Starting phenix.real_space_refine on Sun Jun 22 19:52:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctm_45911/06_2025/9ctm_45911.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctm_45911/06_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_45911/06_2025/9ctm_45911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctm_45911/06_2025/9ctm_45911.map" model { file = "/net/cci-nas-00/data/ceres_data/9ctm_45911/06_2025/9ctm_45911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctm_45911/06_2025/9ctm_45911.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 1, 'SCY:plan-1': 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: {'TYR:plan': 1, 'SCY:plan-1': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 15.55, per 1000 atoms: 0.59 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: 7.67 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.61 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: 16.82 Time building geometry restraints manager: 8.95 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: 0.12 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: 190.570 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: 0.540 Extract box with map and model: 1.100 Check model and map are aligned: 0.240 Set scattering table: 0.230 Process input model: 68.100 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:17.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 279.990 ------------------------------------------------------------------------------- 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 : 7.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP B 651 HIS 0.019 0.001 HIS A 829 PHE 0.011 0.001 PHE A 819 TYR 0.011 0.001 TYR A 706 ARG 0.004 0.000 ARG B 621 Details of bonding type rmsd hydrogen bonds : bond 0.15947 ( 553) hydrogen bonds : angle 6.54100 ( 1545) covalent geometry : bond 0.00288 (13530) covalent geometry : angle 0.54849 (18334) *********************** 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 : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.7848 (mtt) cc_final: 0.7631 (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: 0.7187 (mt-10) outliers start: 6 outliers final: 3 residues processed: 246 average time/residue: 1.8278 time to fit residues: 515.6902 Evaluate side-chains 172 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 168 time to evaluate : 2.081 ------------------------------------------------------------------------------- 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 145 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 328 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.098267 restraints weight = 49913.678| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.90 r_work: 0.3099 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 13530 Z= 0.276 Angle : 0.709 15.645 18334 Z= 0.370 Chirality : 0.061 1.652 2022 Planarity : 0.006 0.062 2390 Dihedral : 4.673 51.003 1841 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.48 % Allowed : 23.47 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.20), residues: 1714 helix: 0.45 (0.20), residues: 684 sheet: -1.15 (0.39), residues: 150 loop : -0.67 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 651 HIS 0.010 0.002 HIS A 829 PHE 0.023 0.002 PHE B 819 TYR 0.022 0.002 TYR B 520 ARG 0.009 0.001 ARG B 492 Details of bonding type rmsd hydrogen bonds : bond 0.05613 ( 553) hydrogen bonds : angle 5.06035 ( 1545) covalent geometry : bond 0.00648 (13530) covalent geometry : angle 0.70883 (18334) *********************** 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 221 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7136 (tp30) cc_final: 0.6778 (tp30) REVERT: A 669 SER cc_start: 0.8046 (t) cc_final: 0.7449 (p) REVERT: A 671 ASP cc_start: 0.7440 (t0) cc_final: 0.7181 (t0) REVERT: A 695 THR cc_start: 0.7730 (OUTLIER) cc_final: 0.7397 (p) REVERT: A 744 ARG cc_start: 0.7112 (ttp80) cc_final: 0.6888 (ttp-110) REVERT: A 752 THR cc_start: 0.6935 (OUTLIER) cc_final: 0.6343 (t) REVERT: A 795 LYS cc_start: 0.8711 (tppt) cc_final: 0.7729 (ttmt) REVERT: B 224 LYS cc_start: 0.8252 (mtpp) cc_final: 0.7747 (mtpp) REVERT: B 626 SER cc_start: 0.7787 (OUTLIER) cc_final: 0.7507 (m) REVERT: B 648 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7026 (mm-30) REVERT: B 680 GLN cc_start: 0.6713 (mp10) cc_final: 0.6509 (mp10) REVERT: B 686 MET cc_start: 0.8152 (mtp) cc_final: 0.7919 (mtp) REVERT: B 796 LYS cc_start: 0.7719 (ttmm) cc_final: 0.7134 (mmmt) REVERT: B 831 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8480 (m) REVERT: B 873 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7933 (mp0) outliers start: 50 outliers final: 20 residues processed: 208 average time/residue: 2.0750 time to fit residues: 488.2550 Evaluate side-chains 178 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 