Starting phenix.real_space_refine on Mon Aug 25 07:53:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctm_45911/08_2025/9ctm_45911.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctm_45911/08_2025/9ctm_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ctm_45911/08_2025/9ctm_45911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctm_45911/08_2025/9ctm_45911.map" model { file = "/net/cci-nas-00/data/ceres_data/9ctm_45911/08_2025/9ctm_45911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctm_45911/08_2025/9ctm_45911.cif" } 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-2.0-5787/lib/python3.9/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: 8 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: 8 Planarities with less than four sites: {'SCY:plan-1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.99, per 1000 atoms: 0.19 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: 2.55 Conformation dependent library (CDL) restraints added in 862.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.79 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: 6.88 Time building geometry restraints manager: 3.44 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 1.703 1.816 -0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" SG SCY B 187 " pdb=" CD SCY B 187 " ideal model delta sigma weight residual 1.703 1.815 -0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" CD SCY A 187 " pdb=" OCD SCY A 187 " ideal model delta sigma weight residual 1.239 1.185 0.054 2.00e-02 2.50e+03 7.28e+00 bond pdb=" CD SCY B 187 " pdb=" OCD SCY B 187 " ideal model delta sigma weight residual 1.239 1.185 0.054 2.00e-02 2.50e+03 7.17e+00 bond pdb=" CA SCY B 187 " pdb=" C SCY B 187 " ideal model delta sigma weight residual 1.575 1.530 0.045 2.00e-02 2.50e+03 5.12e+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: 1170 35.89 - 53.83: 352 53.83 - 71.77: 105 71.77 - 89.72: 18 Dihedral angle restraints: 12608 sinusoidal: 6862 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 12605 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=" CA SCY B 187 " pdb=" N SCY B 187 " pdb=" C SCY B 187 " pdb=" CB SCY B 187 " both_signs ideal model delta sigma weight residual False 2.39 2.57 -0.18 2.00e-01 2.50e+01 8.24e-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 ... (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: 0.03 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: 0.170 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.500 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 13530 Z= 0.132 Angle : 0.548 14.437 18334 Z= 0.269 Chirality : 0.054 1.593 2022 Planarity : 0.004 0.088 2390 Dihedral : 17.011 89.718 4978 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 aren 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 covalent geometry : bond 0.00288 (13530) covalent geometry : angle 0.54849 (18334) hydrogen bonds : bond 0.15947 ( 553) hydrogen bonds : angle 6.54100 ( 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 : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.7848 (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: 0.7719 (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: 0.7337 (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: 0.9695 time to fit residues: 271.7306 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 : 0.782 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3672 r_free = 0.3672 target = 0.135436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100875 restraints weight = 49686.915| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.90 r_work: 0.3137 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 13530 Z= 0.212 Angle : 0.652 15.730 18334 Z= 0.338 Chirality : 0.059 1.650 2022 Planarity : 0.005 0.049 2390 Dihedral : 4.273 50.383 1841 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.13 % Allowed : 23.96 % 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 aren not related in a simple way. whole: -0.04 (0.20), residues: 1714 helix: 0.79 (0.20), residues: 686 sheet: -0.89 (0.39), residues: 156 loop : -0.44 (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 0.020 0.002 PHE B 819 TRP 0.014 0.002 TRP B 651 HIS 0.010 0.002 HIS B 604 Details of bonding type rmsd covalent geometry : bond 0.00485 (13530) covalent geometry : angle 0.65230 (18334) hydrogen