Starting phenix.real_space_refine on Sun Jul 5 07:08:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctm_45911/07_2026/9ctm_45911.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctm_45911/07_2026/9ctm_45911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ctm_45911/07_2026/9ctm_45911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctm_45911/07_2026/9ctm_45911.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ctm_45911/07_2026/9ctm_45911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctm_45911/07_2026/9ctm_45911.map" } resolution = 2.92 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= 0.002 sd= 0.058 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: 5 Type Number sf(0) Gaussians S 98 5.16 5 C 8360 2.51 5 N 2242 2.21 5 O 2534 1.98 5 H 13032 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s 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: 26266 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 13133 Classifications: {'peptide': 862} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 815} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'SCY:plan-1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 13133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 13133 Classifications: {'peptide': 862} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 815} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'SCY:plan-1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.76, per 1000 atoms: 0.18 Number of scatterers: 26266 At special positions: 0 Unit cell: (103.88, 99.64, 189.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 O 2534 8.00 N 2242 7.00 C 8360 6.00 H 13032 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 686.3 milliseconds 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3168 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 10 sheets defined 46.4% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 44 through 54 Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 102 through 119 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 140 through 148 removed outlier: 4.305A pdb=" N THR A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 162 removed outlier: 3.785A pdb=" N HIS A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.783A pdb=" N ASN A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 170 " --> pdb=" O TYR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 203 Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.568A pdb=" N THR A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 305 removed outlier: 3.521A pdb=" N HIS A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 454 through 468 Processing helix chain 'A' and resid 471 through 480 removed outlier: 3.829A pdb=" N HIS A 475 " --> pdb=" O ASN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 537 through 552 Processing helix chain 'A' and resid 553 through 555 No H-bonds generated for 'chain 'A' and resid 553 through 555' Processing helix chain 'A' and resid 557 through 564 Processing helix chain 'A' and resid 566 through 572 removed outlier: 3.785A pdb=" N GLU A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 595 removed outlier: 3.738A pdb=" N PHE A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 616 Processing helix chain 'A' and resid 619 through 637 Processing helix chain 'A' and resid 650 through 658 Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 711 through 723 removed outlier: 3.608A pdb=" N ALA A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 745 Processing helix chain 'A' and resid 747 through 752 removed outlier: 4.161A pdb=" N THR A 752 " --> pdb=" O GLU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 767 through 774 removed outlier: 3.671A pdb=" N LYS A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 799 removed outlier: 3.519A pdb=" N GLY A 799 " --> pdb=" O LYS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 829 removed outlier: 3.567A pdb=" N VAL A 818 " --> pdb=" O ASN A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 839 removed outlier: 3.990A pdb=" N LEU A 838 " --> pdb=" O PRO A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 859 removed outlier: 3.688A pdb=" N VAL A 857 " --> pdb=" O LEU A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 876 removed outlier: 3.604A pdb=" N GLU A 876 " --> pdb=" O GLU A 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 94 through 100 Processing helix chain 'B' and resid 102 through 119 Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 140 through 148 removed outlier: 4.283A pdb=" N THR B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.711A pdb=" N ASN B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 170 " --> pdb=" O TYR B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 203 Processing helix chain 'B' and resid 219 through 229 removed outlier: 3.586A pdb=" N THR B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 305 removed outlier: 3.559A pdb=" N HIS B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 325 through 337 Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 360 through 375 Processing helix chain 'B' and resid 391 through 395 removed outlier: 3.533A pdb=" N LEU B 394 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'B' and resid 454 through 468 Processing helix chain 'B' and resid 471 through 480 removed outlier: 3.800A pdb=" N