2.155 ------------------------------------------------------------------------------- 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 444 LYS 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 82 THR 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 533 SER Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 637 CYS Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 873 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 758 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 = 0.3692 r_free = 0.3692 target = 0.134978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.101174 restraints weight = 49385.428| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.82 r_work: 0.3145 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13530 Z= 0.162 Angle : 0.559 14.750 18334 Z= 0.283 Chirality : 0.056 1.620 2022 Planarity : 0.004 0.042 2390 Dihedral : 4.157 49.855 1839 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.23 % Allowed : 25.07 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1714 helix: 0.92 (0.21), residues: 684 sheet: -1.20 (0.36), residues: 188 loop : -0.45 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 651 HIS 0.005 0.001 HIS A 829 PHE 0.011 0.001 PHE A 247 TYR 0.010 0.001 TYR A 827 ARG 0.004 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.04763 ( 553) hydrogen bonds : angle 4.74059 ( 1545) covalent geometry : bond 0.00375 (13530) covalent geometry : angle 0.55920 (18334) *********************** 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 190 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7032 (tp30) cc_final: 0.6713 (tp30) REVERT: A 695 THR cc_start: 0.7737 (OUTLIER) cc_final: 0.7405 (p) REVERT: A 752 THR cc_start: 0.7005 (OUTLIER) cc_final: 0.6406 (t) REVERT: A 795 LYS cc_start: 0.8695 (tppt) cc_final: 0.7883 (ttmm) REVERT: B 77 MET cc_start: 0.8431 (ttm) cc_final: 0.8071 (ttm) REVERT: B 224 LYS cc_start: 0.8277 (mtpp) cc_final: 0.7743 (mtpp) REVERT: B 464 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6790 (tp30) REVERT: B 620 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6793 (ttm170) REVERT: B 626 SER cc_start: 0.7799 (t) cc_final: 0.7306 (m) REVERT: B 648 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7123 (mm-30) REVERT: B 680 GLN cc_start: 0.6794 (mp10) cc_final: 0.6593 (mp10) REVERT: B 686 MET cc_start: 0.8093 (mtp) cc_final: 0.7880 (mtp) REVERT: B 758 GLN cc_start: 0.6181 (OUTLIER) cc_final: 0.5407 (mp10) REVERT: B 795 LYS cc_start: 0.6562 (tppt) cc_final: 0.6267 (tppt) REVERT: B 831 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8522 (m) outliers start: 32 outliers final: 13 residues processed: 184 average time/residue: 2.1921 time to fit residues: 452.3686 Evaluate side-chains 167 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 794 ILE 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 533 SER Chi-restraints excluded: chain B residue 620 ARG 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 151 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 54 ASN ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101502 restraints weight = 49682.342| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.83 r_work: 0.3150 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4033 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= 0.127 Angle : 0.533 14.687 18334 Z= 0.266 Chirality : 0.055 1.618 2022 Planarity : 0.004 0.043 2390 Dihedral : 3.949 47.528 1838 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.58 % Allowed : 24.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1714 helix: 1.08 (0.21), residues: 684 sheet: -0.76 (0.37), residues: 172 loop : -0.46 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 651 HIS 0.005 0.001 HIS A 829 PHE 0.010 0.001 PHE A 685 TYR 0.011 0.001 TYR B 113 ARG 0.002 0.000 ARG B 514 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 553) hydrogen bonds : angle 4.51318 ( 1545) covalent geometry : bond 0.00303 (13530) covalent geometry : angle 0.53275 (18334) *********************** 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 195 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7078 (tp30) cc_final: 0.6757 (tp30) REVERT: A 507 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7353 (pt0) REVERT: A 671 ASP cc_start: 0.7131 (t0) cc_final: 0.6827 (t0) REVERT: A 695 THR cc_start: 0.7629 (OUTLIER) cc_final: 0.7327 (p) REVERT: A 744 ARG cc_start: 0.7233 (ttp80) cc_final: 0.6938 (ttp80) REVERT: A 752 THR cc_start: 0.7097 (OUTLIER) cc_final: 0.6531 (t) REVERT: A 795 LYS cc_start: 0.8669 (tppt) cc_final: 0.7809 (ttmt) REVERT: B 77 MET cc_start: 0.8320 (ttm) cc_final: 0.7983 (ttm) REVERT: B 224 LYS cc_start: 0.8276 (mtpp) cc_final: 0.7724 (mtpp) REVERT: B 464 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6766 (tp30) REVERT: B 546 