bonds : bond 0.05023 ( 553) hydrogen bonds : angle 4.91753 ( 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 209 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.8573 (tpt) cc_final: 0.8354 (tpt) REVERT: A 464 GLU cc_start: 0.7097 (tp30) cc_final: 0.6723 (tp30) REVERT: A 671 ASP cc_start: 0.7347 (t0) cc_final: 0.7111 (t0) REVERT: A 695 THR cc_start: 0.7710 (OUTLIER) cc_final: 0.7379 (p) REVERT: A 752 THR cc_start: 0.6758 (OUTLIER) cc_final: 0.6160 (t) REVERT: A 795 LYS cc_start: 0.8674 (tppt) cc_final: 0.7736 (ttmt) REVERT: B 58 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.6506 (mpp) REVERT: B 96 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7443 (mtpt) REVERT: B 224 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7659 (mtpt) REVERT: B 648 GLU cc_start: 0.7883 (mt-10) cc_final: 0.6892 (mm-30) REVERT: B 653 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: B 831 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8260 (m) outliers start: 45 outliers final: 19 residues processed: 198 average time/residue: 1.0796 time to fit residues: 240.7425 Evaluate side-chains 169 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 694 VAL 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 330 THR 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 653 GLU 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: 0.0670 chunk 135 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3740 r_free = 0.3740 target = 0.138917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105344 restraints weight = 49685.003| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.82 r_work: 0.3208 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13530 Z= 0.115 Angle : 0.529 14.796 18334 Z= 0.263 Chirality : 0.055 1.634 2022 Planarity : 0.004 0.042 2390 Dihedral : 3.886 48.891 1839 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.16 % Allowed : 24.65 % 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 aren not related in a simple way. whole: 0.30 (0.21), residues: 1714 helix: 1.21 (0.21), residues: 686 sheet: -0.98 (0.36), residues: 186 loop : -0.28 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 199 TYR 0.010 0.001 TYR A 113 PHE 0.012 0.001 PHE A 685 TRP 0.012 0.001 TRP B 651 HIS 0.009 0.001 HIS B 667 Details of bonding type rmsd covalent geometry : bond 0.00271 (13530) covalent geometry : angle 0.52854 (18334) hydrogen bonds : bond 0.04369 ( 553) hydrogen bonds : angle 4.60363 ( 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 193 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.6896 (tp30) cc_final: 0.6551 (tp30) REVERT: A 671 ASP cc_start: 0.7425 (t0) cc_final: 0.7190 (t0) REVERT: A 695 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7310 (p) REVERT: A 752 THR cc_start: 0.6771 (OUTLIER) cc_final: 0.6177 (t) REVERT: A 795 LYS cc_start: 0.8560 (tppt) cc_final: 0.7640 (ttmt) REVERT: B 58 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.6643 (mpp) REVERT: B 224 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7596 (mtpt) REVERT: B 373 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8290 (tpp) REVERT: B 648 GLU cc_start: 0.7794 (mt-10) cc_final: 0.6847 (mm-30) REVERT: B 796 LYS cc_start: 0.7642 (ttmm) cc_final: 0.7100 (mmmt) REVERT: B 831 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8311 (m) outliers start: 31 outliers final: 10 residues processed: 185 average time/residue: 1.1573 time to fit residues: 239.6746 Evaluate side-chains 163 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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 373 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: 1.9990 chunk 117 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 507 GLN ** B 581 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 = 0.3693 r_free = 0.3693 target = 0.134967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.101004 restraints weight = 49399.589| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.82 r_work: 0.3143 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13530 Z= 0.176 Angle : 0.566 13.645 18334 Z= 0.287 Chirality : 0.056 1.609 2022 Planarity : 0.004 0.043 2390 Dihedral : 3.975 47.555 1838 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.65 % Allowed : 24.44 % 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 aren not related in a simple