HIS B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 537 through 552 Processing helix chain 'B' and resid 553 through 555 No H-bonds generated for 'chain 'B' and resid 553 through 555' Processing helix chain 'B' and resid 557 through 565 Processing helix chain 'B' and resid 566 through 572 removed outlier: 3.766A pdb=" N GLU B 572 " --> pdb=" O ASP B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 607 through 615 Processing helix chain 'B' and resid 619 through 637 removed outlier: 3.624A pdb=" N VAL B 634 " --> pdb=" O ARG B 630 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N CYS B 637 " --> pdb=" O ALA B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 658 removed outlier: 3.765A pdb=" N ARG B 656 " --> pdb=" O GLU B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 692 removed outlier: 3.549A pdb=" N THR B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 692 " --> pdb=" O GLU B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 711 through 723 Processing helix chain 'B' and resid 741 through 745 Processing helix chain 'B' and resid 747 through 752 removed outlier: 4.144A pdb=" N THR B 752 " --> pdb=" O GLU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 764 Processing helix chain 'B' and resid 767 through 775 removed outlier: 3.627A pdb=" N LYS B 774 " --> pdb=" O GLU B 770 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 799 Processing helix chain 'B' and resid 814 through 829 removed outlier: 3.544A pdb=" N VAL B 818 " --> pdb=" O ASN B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 839 removed outlier: 3.778A pdb=" N LEU B 838 " --> pdb=" O PRO B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 859 removed outlier: 3.693A pdb=" N VAL B 857 " --> pdb=" O LEU B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 876 removed outlier: 3.610A pdb=" N GLU B 876 " --> pdb=" O GLU B 873 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 212 through 213 removed outlier: 7.734A pdb=" N GLY A 212 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR A 134 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR A 181 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL A 133 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N TYR A 183 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE A 135 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N THR B 181 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL B 133 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR B 183 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE B 135 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY B 212 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 399 through 401 removed outlier: 5.968A pdb=" N LEU A 345 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS A 313 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N GLY A 348 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE A 315 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU A 412 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR A 314 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASN A 424 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU A 276 " --> pdb=" O ASN A 424 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N HIS A 426 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER A 274 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 428 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS A 269 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL A 30 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 257 " --> pdb=" O CYS A 33 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU A 35 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA A 255 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR A 181 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL A 133 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N TYR A 183 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE A 135 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N THR B 181 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL B 133 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR B 183 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE B 135 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA B 255 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU B 35 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU B 257 " --> pdb=" O CYS B 33 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL B 30 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS B 269 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE B 428 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER B 274 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N HIS B 426 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU B 276 " --> pdb=" O ASN B 424 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN B 424 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 412 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR B 314 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS B 313 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLY B 348 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE B 315 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU B 345 " --> pdb=" O LYS B 400 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA4, first strand: chain 'A' and resid 446 through 452 Processing sheet