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7430 (mt-10) REVERT: B 626 SER cc_start: 0.7761 (t) cc_final: 0.7308 (m) REVERT: B 648 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7173 (mm-30) REVERT: B 758 GLN cc_start: 0.6351 (OUTLIER) cc_final: 0.5515 (mp10) REVERT: B 795 LYS cc_start: 0.6646 (tppt) cc_final: 0.6325 (tppt) REVERT: B 831 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8559 (m) outliers start: 37 outliers final: 13 residues processed: 185 average time/residue: 2.1769 time to fit residues: 451.9809 Evaluate side-chains 171 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 2.055 ------------------------------------------------------------------------------- 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 507 GLN 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 464 GLU Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 546 GLU 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 93 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN B 168 ASN ** 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 = 0.3653 r_free = 0.3653 target = 0.131799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.097780 restraints weight = 49679.981| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.83 r_work: 0.3094 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 13530 Z= 0.214 Angle : 0.580 14.873 18334 Z= 0.295 Chirality : 0.057 1.596 2022 Planarity : 0.004 0.046 2390 Dihedral : 4.117 46.845 1838 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.06 % Allowed : 24.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1714 helix: 0.91 (0.21), residues: 686 sheet: -0.70 (0.37), residues: 186 loop : -0.49 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 527 HIS 0.008 0.001 HIS B 667 PHE 0.015 0.001 PHE A 685 TYR 0.011 0.001 TYR B 113 ARG 0.004 0.000 ARG B 620 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 553) hydrogen bonds : angle 4.60066 ( 1545) covalent geometry : bond 0.00507 (13530) covalent geometry : angle 0.58010 (18334) *********************** 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 206 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 5.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7149 (tp30) cc_final: 0.6803 (tp30) REVERT: A 695 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7346 (p) REVERT: A 744 ARG cc_start: 0.7325 (ttp80) cc_final: 0.7046 (ttp80) REVERT: A 752 THR cc_start: 0.7257 (OUTLIER) cc_final: 0.6696 (t) REVERT: A 795 LYS cc_start: 0.8712 (tppt) cc_final: 0.7925 (ttmt) REVERT: B 464 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6878 (tp30) REVERT: B 533 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8268 (t) REVERT: B 546 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: B 572 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5253 (mp0) REVERT: B 626 SER cc_start: 0.7744 (OUTLIER) cc_final: 0.7325 (m) REVERT: B 648 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7332 (mm-30) REVERT: B 758 GLN cc_start: 0.6351 (OUTLIER) cc_final: 0.5649 (mp10) REVERT: B 795 LYS cc_start: 0.6796 (tppt) cc_final: 0.6414 (tppt) outliers start: 44 outliers final: 19 residues processed: 195 average time/residue: 3.1977 time to fit residues: 727.9748 Evaluate side-chains 179 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 6.408 ------------------------------------------------------------------------------- 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 572 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 330 THR 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.0570 chunk 68 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 45 optimal weight: 0.0050 chunk 158 optimal weight: 4.9990 overall best weight: 0.5512 ------------------------------------------------------------------------------- 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 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.100447 restraints weight = 49247.417| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.83 r_work: 0.3135 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13530 Z= 0.107 Angle : 0.531 14.798 18334 Z= 0.264 Chirality : 0.055 1.620 2022 Planarity : 0.004 0.064 2390 Dihedral : 3.919 44.633 1838 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.30 % Allowed : 24.93 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1714 helix: 1.14 (0.21), residues: 686 sheet: -0.88 (0.36), residues: 176 loop : -0.40 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 527 HIS 0.003 0.001 HIS B 667 PHE 0.007 0.001 PHE A 819 TYR 0.011 0.001 TYR B 113 ARG 0.006 0.000 ARG A 656 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 553) hydrogen bonds : angle 4.44247 ( 1545) covalent geometry : bond 0.00252 (13530) covalent geometry : angle 0.53118 (18334) *********************** 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 