way. whole: 0.22 (0.21), residues: 1714 helix: 1.11 (0.21), residues: 684 sheet: -0.57 (0.37), residues: 184 loop : -0.43 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 514 TYR 0.013 0.001 TYR B 757 PHE 0.010 0.001 PHE A 247 TRP 0.016 0.001 TRP B 651 HIS 0.017 0.001 HIS B 667 Details of bonding type rmsd covalent geometry : bond 0.00426 (13530) covalent geometry : angle 0.56592 (18334) hydrogen bonds : bond 0.04450 ( 553) hydrogen bonds : angle 4.54212 ( 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 201 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7105 (tp30) cc_final: 0.6764 (tp30) REVERT: A 523 MET cc_start: 0.8259 (mmm) cc_final: 0.7864 (mmm) REVERT: A 695 THR cc_start: 0.7626 (OUTLIER) cc_final: 0.7304 (p) REVERT: A 744 ARG cc_start: 0.7414 (ttp80) cc_final: 0.7042 (ttp80) REVERT: A 752 THR cc_start: 0.7029 (OUTLIER) cc_final: 0.6444 (t) REVERT: A 795 LYS cc_start: 0.8671 (tppt) cc_final: 0.7841 (ttmt) REVERT: B 58 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8297 (mtp) REVERT: B 224 LYS cc_start: 0.8251 (mtpp) cc_final: 0.7715 (mtpp) REVERT: B 546 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: B 572 GLU cc_start: 0.5941 (OUTLIER) cc_final: 0.5131 (mp0) REVERT: B 626 SER cc_start: 0.7805 (OUTLIER) cc_final: 0.7390 (m) REVERT: B 648 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7171 (mm-30) REVERT: B 651 TRP cc_start: 0.7669 (t-100) cc_final: 0.7373 (t-100) REVERT: B 758 GLN cc_start: 0.6414 (OUTLIER) cc_final: 0.5555 (mp10) REVERT: B 831 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8483 (p) outliers start: 38 outliers final: 14 residues processed: 193 average time/residue: 1.1839 time to fit residues: 254.7386 Evaluate side-chains 173 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 363 ILE 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 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 831 VAL 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: 2.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3691 r_free = 0.3691 target = 0.134920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.100930 restraints weight = 49202.693| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.82 r_work: 0.3142 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13530 Z= 0.140 Angle : 0.539 14.869 18334 Z= 0.269 Chirality : 0.055 1.609 2022 Planarity : 0.004 0.044 2390 Dihedral : 3.914 45.869 1838 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.72 % Allowed : 24.65 % Favored : 72.63 % 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 aren not related in a simple way. whole: 0.22 (0.21), residues: 1714 helix: 1.14 (0.21), residues: 688 sheet: -0.68 (0.37), residues: 172 loop : -0.43 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.010 0.001 TYR A 113 PHE 0.022 0.001 PHE A 685 TRP 0.009 0.001 TRP B 527 HIS 0.004 0.001 HIS A 829 Details of bonding type rmsd covalent geometry : bond 0.00334 (13530) covalent geometry : angle 0.53867 (18334) hydrogen bonds : bond 0.04161 ( 553) hydrogen bonds : angle 4.46699 ( 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 202 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7096 (tp30) cc_final: 0.6769 (tp30) REVERT: A 671 ASP cc_start: 0.7122 (t0) cc_final: 0.6793 (t0) REVERT: A 695 THR cc_start: 0.7449 (OUTLIER) cc_final: 0.7153 (p) REVERT: A 752 THR cc_start: 0.7139 (OUTLIER) cc_final: 0.6574 (t) REVERT: A 795 LYS cc_start: 0.8627 (tppt) cc_final: 0.7835 (ttmt) REVERT: B 58 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.6826 (mpp) REVERT: B 224 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7742 (mtpp) REVERT: B 464 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6805 (tp30) REVERT: B 546 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: B 572 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5204 (mp0) REVERT: B 626 SER cc_start: 0.7692 (t) cc_final: 0.7293 (m) REVERT: B 648 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7225 (mm-30) REVERT: B 651 TRP cc_start: 0.7598 (t-100) cc_final: 0.7275 (t-100) REVERT: B 674 THR cc_start: 0.7685 (m) cc_final: 0.7455 (m) REVERT: B 758 GLN cc_start: 0.6309 (OUTLIER) cc_final: 0.5597 (mp10) REVERT: B 831 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8522 (p) outliers start: 39 outliers final: 17 residues processed: 194 average time/residue: 1.1734 time