with id=AA5, first strand: chain 'A' and resid 600 through 603 removed outlier: 6.621A pdb=" N TRP A 517 " --> pdb=" O ILE A 782 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE A 784 " --> pdb=" O TRP A 517 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL A 519 " --> pdb=" O ILE A 784 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 662 through 663 removed outlier: 4.464A pdb=" N MET A 644 " --> pdb=" O VAL A 699 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 667 through 669 removed outlier: 3.693A pdb=" N SER A 669 " --> pdb=" O SER A 672 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 446 through 452 Processing sheet with id=AA9, first strand: chain 'B' and resid 600 through 603 Processing sheet with id=AB1, first strand: chain 'B' and resid 663 through 669 removed outlier: 6.665A pdb=" N THR B 674 " --> pdb=" O ALA B 665 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N HIS B 667 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N SER B 672 " --> pdb=" O HIS B 667 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET B 644 " --> pdb=" O VAL B 699 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1545 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: 6.26 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12994 1.03 - 1.23: 51 1.23 - 1.43: 5581 1.43 - 1.62: 7778 1.62 - 1.82: 158 Bond restraints: 26562 Sorted by residual: bond pdb=" SG SCY A 187 " pdb=" CD SCY A 187 " ideal model delta sigma weight residual 1.771 1.816 -0.045 2.00e-02 2.50e+03 5.04e+00 bond pdb=" SG SCY B 187 " pdb=" CD SCY B 187 " ideal model delta sigma weight residual 1.771 1.815 -0.044 2.00e-02 2.50e+03 4.75e+00 bond pdb=" CB CYS B 334 " pdb=" SG CYS B 334 " ideal model delta sigma weight residual 1.808 1.760 0.048 3.30e-02 9.18e+02 2.10e+00 bond pdb=" C SCY A 187 " pdb=" O SCY A 187 " ideal model delta sigma weight residual 1.231 1.258 -0.027 2.00e-02 2.50e+03 1.79e+00 bond pdb=" C SCY B 187 " pdb=" O SCY B 187 " ideal model delta sigma weight residual 1.231 1.258 -0.027 2.00e-02 2.50e+03 1.78e+00 ... (remaining 26557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.26: 48047 5.26 - 10.51: 9 10.51 - 15.77: 1 15.77 - 21.02: 0 21.02 - 26.28: 3 Bond angle restraints: 48060 Sorted by residual: angle pdb=" CG2 ILE B 573 " pdb=" CB ILE B 573 " pdb=" HB ILE B 573 " ideal model delta sigma weight residual 109.00 82.72 26.28 3.00e+00 1.11e-01 7.67e+01 angle pdb=" CG1 ILE B 573 " pdb=" CB ILE B 573 " pdb=" HB ILE B 573 " ideal model delta sigma weight residual 109.00 82.82 26.18 3.00e+00 1.11e-01 7.61e+01 angle pdb=" CA ILE B 573 " pdb=" CB ILE B 573 " pdb=" HB ILE B 573 " ideal model delta sigma weight residual 109.00 85.58 23.42 3.00e+00 1.11e-01 6.09e+01 angle pdb=" CG1 ILE B 573 " pdb=" CB ILE B 573 " pdb=" CG2 ILE B 573 " ideal model delta sigma weight residual 110.70 125.14 -14.44 3.00e+00 1.11e-01 2.32e+01 angle pdb=" CA ILE B 573 " pdb=" CB ILE B 573 " pdb=" CG1 ILE B 573 " ideal model delta sigma weight residual 110.40 116.25 -5.85 1.70e+00 3.46e-01 1.18e+01 ... (remaining 48055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10963 17.94 - 35.89: 1180 35.89 - 53.83: 352 53.83 - 71.77: 112 71.77 - 89.72: 17 Dihedral angle restraints: 12624 sinusoidal: 6878 harmonic: 5746 Sorted by residual: dihedral pdb=" CB GLU A 622 " pdb=" CG GLU A 622 " pdb=" CD GLU A 622 " pdb=" OE1 GLU A 622 " ideal model delta sinusoidal sigma weight residual 0.00 -86.82 86.82 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB MET A 711 " pdb=" CG MET A 711 " pdb=" SD MET A 711 " pdb=" CE MET A 711 " ideal model delta sinusoidal sigma weight residual 180.00 120.61 59.39 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 227 " pdb=" CG MET A 227 " pdb=" SD MET A 227 " pdb=" CE MET A 227 " ideal model delta sinusoidal sigma weight residual 60.00 0.78 59.22 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 12621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.319: 2021 0.319 - 0.637: 0 0.637 - 0.956: 0 0.956 - 1.275: 0 1.275 - 1.593: 1 Chirality restraints: 2022 Sorted by residual: chirality pdb=" CB ILE B 573 " pdb=" CA ILE B 573 " pdb=" CG1 ILE B 573 " pdb=" CG2 ILE B 573 " both_signs ideal model delta sigma weight residual False 2.64 1.05 1.59 2.00e-01 2.50e+01 6.35e+01 chirality pdb=" CB ILE B 635 " pdb=" CA ILE B 635 " pdb=" CG1 ILE B 635 " pdb=" CG2 ILE B 635 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE B 740 " pdb=" N ILE B 740 " pdb=" C ILE B 740 " pdb=" CB ILE B 740 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 2019 not shown) Planarity restraints: 4020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 656 " -0.201 9.50e-02 1.11e+02 6.72e-02 4.93e+00 pdb=" NE ARG B 656 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 656 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 656 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 656 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 656 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 656 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 656 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG B 656 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 575 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO B 576 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 576 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 576 