193 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7079 (tp30) cc_final: 0.6773 (tp30) REVERT: A 528 VAL cc_start: 0.8195 (t) cc_final: 0.7946 (m) REVERT: A 671 ASP cc_start: 0.7200 (t0) cc_final: 0.6870 (t0) REVERT: A 695 THR cc_start: 0.7444 (OUTLIER) cc_final: 0.7172 (p) REVERT: A 744 ARG cc_start: 0.7263 (ttp80) cc_final: 0.6988 (ttp80) REVERT: A 795 LYS cc_start: 0.8606 (tppt) cc_final: 0.7855 (ttmt) REVERT: B 58 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8640 (mtm) REVERT: B 77 MET cc_start: 0.8269 (ttm) cc_final: 0.7909 (ttm) REVERT: B 331 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7712 (ttm170) REVERT: B 464 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6825 (tp30) REVERT: B 533 SER cc_start: 0.8620 (m) cc_final: 0.8281 (t) REVERT: B 535 MET cc_start: 0.8411 (mmt) cc_final: 0.8203 (mmm) REVERT: B 546 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: B 572 GLU cc_start: 0.6079 (OUTLIER) cc_final: 0.5286 (mp0) REVERT: B 626 SER cc_start: 0.7722 (t) cc_final: 0.7288 (m) REVERT: B 648 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7344 (mm-30) REVERT: B 758 GLN cc_start: 0.6214 (OUTLIER) cc_final: 0.5634 (mp10) REVERT: B 795 LYS cc_start: 0.6790 (tppt) cc_final: 0.6452 (tppt) outliers start: 33 outliers final: 14 residues processed: 185 average time/residue: 2.2178 time to fit residues: 459.7280 Evaluate side-chains 175 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.991 ------------------------------------------------------------------------------- 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 694 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain B residue 58 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 521 SER 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 62 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 773 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.131324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.097584 restraints weight = 49649.568| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.82 r_work: 0.3092 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13530 Z= 0.180 Angle : 0.566 14.992 18334 Z= 0.285 Chirality : 0.056 1.602 2022 Planarity : 0.004 0.045 2390 Dihedral : 4.021 43.549 1838 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.65 % Allowed : 24.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1714 helix: 1.03 (0.21), residues: 688 sheet: -0.64 (0.37), residues: 188 loop : -0.46 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 527 HIS 0.005 0.001 HIS B 667 PHE 0.011 0.001 PHE A 247 TYR 0.011 0.001 TYR A 113 ARG 0.007 0.000 ARG A 656 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 553) hydrogen bonds : angle 4.49882 ( 1545) covalent geometry : bond 0.00435 (13530) covalent geometry : angle 0.56631 (18334) *********************** 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 202 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7146 (tp30) cc_final: 0.6824 (tp30) REVERT: A 528 VAL cc_start: 0.8299 (t) cc_final: 0.8058 (m) REVERT: A 671 ASP cc_start: 0.7205 (t0) cc_final: 0.6923 (t0) REVERT: A 695 THR cc_start: 0.7521 (OUTLIER) cc_final: 0.7264 (p) REVERT: A 744 ARG cc_start: 0.7377 (ttp80) cc_final: 0.7069 (ttp80) REVERT: B 464 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6943 (tp30) REVERT: B 533 SER cc_start: 0.8601 (m) cc_final: 0.8335 (t) REVERT: B 546 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: B 572 GLU cc_start: 0.6069 (OUTLIER) cc_final: 0.5269 (mp0) REVERT: B 625 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6670 (mp) REVERT: B 626 SER cc_start: 0.7726 (t) cc_final: 0.7339 (m) REVERT: B 648 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7366 (mm-30) REVERT: B 719 LYS cc_start: 0.7047 (ttmt) cc_final: 0.6558 (tptt) REVERT: B 751 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7832 (mm110) REVERT: B 758 GLN cc_start: 0.6353 (OUTLIER) cc_final: 0.5729 (mp10) REVERT: B 769 TYR cc_start: 0.7881 (t80) cc_final: 0.7675 (t80) REVERT: B 795 LYS cc_start: 0.6944 (tppt) cc_final: 0.6681 (tppt) outliers start: 38 outliers final: 22 residues processed: 193 average time/residue: 2.2546 time to fit residues: 486.0961 Evaluate side-chains 187 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 2.234 ------------------------------------------------------------------------------- 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 403 THR 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 767 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 855 SER 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 521 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 663 VAL Chi-restraints excluded: chain B residue 694 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 165 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.091992 