to fit residues: 253.5805 Evaluate side-chains 180 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 561 LEU 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 A residue 794 ILE 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 303 SER 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 546 GLU Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 758 GLN Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 831 VAL 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: 8.9990 chunk 17 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3659 r_free = 0.3659 target = 0.132352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.098167 restraints weight = 49739.229| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.84 r_work: 0.3102 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13530 Z= 0.184 Angle : 0.564 14.759 18334 Z= 0.284 Chirality : 0.056 1.608 2022 Planarity : 0.004 0.043 2390 Dihedral : 4.010 44.667 1838 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.65 % Allowed : 24.16 % 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 aren not related in a simple way. whole: 0.14 (0.21), residues: 1714 helix: 1.03 (0.21), residues: 686 sheet: -0.56 (0.37), residues: 184 loop : -0.47 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.011 0.001 TYR B 113 PHE 0.011 0.001 PHE A 247 TRP 0.008 0.001 TRP B 527 HIS 0.005 0.001 HIS A 829 Details of bonding type rmsd covalent geometry : bond 0.00449 (13530) covalent geometry : angle 0.56397 (18334) hydrogen bonds : bond 0.04373 ( 553) hydrogen bonds : angle 4.49606 ( 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 204 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7155 (tp30) cc_final: 0.6828 (tp30) REVERT: A 671 ASP cc_start: 0.7132 (t0) cc_final: 0.6838 (t0) REVERT: A 695 THR cc_start: 0.7353 (OUTLIER) cc_final: 0.7059 (p) REVERT: A 744 ARG cc_start: 0.7243 (ttp80) cc_final: 0.6966 (ttp80) REVERT: A 752 THR cc_start: 0.7261 (OUTLIER) cc_final: 0.6711 (t) REVERT: A 795 LYS cc_start: 0.8663 (tppt) cc_final: 0.7870 (ttmt) REVERT: B 464 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6866 (tp30) REVERT: B 533 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8273 (t) REVERT: B 535 MET cc_start: 0.8430 (mmt) cc_final: 0.8132 (mmm) REVERT: B 546 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: B 572 GLU cc_start: 0.5979 (OUTLIER) cc_final: 0.5174 (mp0) REVERT: B 620 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7293 (ttm170) REVERT: B 626 SER cc_start: 0.7702 (OUTLIER) cc_final: 0.7319 (m) REVERT: B 648 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7372 (mm-30) REVERT: B 651 TRP cc_start: 0.7511 (t-100) cc_final: 0.7214 (t-100) REVERT: B 758 GLN cc_start: 0.6435 (OUTLIER) cc_final: 0.5615 (mp10) REVERT: B 831 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8609 (p) REVERT: B 876 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7469 (mt-10) outliers start: 38 outliers final: 19 residues processed: 195 average time/residue: 1.2210 time to fit residues: 265.0914 Evaluate side-chains 189 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 205 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 561 LEU 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 82 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 276 LEU 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 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 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 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: 3.9990 chunk 148 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 122 optimal weight: 0.0970 chunk 126 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 167 optimal weight: 0.3980 chunk 66 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.133128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.099301 restraints weight = 49520.094| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.84 r_work: 0.3119 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13530 Z= 0.129 Angle : 0.541 14.860 18334 Z= 0.270 Chirality : 0.055 1.615 2022 Planarity : 0.004 0.070 2390 Dihedral : 3.922 42.951 1838 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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 aren not related in a simple way. whole: 0.26 (0.21), residues: 1714 helix: 1.15 (0.21), residues: 