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET B 682 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C MET B 682 " -0.029 2.00e-02 2.50e+03 pdb=" O MET B 682 " 0.011 2.00e-02 2.50e+03 pdb=" N THR B 683 " 0.010 2.00e-02 2.50e+03 ... (remaining 4017 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1376 2.18 - 2.78: 52389 2.78 - 3.39: 76159 3.39 - 3.99: 100709 3.99 - 4.60: 157697 Nonbonded interactions: 388330 Sorted by model distance: nonbonded pdb=" O ALA B 186 " pdb=" HG1 THR B 189 " model vdw 1.570 2.450 nonbonded pdb=" OE1 GLU A 89 " pdb=" H GLU A 89 " model vdw 1.601 2.450 nonbonded pdb=" O ASN B 139 " pdb=" HE2 HIS B 163 " model vdw 1.621 2.450 nonbonded pdb="HH11 ARG A 453 " pdb=" O SER A 488 " model vdw 1.636 2.450 nonbonded pdb=" HH TYR A 520 " pdb=" OG1 THR A 588 " model vdw 1.638 2.450 ... (remaining 388325 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.810 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: 0.110 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.640 Find NCS groups from input model: 0.370 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:7.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 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 : 0.002 0.048 13530 Z= 0.108 Angle : 0.541 14.437 18334 Z= 0.268 Chirality : 0.054 1.593 2022 Planarity : 0.004 0.088 2390 Dihedral : 17.110 89.718 4990 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.42 % Allowed : 25.56 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.33 (0.21), residues: 1714 helix: 1.10 (0.21), residues: 676 sheet: -0.75 (0.39), residues: 174 loop : -0.18 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 621 TYR 0.011 0.001 TYR A 706 PHE 0.011 0.001 PHE A 819 TRP 0.013 0.001 TRP B 651 HIS 0.019 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (13530) covalent geometry : angle 0.54060 / 0.27 (18334) hydrogen bonds : bond 0.15947 / 10.49 ( 553) hydrogen bonds : angle 6.54100 / 4.73 ( 1545) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 241 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.7847 (mtt) cc_final: 0.7630 (mtp) REVERT: A 242 GLU cc_start: 0.6695 (pt0) cc_final: 0.6425 (tm-30) REVERT: A 245 ASP cc_start: 0.7193 (p0) cc_final: 0.6967 (p0) REVERT: A 302 TYR cc_start: 0.7718 (m-80) cc_final: 0.7503 (m-80) REVERT: A 523 MET cc_start: 0.7623 (mmm) cc_final: 0.7272 (mmm) REVERT: A 669 SER cc_start: 0.8298 (t) cc_final: 0.7747 (p) REVERT: A 695 THR cc_start: 0.7867 (OUTLIER) cc_final: 0.7544 (p) REVERT: A 795 LYS cc_start: 0.8638 (tppt) cc_final: 0.7712 (ttmt) REVERT: B 224 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7743 (mtpt) REVERT: B 648 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6770 (mm-30) REVERT: B 796 LYS cc_start: 0.7338 (ttmm) cc_final: 0.6867 (mmmt) REVERT: B 876 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7188 (mt-10) outliers start: 6 outliers final: 3 residues processed: 246 average time/residue: 0.8253 time to fit residues: 233.7469 Evaluate side-chains 171 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 167 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain B residue 637 CYS Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 801 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0270 chunk 91 optimal weight: 0.4980 chunk 149 optimal weight: 9.9990 overall best weight: 1.7044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 140 ASN A 356 HIS ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 377 GLN ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.136171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102083 restraints weight = 50411.952| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.88 r_work: 0.3134 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13530 Z= 0.216 Angle : 0.635 15.407 18334 Z= 0.330 Chirality : 0.059 1.655 2022 Planarity : 0.005 0.052 2390 Dihedral : 5.397 75.930 1853 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.99 % Allowed : 24.03 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.04 (0.20), residues: 1714 helix: 0.80 (0.20), residues: 686 sheet: -0.86 (0.39), residues: 156 loop : -0.46 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 492 TYR 0.015 0.002 TYR B 113 PHE 0.019 0.002 PHE B 819 TRP 0.013 0.001 TRP B 651 HIS 0.007 0.002 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (13530) covalent geometry : angle 0.63544 / 0.33 (18334) hydrogen bonds : bond 0.04834 / 3.28 ( 553) hydrogen bonds : angle 4.89068 / 3.56 ( 1545) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8580 (tpt) cc_final: 0.8365 (tpt) REVERT: A 464 GLU cc_start: 0.6956 (tp30) cc_final: 0.6591 (tp30) REVERT: A 695 THR cc_start: 0.7688 (OUTLIER) cc_final: 0.7358 (p) REVERT: A 752 THR cc_start: 0.6723 (OUTLIER) cc_final: 0.6130 (t) REVERT: A 795 LYS cc_start: 0.8632 (tppt) cc_final: 0.7659 (ttmt) REVERT: B 58 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.6525 (mpp) REVERT: B 77 MET cc_start: 0.8620 (ttm) cc_final: 0.8375 (ttm) REVERT: B 96 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7365 (mtpt) REVERT: B 224 LYS cc_start: 0.8114 (mtpp) cc_final: 0.7588 (mtpt) REVERT: B 648 GLU cc_start: 0.7899 (mt-10) cc_final: 0.6881 (mm-30) REVERT: B 686 MET cc_start: 0.8023 (mtp) cc_final: 0.7800 (mtp) REVERT: B 831 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8256 (m) outliers start: 