restraints weight = 49681.116| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.86 r_work: 0.2982 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13530 Z= 0.176 Angle : 0.572 14.864 18334 Z= 0.286 Chirality : 0.056 1.609 2022 Planarity : 0.004 0.044 2390 Dihedral : 4.040 41.923 1838 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.86 % Allowed : 24.72 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.21), residues: 1714 helix: 0.99 (0.21), residues: 690 sheet: -0.74 (0.37), residues: 186 loop : -0.48 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 527 HIS 0.008 0.001 HIS B 667 PHE 0.013 0.001 PHE B 685 TYR 0.010 0.001 TYR B 113 ARG 0.005 0.000 ARG A 656 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 553) hydrogen bonds : angle 4.49876 ( 1545) covalent geometry : bond 0.00429 (13530) covalent geometry : angle 0.57211 (18334) *********************** 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 210 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7285 (tp30) cc_final: 0.6978 (tp30) REVERT: A 528 VAL cc_start: 0.8338 (t) cc_final: 0.8108 (m) REVERT: A 671 ASP cc_start: 0.7198 (t0) cc_final: 0.6959 (t0) REVERT: A 695 THR cc_start: 0.7545 (OUTLIER) cc_final: 0.7298 (p) REVERT: B 464 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7026 (tp30) REVERT: B 533 SER cc_start: 0.8545 (m) cc_final: 0.8307 (t) REVERT: B 546 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: B 572 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5287 (mp0) REVERT: B 626 SER cc_start: 0.7667 (t) cc_final: 0.7195 (m) REVERT: B 648 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7384 (mm-30) REVERT: B 719 LYS cc_start: 0.7150 (ttmt) cc_final: 0.6793 (tptt) REVERT: B 751 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7972 (mm110) REVERT: B 758 GLN cc_start: 0.6487 (OUTLIER) cc_final: 0.5911 (mp10) REVERT: B 769 TYR cc_start: 0.7991 (t80) cc_final: 0.7667 (t80) outliers start: 41 outliers final: 20 residues processed: 201 average time/residue: 2.2892 time to fit residues: 518.2217 Evaluate side-chains 186 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 2.358 ------------------------------------------------------------------------------- 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 403 THR 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 805 VAL Chi-restraints excluded: chain A residue 855 SER 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 521 SER 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 676 SER Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 758 GLN Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 802 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 74 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.126670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.092053 restraints weight = 49985.920| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.88 r_work: 0.2986 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13530 Z= 0.154 Angle : 0.560 14.894 18334 Z= 0.280 Chirality : 0.057 1.685 2022 Planarity : 0.004 0.056 2390 Dihedral : 3.967 40.257 1837 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.44 % Allowed : 25.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1714 helix: 1.06 (0.21), residues: 688 sheet: -0.87 (0.37), residues: 176 loop : -0.50 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 527 HIS 0.004 0.001 HIS A 829 PHE 0.009 0.001 PHE A 247 TYR 0.011 0.001 TYR B 113 ARG 0.005 0.000 ARG B 435 Details of bonding type rmsd hydrogen bonds : bond 0.04162 ( 553) hydrogen bonds : angle 4.46613 ( 1545) covalent geometry : bond 0.00377 (13530) covalent geometry : angle 0.56002 (18334) *********************** 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 199 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7291 (tp30) cc_final: 0.6973 (tp30) REVERT: A 528 VAL cc_start: 0.8373 (t) cc_final: 0.8152 (m) REVERT: A 744 ARG cc_start: 0.7397 (ttp80) cc_final: 0.7075 (ttp80) REVERT: B 444 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8015 (mttt) REVERT: B 464 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7047 (tp30) REVERT: B 533 SER cc_start: 0.8520 (m) cc_final: 0.8291 (t) REVERT: B 545 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7464 (mp0) REVERT: B 546 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: B 572 GLU cc_start: 0.6235 (OUTLIER) cc_final: 0.5421 (mp0) REVERT: B 626 SER cc_start: 0.7721 (t) cc_final: 0.7252 (m) REVERT: B 648 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7384 (mm-30) REVERT: B 719 LYS cc_start: 0.7385 (ttmt) cc_final: 0.6923 (tptt) REVERT: B 751 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7948 (mm110) REVERT: B 758 GLN cc_start: 0.6515 (OUTLIER) cc_final: 0.5963 (mp10) REVERT: B 769 TYR cc_start: 0.7989 (t80) cc_final: 0.7716 (t80) outliers