688 sheet: -0.53 (0.37), residues: 184 loop : -0.42 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 656 TYR 0.011 0.001 TYR B 113 PHE 0.012 0.001 PHE A 418 TRP 0.008 0.001 TRP B 527 HIS 0.006 0.001 HIS B 667 Details of bonding type rmsd covalent geometry : bond 0.00314 (13530) covalent geometry : angle 0.54066 (18334) hydrogen bonds : bond 0.04023 ( 553) hydrogen bonds : angle 4.41621 ( 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 200 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7144 (tp30) cc_final: 0.6820 (tp30) REVERT: A 744 ARG cc_start: 0.7227 (ttp80) cc_final: 0.6932 (ttp80) REVERT: B 464 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6879 (tp30) REVERT: B 533 SER cc_start: 0.8642 (m) cc_final: 0.8335 (t) REVERT: B 535 MET cc_start: 0.8437 (mmt) cc_final: 0.8130 (mmm) REVERT: B 546 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: B 572 GLU cc_start: 0.6040 (OUTLIER) cc_final: 0.5269 (mp0) REVERT: B 625 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6684 (mp) REVERT: B 626 SER cc_start: 0.7675 (t) cc_final: 0.7318 (m) REVERT: B 648 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7394 (mm-30) REVERT: B 651 TRP cc_start: 0.7562 (t-100) cc_final: 0.7331 (t-100) REVERT: B 719 LYS cc_start: 0.6975 (ttmt) cc_final: 0.6495 (tptt) REVERT: B 751 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7818 (mm110) REVERT: B 758 GLN cc_start: 0.6422 (OUTLIER) cc_final: 0.5641 (mp10) REVERT: B 831 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8592 (p) REVERT: B 876 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7414 (mt-10) outliers start: 36 outliers final: 18 residues processed: 189 average time/residue: 1.2194 time to fit residues: 257.3514 Evaluate side-chains 179 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 561 LEU 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 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 617 CYS Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 697 LYS 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=2.00 ------------------------------------------------------------------------------- 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: 2.9990 chunk 92 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3616 r_free = 0.3616 target = 0.128856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.095040 restraints weight = 49888.668| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.81 r_work: 0.3051 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13530 Z= 0.253 Angle : 0.632 14.977 18334 Z= 0.321 Chirality : 0.058 1.594 2022 Planarity : 0.005 0.062 2390 Dihedral : 4.116 17.602 1836 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.58 % Allowed : 24.93 % Favored : 72.49 % 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 aren not related in a simple way. whole: -0.13 (0.20), residues: 1714 helix: 0.80 (0.20), residues: 688 sheet: -0.69 (0.37), residues: 188 loop : -0.61 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 435 TYR 0.013 0.002 TYR B 302 PHE 0.015 0.002 PHE A 247 TRP 0.010 0.002 TRP B 629 HIS 0.008 0.002 HIS B 667 Details of bonding type rmsd covalent geometry : bond 0.00615 (13530) covalent geometry : angle 0.63191 (18334) hydrogen bonds : bond 0.04926 ( 553) hydrogen bonds : angle 4.63018 ( 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 213 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7852 (mtm) REVERT: A 373 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8732 (mtp) REVERT: A 464 GLU cc_start: 0.7145 (tp30) cc_final: 0.6824 (tp30) REVERT: A 669 SER cc_start: 0.7791 (t) cc_final: 0.7364 (p) REVERT: A 671 ASP cc_start: 0.7179 (t0) cc_final: 0.6940 (t0) REVERT: A 697 LYS cc_start: 0.7464 (ttmt) cc_final: 0.7243 (ttmm) REVERT: A 770 GLU cc_start: 0.8207 (mp0) cc_final: 0.7927 (mp0) REVERT: B 58 MET cc_start: 0.8972 (mtp) cc_final: 0.8712 (mtm) REVERT: B 404 GLU cc_start: 0.7718 (pt0) cc_final: 0.7490 (mt-10) REVERT: B 464 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6988 (tp30) REVERT: B 533 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8336 (t) REVERT: B 545 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7433 (mp0) REVERT: B 546 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: B 572 GLU cc_start: 0.6199 (OUTLIER) cc_final: 0.5364 (mp0) REVERT: B 620 