43 outliers final: 17 residues processed: 192 average time/residue: 0.9184 time to fit residues: 198.7970 Evaluate side-chains 165 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 637 CYS Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 169 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN A 507 GLN ** B 581 ASN ** 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 = 0.3743 r_free = 0.3743 target = 0.139250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.105664 restraints weight = 49665.269| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.82 r_work: 0.3213 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13530 Z= 0.109 Angle : 0.524 14.708 18334 Z= 0.262 Chirality : 0.055 1.633 2022 Planarity : 0.004 0.041 2390 Dihedral : 5.004 74.828 1851 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.16 % Allowed : 24.51 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.29 (0.21), residues: 1714 helix: 1.20 (0.21), residues: 686 sheet: -0.94 (0.36), residues: 186 loop : -0.29 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 430 TYR 0.010 0.001 TYR A 113 PHE 0.015 0.001 PHE A 685 TRP 0.010 0.001 TRP B 651 HIS 0.012 0.001 HIS B 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (13530) covalent geometry : angle 0.52406 / 0.26 (18334) hydrogen bonds : bond 0.04177 / 2.77 ( 553) hydrogen bonds : angle 4.59374 / 3.36 ( 1545) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.6894 (tp30) cc_final: 0.6552 (tp30) REVERT: A 671 ASP cc_start: 0.7081 (t0) cc_final: 0.6779 (t0) REVERT: A 695 THR cc_start: 0.7595 (OUTLIER) cc_final: 0.7264 (p) REVERT: A 752 THR cc_start: 0.6761 (OUTLIER) cc_final: 0.6168 (t) REVERT: A 795 LYS cc_start: 0.8606 (tppt) cc_final: 0.7700 (ttmt) REVERT: B 58 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.6631 (mpp) REVERT: B 77 MET cc_start: 0.8389 (ttm) cc_final: 0.8161 (ttm) REVERT: B 224 LYS cc_start: 0.8121 (mtpp) cc_final: 0.7612 (mtpp) REVERT: B 373 MET cc_start: 0.8684 (tpp) cc_final: 0.8203 (tpp) REVERT: B 648 GLU cc_start: 0.7791 (mt-10) cc_final: 0.6853 (mm-30) REVERT: B 686 MET cc_start: 0.7940 (mtp) cc_final: 0.7708 (mtp) REVERT: B 796 LYS cc_start: 0.7627 (ttmm) cc_final: 0.7090 (mmmt) REVERT: B 831 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8319 (m) outliers start: 31 outliers final: 10 residues processed: 181 average time/residue: 0.9737 time to fit residues: 198.2692 Evaluate side-chains 159 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 10 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN A 507 GLN ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.099937 restraints weight = 49349.685| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.81 r_work: 0.3123 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13530 Z= 0.188 Angle : 0.593 13.995 18334 Z= 0.302 Chirality : 0.057 1.614 2022 Planarity : 0.005 0.046 2390 Dihedral : 5.137 77.494 1850 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.92 % Allowed : 24.30 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.12 (0.20), residues: 1714 helix: 1.05 (0.21), residues: 684 sheet: -0.61 (0.36), residues: 184 loop : -0.50 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 514 TYR 0.015 0.002 TYR B 757 PHE 0.035 0.002 PHE A 685 TRP 0.018 0.001 TRP B 651 HIS 0.021 0.002 HIS B 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (13530) covalent geometry : angle 0.59265 / 0.30 (18334) hydrogen bonds : bond 0.04534 / 3.03 ( 553) hydrogen bonds : angle 4.54656 / 3.32 ( 1545) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7109 (tp30) cc_final: 0.6776 (tp30) REVERT: A 695 THR cc_start: 0.7359 (OUTLIER) cc_final: 0.7040 (p) REVERT: A 744 ARG cc_start: 0.7429 (ttp80) cc_final: 0.7073 (ttp80) REVERT: A 752 THR cc_start: 0.7160 (OUTLIER) cc_final: 0.6597 (t) REVERT: A 795 LYS cc_start: 0.8696 (tppt) cc_final: 0.7800 (ttmt) REVERT: B 58 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8333 (mtp) REVERT: B 224 LYS cc_start: 0.8238 (mtpp) cc_final: 0.7692 (mtpp) REVERT: B 546 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: B 572 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.5150 (mp0) REVERT: B 626 SER cc_start: 0.7738 (OUTLIER) cc_final: 0.7296 (m) REVERT: B 648 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7218 (mm-30) REVERT: B 758 GLN cc_start: 0.6426 (OUTLIER) cc_final: 0.5445 (mp10) REVERT: B 873 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7924 (mp0) outliers start: 42 outliers final: 14 residues processed: 197 average time/residue: 0.9420 time to fit residues: 208.7358 Evaluate side-chains 179 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 758 GLN Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 873 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 121 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN A 507 GLN ** B 581 ASN ** 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 = 0.3686 r_free = 0.3686 target = 0.134524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100444 restraints weight = 49191.454| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.84 r_work: 0.3136 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13530 Z= 0.139 Angle : 0.534 14.709 18334 Z= 0.268 Chirality : 0.055 1.612 2022 Planarity : 0.004 0.044 2390 Dihedral : 5.015 77.708 1850 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.51 % Allowed : 