start: 35 outliers final: 21 residues processed: 191 average time/residue: 2.2600 time to fit residues: 483.6848 Evaluate side-chains 186 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.992 ------------------------------------------------------------------------------- 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 403 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 855 SER 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 444 LYS Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 521 SER 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 694 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 758 GLN Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 855 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 21 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 702 ASN A 800 GLN B 168 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.125860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.091298 restraints weight = 49934.246| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.87 r_work: 0.2975 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13530 Z= 0.183 Angle : 0.578 15.241 18334 Z= 0.291 Chirality : 0.057 1.667 2022 Planarity : 0.004 0.045 2390 Dihedral : 3.905 17.484 1836 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.16 % Allowed : 25.42 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1714 helix: 1.00 (0.21), residues: 688 sheet: -0.85 (0.38), residues: 176 loop : -0.52 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 629 HIS 0.004 0.001 HIS A 829 PHE 0.011 0.001 PHE A 247 TYR 0.011 0.001 TYR A 113 ARG 0.010 0.000 ARG B 435 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 553) hydrogen bonds : angle 4.48768 ( 1545) covalent geometry : bond 0.00448 (13530) covalent geometry : angle 0.57800 (18334) ********************** 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 193 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7275 (tp30) cc_final: 0.6978 (tp30) REVERT: A 528 VAL cc_start: 0.8454 (t) cc_final: 0.8245 (m) REVERT: A 744 ARG cc_start: 0.7511 (ttp80) cc_final: 0.7182 (ttp80) REVERT: B 444 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8026 (mttt) REVERT: B 464 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7009 (tp30) REVERT: B 533 SER cc_start: 0.8494 (m) cc_final: 0.8277 (t) REVERT: B 545 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7471 (mp0) REVERT: B 546 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: B 572 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5431 (mp0) REVERT: B 626 SER cc_start: 0.7689 (t) cc_final: 0.7236 (m) REVERT: B 648 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7261 (mm-30) REVERT: B 719 LYS cc_start: 0.7389 (ttmt) cc_final: 0.7022 (tptt) REVERT: B 751 GLN cc_start: 0.8310 (mm-40) cc_final: 0.8034 (mm110) REVERT: B 758 GLN cc_start: 0.6533 (OUTLIER) cc_final: 0.6017 (mp10) REVERT: B 769 TYR cc_start: 0.8006 (t80) cc_final: 0.7773 (t80) outliers start: 31 outliers final: 22 residues processed: 187 average time/residue: 2.2498 time to fit residues: 470.3993 Evaluate side-chains 189 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 2.245 ------------------------------------------------------------------------------- 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 403 THR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 855 SER 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 444 LYS 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 663 VAL Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 758 GLN Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 855 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 108 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 B 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.127173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.092904 restraints weight = 49709.652| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.87 r_work: 0.2998 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13530 Z= 0.123 Angle : 0.551 15.098 18334 Z= 0.275 Chirality : 0.056 1.654 2022 Planarity : 0.004 0.049 2390 Dihedral : 3.804 19.048 1836 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.74 % Allowed : 25.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1714 helix: 1.15 (0.21), residues: 688 sheet: -0.99 (0.36), residues: 182 loop : -0.44 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 527 HIS 0.005 0.001 HIS A 426 PHE 0.008 0.001 PHE A 819 TYR 0.011 0.001 TYR B 113 ARG 0.009 0.000 ARG B 435 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 553) hydrogen bonds : angle 4.40703 ( 1545) covalent geometry : bond 0.00299 (13530) covalent geometry : angle 0.55139 (18334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18957.96 seconds wall clock time: 326 minutes 58.56 seconds (19618.56 seconds total)