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7741 (ttm110) REVERT: B 625 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6734 (mp) REVERT: B 626 SER cc_start: 0.7614 (OUTLIER) cc_final: 0.7166 (m) REVERT: B 648 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7265 (mm-30) REVERT: B 719 LYS cc_start: 0.7228 (ttmt) cc_final: 0.6906 (tptt) REVERT: B 751 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7968 (mm110) REVERT: B 758 GLN cc_start: 0.6504 (OUTLIER) cc_final: 0.5744 (mp10) REVERT: B 769 TYR cc_start: 0.7976 (t80) cc_final: 0.7764 (t80) REVERT: B 831 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8648 (p) REVERT: B 876 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7541 (mt-10) outliers start: 37 outliers final: 17 residues processed: 203 average time/residue: 1.0701 time to fit residues: 240.9306 Evaluate side-chains 198 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 561 LEU 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 767 LEU 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 620 ARG Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 676 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 90 optimal weight: 0.0170 chunk 104 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 139 optimal weight: 0.2980 chunk 69 optimal weight: 2.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN B 773 GLN ** 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 = 0.3645 r_free = 0.3645 target = 0.131333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.097694 restraints weight = 49534.072| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.84 r_work: 0.3094 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13530 Z= 0.122 Angle : 0.559 14.937 18334 Z= 0.280 Chirality : 0.056 1.692 2022 Planarity : 0.004 0.044 2390 Dihedral : 3.914 19.293 1836 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.09 % Allowed : 25.77 % Favored : 72.14 % 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 aren not related in a simple way. whole: 0.12 (0.21), residues: 1714 helix: 1.04 (0.21), residues: 688 sheet: -0.59 (0.37), residues: 184 loop : -0.51 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 656 TYR 0.012 0.001 TYR B 113 PHE 0.013 0.001 PHE B 577 TRP 0.013 0.001 TRP B 651 HIS 0.005 0.001 HIS A 829 Details of bonding type rmsd covalent geometry : bond 0.00293 (13530) covalent geometry : angle 0.55862 (18334) hydrogen bonds : bond 0.04123 ( 553) hydrogen bonds : angle 4.47174 ( 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 197 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7181 (tp30) cc_final: 0.6875 (tp30) REVERT: A 528 VAL cc_start: 0.8334 (t) cc_final: 0.8107 (m) REVERT: A 697 LYS cc_start: 0.7481 (ttmt) cc_final: 0.7271 (ttmm) REVERT: A 744 ARG cc_start: 0.7373 (ttp80) cc_final: 0.7046 (ttp80) REVERT: B 58 MET cc_start: 0.8939 (mtp) cc_final: 0.8583 (mtm) REVERT: B 404 GLU cc_start: 0.7690 (pt0) cc_final: 0.7485 (mt-10) REVERT: B 464 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6870 (tp30) REVERT: B 533 SER cc_start: 0.8537 (m) cc_final: 0.8313 (t) REVERT: B 545 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7564 (mp0) REVERT: B 546 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: B 572 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5435 (mp0) REVERT: B 620 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7651 (ttm110) REVERT: B 626 SER cc_start: 0.7535 (t) cc_final: 0.7162 (m) REVERT: B 648 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7295 (mm-30) REVERT: B 719 LYS cc_start: 0.7375 (ttmt) cc_final: 0.6924 (tptt) REVERT: B 744 ARG cc_start: 0.7478 (mtm110) cc_final: 0.7212 (mtp180) REVERT: B 751 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7910 (mm110) REVERT: B 769 TYR cc_start: 0.8027 (t80) cc_final: 0.7738 (t80) REVERT: B 831 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8615 (p) REVERT: B 876 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7473 (mt-10) outliers start: 30 outliers final: 13 residues processed: 187 average time/residue: 1.1368 time to fit residues: 235.1534 Evaluate side-chains 180 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 794 ILE 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 572 GLU Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 697 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 85 