24.16 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.23 (0.21), residues: 1714 helix: 1.12 (0.21), residues: 686 sheet: -0.49 (0.37), residues: 184 loop : -0.45 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 106 TYR 0.010 0.001 TYR A 113 PHE 0.017 0.001 PHE A 685 TRP 0.012 0.001 TRP B 651 HIS 0.005 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (13530) covalent geometry : angle 0.53443 / 0.27 (18334) hydrogen bonds : bond 0.04140 / 2.77 ( 553) hydrogen bonds : angle 4.44044 / 3.25 ( 1545) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7104 (tp30) cc_final: 0.6796 (tp30) REVERT: A 671 ASP cc_start: 0.7064 (t0) cc_final: 0.6834 (t0) REVERT: A 695 THR cc_start: 0.7264 (OUTLIER) cc_final: 0.6951 (p) REVERT: A 795 LYS cc_start: 0.8623 (tppt) cc_final: 0.7792 (ttmt) REVERT: B 464 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6843 (tp30) REVERT: B 535 MET cc_start: 0.8384 (mmt) cc_final: 0.8046 (mmm) REVERT: B 546 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7524 (mt-10) REVERT: B 572 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5170 (mp0) REVERT: B 626 SER cc_start: 0.7701 (t) cc_final: 0.7285 (m) REVERT: B 648 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7248 (mm-30) REVERT: B 758 GLN cc_start: 0.6356 (OUTLIER) cc_final: 0.5587 (mp10) REVERT: B 876 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7460 (mt-10) outliers start: 36 outliers final: 15 residues processed: 191 average time/residue: 0.9367 time to fit residues: 200.3157 Evaluate side-chains 171 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 758 GLN Chi-restraints excluded: chain B residue 802 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 22 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN A 507 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.131865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.097936 restraints weight = 49778.788| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.82 r_work: 0.3097 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13530 Z= 0.188 Angle : 0.564 14.812 18334 Z= 0.286 Chirality : 0.056 1.600 2022 Planarity : 0.005 0.065 2390 Dihedral : 5.140 78.647 1850 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.58 % Allowed : 23.75 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.12 (0.21), residues: 1714 helix: 1.00 (0.21), residues: 688 sheet: -0.55 (0.38), residues: 184 loop : -0.48 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 656 TYR 0.011 0.001 TYR B 113 PHE 0.019 0.001 PHE A 685 TRP 0.008 0.001 TRP B 651 HIS 0.007 0.001 HIS B 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (13530) covalent geometry : angle 0.56399 / 0.29 (18334) hydrogen bonds : bond 0.04391 / 2.94 ( 553) hydrogen bonds : angle 4.47394 / 3.27 ( 1545) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7159 (tp30) cc_final: 0.6814 (tp30) REVERT: A 572 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.6049 (tm-30) REVERT: A 671 ASP cc_start: 0.7097 (t0) cc_final: 0.6845 (t0) REVERT: A 695 THR cc_start: 0.7310 (OUTLIER) cc_final: 0.7017 (p) REVERT: A 744 ARG cc_start: 0.7318 (ttp80) cc_final: 0.7029 (ttp80) REVERT: A 752 THR cc_start: 0.7322 (OUTLIER) cc_final: 0.6801 (t) REVERT: A 795 LYS cc_start: 0.8638 (tppt) cc_final: 0.7845 (ttmt) REVERT: B 58 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8467 (mtm) REVERT: B 464 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6871 (tp30) REVERT: B 533 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8307 (t) REVERT: B 546 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: B 572 GLU cc_start: 0.6034 (OUTLIER) cc_final: 0.5233 (mp0) REVERT: B 626 SER cc_start: 0.7695 (OUTLIER) cc_final: 0.7320 (m) REVERT: B 648 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7362 (mm-30) REVERT: B 758 GLN cc_start: 0.6432 (OUTLIER) cc_final: 0.5629 (mp10) REVERT: B 831 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8581 (p) REVERT: B 876 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7518 (mt-10) outliers start: 37 outliers final: 16 residues processed: 194 average time/residue: 0.9997 time to fit residues: 217.6392 Evaluate side-chains 182 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 758 GLN Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 93 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 167 optimal weight: 0.0980 chunk 66 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN B 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.132432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.098784 restraints weight = 49476.233| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.82 r_work: 0.3112 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13530 Z= 0.143 Angle : 0.540 14.891 18334 Z= 0.271 Chirality : 0.055 1.610 2022 Planarity : 0.004 0.046 2390 Dihedral : 5.035 79.057 1849 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.51 % Allowed : 24.30 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.22 (0.21), residues: 1714 helix: 1.10 (0.21), residues: 688 sheet: -0.46 (0.38), residues: 184 loop : -0.44 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 656 TYR 0.011 0.001 TYR B 113 PHE 0.009 0.001 PHE A 247 TRP 0.014 0.001 TRP B 651 HIS 0.006 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 (13530) covalent geometry : angle 0.53991 / 0.27 (18334) hydrogen bonds : bond 0.04087 / 2.74 ( 553) hydrogen bonds : angle 4.42959 / 3.24 ( 1545) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7118 (tp30) cc_final: 0.6809 (tp30) REVERT: A 671 ASP cc_start: 0.7123 (t0) cc_final: 0.6764 (t0) REVERT: A 744 ARG cc_start: 0.7268 (ttp80) cc_final: 0.6985 (ttp80) REVERT: B 58 MET cc_start: 0.8872 (mtp) cc_final: 0.8408 (mtm) REVERT: B 464 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6848 (tp30) REVERT: B 533 SER cc_start: 0.8650 (m) cc_final: 0.8349 (t) REVERT: B 545 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7353 (mp0) REVERT: B 546 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: B 572 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.5239 (mp0) REVERT: B 625 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6717 (mp) REVERT: B 626 SER cc_start: 0.7622 (t) cc_final: 0.7271 (m) REVERT: B 648 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7351 (mm-30) REVERT: B 719 LYS cc_start: 0.6996 (ttmt) cc_final: 0.6633 (tptt) REVERT: B 751 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7839 (mm-40) REVERT: B 758 GLN cc_start: 0.6392 (OUTLIER) cc_final: 0.5679 (mp10) REVERT: B 769 TYR cc_start: 0.7877 (t80) cc_final: 0.7624 (t80) REVERT: B 876 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7460 (mt-10) outliers start: 36 outliers final: 16 residues processed: 194 average time/residue: 1.0022 time to fit residues: 217.8528 Evaluate side-chains 179 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 758 GLN Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 802 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 63 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 92 optimal weight: 0.0170 chunk 31 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN B 773 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.096074 restraints weight = 49878.378| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.83 r_work: 0.3070 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13530 Z= 0.211 Angle : 0.587 14.951 18334 Z= 0.298 Chirality : 0.057 1.600 2022 Planarity : 0.005 0.065 2390 Dihedral : 5.127 79.800 1848 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.37 % Allowed : 24.72 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.05 (0.21), residues: 1714 helix: 0.93 (0.21), residues: 690 sheet: -0.61 (0.37), residues: 188 loop : -0.50 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 435 TYR 0.012 0.002 TYR B 757 PHE 0.013 0.002 PHE A 247 TRP 0.014 0.001 TRP B 651 HIS 0.005 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (13530) covalent geometry : angle 0.58688 / 0.30 (18334) hydrogen bonds : bond 0.04522 / 3.03 ( 553) hydrogen bonds : angle 4.51178 / 3.28 ( 1545) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7216 (tp30) cc_final: 0.6894 (tp30) REVERT: A 770 GLU cc_start: 0.8208 (mp0) cc_final: 0.7938 (mp0) REVERT: B 58 MET cc_start: 0.8975 (mtp) cc_final: 0.8502 (mtm) REVERT: B 464 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6957 (tp30) REVERT: B 533 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.8324 (t) REVERT: B 545 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7416 (mp0) REVERT: B 546 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: B 572 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5329 (mp0) REVERT: B 625 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6652 (mp) REVERT: B 626 SER cc_start: 0.7591 (t) cc_final: 0.7136 (m) REVERT: B 648 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7287 (mm-30) REVERT: B 719 LYS cc_start: 0.7357 (ttmt) cc_final: 0.6906 (tptt) REVERT: B 733 LYS cc_start: 0.8472 (tppt) cc_final: 0.8012 (pttm) REVERT: B 751 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7948 (mm110) REVERT: B 758 GLN cc_start: 0.6431 (OUTLIER) cc_final: 0.5691 (mp10) REVERT: B 795 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6882 (tppt) REVERT: B 817 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: B 831 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8652 (p) REVERT: B 876 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7578 (mt-10) outliers start: 34 outliers final: 18 residues processed: 197 average time/residue: 0.9664 time to fit residues: 213.6466 Evaluate side-chains 191 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 278 ASN Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 758 GLN Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.097036 restraints weight = 50039.399| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.82 r_work: 0.3081 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13530 Z= 0.179 Angle : 0.568 15.124 18334 Z= 0.288 Chirality : 0.057 1.670 2022 Planarity : 0.004 0.044 2390 Dihedral : 5.106 79.980 1848 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.23 % Allowed : 24.93 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.08 (0.21), residues: 1714 helix: 0.96 (0.21), residues: 688 sheet: -0.61 (0.37), residues: 188 loop : -0.48 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 656 TYR 0.010 0.001 TYR B 113 PHE 0.012 0.001 PHE A 247 TRP 0.012 0.001 TRP B 651 HIS 0.004 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (13530) covalent geometry : angle 0.56847 / 0.29 (18334) hydrogen bonds : bond 0.04340 / 2.91 ( 553) hydrogen bonds : angle 4.49973 / 3.28 ( 1545) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7175 (tp30) cc_final: 