc_start: 0.6678 (ptp) cc_final: 0.6449 (ptm) REVERT: A 564 ASP cc_start: 0.8816 (m-30) cc_final: 0.8590 (m-30) REVERT: B 389 LYS cc_start: 0.9183 (ttmt) cc_final: 0.8959 (ttmt) REVERT: B 561 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8271 (mt-10) REVERT: B 668 LYS cc_start: 0.9130 (mmpt) cc_final: 0.8843 (mmpt) REVERT: C 236 LYS cc_start: 0.7781 (pptt) cc_final: 0.7453 (pttm) REVERT: C 256 ARG cc_start: 0.7654 (mtt-85) cc_final: 0.6909 (mtp180) REVERT: C 292 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8204 (mm-30) REVERT: C 352 SER cc_start: 0.9228 (m) cc_final: 0.8926 (t) REVERT: C 358 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8502 (mtm180) REVERT: D 275 MET cc_start: 0.9327 (mmm) cc_final: 0.8914 (mmp) REVERT: D 321 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8304 (mt-10) REVERT: D 397 GLU cc_start: 0.8548 (tt0) cc_final: 0.8234 (mp0) REVERT: D 564 ASP cc_start: 0.8831 (m-30) cc_final: 0.8621 (m-30) REVERT: D 764 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7384 (mp10) REVERT: E 389 LYS cc_start: 0.9181 (ttmt) cc_final: 0.8962 (ttmt) REVERT: E 397 GLU cc_start: 0.8594 (tt0) cc_final: 0.8115 (tp30) REVERT: E 508 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7998 (tmm) REVERT: E 561 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8284 (mt-10) REVERT: E 668 LYS cc_start: 0.9294 (mmmm) cc_final: 0.9071 (mmtm) REVERT: F 236 LYS cc_start: 0.7740 (pptt) cc_final: 0.7367 (pttm) REVERT: F 256 ARG cc_start: 0.7632 (mtt-85) cc_final: 0.6860 (mtp180) REVERT: F 292 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8221 (mm-30) REVERT: F 352 SER cc_start: 0.9236 (m) cc_final: 0.8942 (t) REVERT: F 358 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8393 (mtm180) REVERT: F 704 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7869 (mp0) outliers start: 49 outliers final: 35 residues processed: 302 average time/residue: 0.7401 time to fit residues: 255.3071 Evaluate side-chains 300 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 260 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 702 SER Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain D residue 764 GLN Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 358 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 704 GLU Chi-restraints excluded: chain F residue 744 ARG Chi-restraints excluded: chain F residue 757 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 218 optimal weight: 0.6980 chunk 307 optimal weight: 0.7980 chunk 241 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 262 optimal weight: 4.9990 chunk 234 optimal weight: 0.0270 chunk 265 optimal weight: 1.9990 chunk 319 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.123825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.088196 restraints weight = 35879.213| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.74 r_work: 0.2904 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 26436 Z= 0.139 Angle : 0.593 11.061 35754 Z= 0.288 Chirality : 0.042 0.191 3996 Planarity : 0.005 0.066 4668 Dihedral : 16.664 178.416 3996 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.73 % Favored : 95.99 % Rotamer: Outliers : 1.76 % Allowed : 18.46 % Favored : 79.78 % 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: 1.37 (0.13), residues: 1746 sheet: -0.22 (0.25), residues: 378 loop : 1.04 (0.22), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 256 TYR 0.008 0.001 TYR D 244 PHE 0.010 0.001 PHE F 302 TRP 0.013 0.002 TRP D 551 HIS 0.004 0.001 HIS C 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (26430) covalent geometry : angle 0.59324 / 0.29 (35754) hydrogen bonds : bond 0.03284 / 2.21 ( 1235) hydrogen bonds : angle 3.77429 / 2.68 ( 3480) Misc. bond : bond 0.00131 / 0.07 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8795.94 seconds wall clock time: 166 minutes 26.29 seconds (9986.29 seconds total)