optimal weight: 0.0370 chunk 145 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN B 54 ASN B 278 ASN B 791 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098619 restraints weight = 49270.891| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.84 r_work: 0.3108 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13530 Z= 0.115 Angle : 0.551 15.154 18334 Z= 0.274 Chirality : 0.056 1.669 2022 Planarity : 0.004 0.045 2390 Dihedral : 3.802 19.759 1836 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.32 % Allowed : 26.39 % Favored : 72.28 % 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 aren not related in a simple way. whole: 0.19 (0.21), residues: 1714 helix: 1.16 (0.21), residues: 688 sheet: -0.76 (0.37), residues: 172 loop : -0.48 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 656 TYR 0.011 0.001 TYR B 757 PHE 0.008 0.001 PHE A 418 TRP 0.015 0.001 TRP B 651 HIS 0.005 0.001 HIS A 829 Details of bonding type rmsd covalent geometry : bond 0.00280 (13530) covalent geometry : angle 0.55088 (18334) hydrogen bonds : bond 0.03933 ( 553) hydrogen bonds : angle 4.38460 ( 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 184 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7149 (tp30) cc_final: 0.6843 (tp30) REVERT: A 528 VAL cc_start: 0.8340 (t) cc_final: 0.8116 (m) REVERT: A 697 LYS cc_start: 0.7317 (ttmt) cc_final: 0.7103 (ttmm) REVERT: A 744 ARG cc_start: 0.7423 (ttp80) cc_final: 0.7065 (ttp80) REVERT: B 58 MET cc_start: 0.8939 (mtp) cc_final: 0.8581 (mtm) REVERT: B 404 GLU cc_start: 0.7720 (pt0) cc_final: 0.7506 (mt-10) REVERT: B 464 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6857 (tp30) REVERT: B 533 SER cc_start: 0.8519 (m) cc_final: 0.8298 (t) REVERT: B 545 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7559 (mp0) REVERT: B 546 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: B 572 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5451 (mp0) REVERT: B 620 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7618 (ttm110) REVERT: B 626 SER cc_start: 0.7648 (t) cc_final: 0.7215 (m) REVERT: B 644 MET cc_start: 0.7842 (mtt) cc_final: 0.7439 (mtt) REVERT: B 648 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7402 (mm-30) REVERT: B 719 LYS cc_start: 0.7290 (ttmt) cc_final: 0.6903 (tptt) REVERT: B 744 ARG cc_start: 0.7496 (mtm110) cc_final: 0.7226 (mtp180) REVERT: B 751 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7969 (mm110) REVERT: B 769 TYR cc_start: 0.8006 (t80) cc_final: 0.7719 (t80) REVERT: B 831 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8614 (p) REVERT: B 876 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7496 (mt-10) outliers start: 19 outliers final: 11 residues processed: 180 average time/residue: 1.1550 time to fit residues: 229.4850 Evaluate side-chains 179 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 794 ILE Chi-restraints excluded: chain B residue 82 THR 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 676 SER Chi-restraints excluded: chain B residue 697 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 36 optimal weight: 0.0000 chunk 154 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3657 r_free = 0.3657 target = 0.132360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.098879 restraints weight = 49257.758| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.84 r_work: 0.3111 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13530 Z= 0.115 Angle : 0.545 15.033 18334 Z= 0.271 Chirality : 0.056 1.649 2022 Planarity : 0.004 0.045 2390 Dihedral : 3.726 20.014 1836 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.32 % Allowed : 26.11 % Favored : 72.56 % 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 aren not related in a simple way. whole: 0.26 (0.21), residues: 1714 helix: 1.25 (0.21), residues: 688 sheet: -0.74 (0.37), residues: 172 loop : -0.46 (0.22), residues: 854 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 0.008 0.001 PHE A 819 TRP 0.016 0.001 TRP B 651 HIS 0.005 0.001 HIS A 829 Details of bonding type rmsd covalent geometry : bond 0.00278 (13530) covalent geometry : angle 0.54525 (18334) hydrogen bonds : bond 0.03860 ( 553) hydrogen bonds : angle 4.34276 ( 1545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8494.26 seconds wall clock time: 144 minutes 46.19 seconds (8686.19 seconds total)