0.6859 (tp30) REVERT: A 528 VAL cc_start: 0.8370 (t) cc_final: 0.8144 (m) REVERT: A 744 ARG cc_start: 0.7404 (ttp80) cc_final: 0.7066 (ttp80) REVERT: A 770 GLU cc_start: 0.8211 (mp0) cc_final: 0.7935 (mp0) REVERT: B 58 MET cc_start: 0.8964 (mtp) cc_final: 0.7998 (mtt) REVERT: B 464 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6883 (tp30) REVERT: B 533 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8283 (t) REVERT: B 545 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7581 (mp0) REVERT: B 546 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: B 577 PHE cc_start: 0.7987 (m-80) cc_final: 0.7646 (m-80) REVERT: B 626 SER cc_start: 0.7484 (t) cc_final: 0.7069 (m) REVERT: B 648 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7217 (mm-30) REVERT: B 719 LYS cc_start: 0.7304 (ttmt) cc_final: 0.6925 (tptt) REVERT: B 751 GLN cc_start: 0.8259 (mm-40) cc_final: 0.8011 (mm110) REVERT: B 758 GLN cc_start: 0.6479 (OUTLIER) cc_final: 0.5815 (mp10) REVERT: B 795 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6831 (tppt) REVERT: B 817 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: B 831 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8635 (p) REVERT: B 876 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7580 (mt-10) outliers start: 32 outliers final: 17 residues processed: 188 average time/residue: 0.9479 time to fit residues: 199.8028 Evaluate side-chains 188 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 758 GLN Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 817 GLU Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 71 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 156 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 162 optimal weight: 0.5980 chunk 165 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN B 278 ASN ** B 791 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 = 0.131838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098450 restraints weight = 49414.038| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.82 r_work: 0.3106 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13530 Z= 0.116 Angle : 0.546 15.230 18334 Z= 0.272 Chirality : 0.056 1.661 2022 Planarity : 0.004 0.044 2390 Dihedral : 4.980 79.991 1848 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.53 % Allowed : 25.77 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.19 (0.21), residues: 1714 helix: 1.14 (0.21), residues: 688 sheet: -0.70 (0.38), residues: 172 loop : -0.47 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 656 TYR 0.012 0.001 TYR B 113 PHE 0.008 0.001 PHE B 540 TRP 0.015 0.001 TRP B 651 HIS 0.004 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (13530) covalent geometry : angle 0.54602 / 0.27 (18334) hydrogen bonds : bond 0.03926 / 2.62 ( 553) hydrogen bonds : angle 4.38438 / 3.19 ( 1545) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7166 (tp30) cc_final: 0.6881 (tp30) REVERT: A 528 VAL cc_start: 0.8421 (t) cc_final: 0.8201 (m) REVERT: A 744 ARG cc_start: 0.7427 (ttp80) cc_final: 0.7083 (ttp80) REVERT: B 58 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.7977 (mtt) REVERT: B 464 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6893 (tp30) REVERT: B 533 SER cc_start: 0.8496 (m) cc_final: 0.8287 (t) REVERT: B 545 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7734 (mp0) REVERT: B 546 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: B 626 SER cc_start: 0.7593 (t) cc_final: 0.7217 (m) REVERT: B 648 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7166 (mm-30) REVERT: B 719 LYS cc_start: 0.7420 (ttmt) cc_final: 0.7052 (tptt) REVERT: B 751 GLN cc_start: 0.8310 (mm-40) cc_final: 0.8014 (mm110) REVERT: B 795 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6913 (tppt) REVERT: B 831 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8623 (p) REVERT: B 876 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7528 (mt-10) outliers start: 22 outliers final: 12 residues processed: 178 average time/residue: 0.9589 time to fit residues: 191.2142 Evaluate side-chains 179 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 36 optimal weight: 0.0370 chunk 154 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN A 800 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.131466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098111 restraints weight = 49444.485| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.82 r_work: 0.3103 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13530 Z= 0.129 Angle : 0.544 15.159 18334 Z= 0.272 Chirality : 0.056 1.653 2022 Planarity : 0.004 0.045 2390 Dihedral : 4.944 80.168 1848 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.46 % Allowed : 25.77 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.24 (0.21), residues: 1714 helix: 1.19 (0.21), residues: 688 sheet: -0.74 (0.37), residues: 176 loop : -0.43 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 656 TYR 0.012 0.001 TYR B 769 PHE 0.008 0.001 PHE A 819 TRP 0.013 0.001 TRP B 651 HIS 0.004 0.001 HIS A 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (13530) covalent geometry : angle 0.54405 / 0.27 (18334) hydrogen bonds : bond 0.03946 / 2.64 ( 553) hydrogen bonds : angle 4.35466 / 3.17 ( 1545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7670.54 seconds wall clock time: 146 minutes 42.94 seconds (8802.94 seconds total)