Starting phenix.real_space_refine on Thu Sep 18 04:40:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jr9_61748/09_2025/9jr9_61748.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jr9_61748/09_2025/9jr9_61748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jr9_61748/09_2025/9jr9_61748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jr9_61748/09_2025/9jr9_61748.map" model { file = "/net/cci-nas-00/data/ceres_data/9jr9_61748/09_2025/9jr9_61748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jr9_61748/09_2025/9jr9_61748.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.043 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 Zn 2 6.06 5 S 98 5.16 5 C 8856 2.51 5 N 2361 2.21 5 O 2549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13866 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6957 Classifications: {'peptide': 869} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 829} Chain breaks: 2 Chain: "B" Number of atoms: 6907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6907 Classifications: {'peptide': 862} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 823} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2147 SG CYS A 284 78.069 78.558 75.101 1.00 53.75 S ATOM 2421 SG CYS A 318 76.844 79.525 78.560 1.00 47.44 S ATOM 2427 SG CYS A 319 76.004 76.024 77.200 1.00 47.53 S ATOM 9104 SG CYS B 284 40.076 43.001 75.145 1.00 55.27 S ATOM 9378 SG CYS B 318 41.716 41.813 78.366 1.00 48.37 S ATOM 9384 SG CYS B 319 42.299 45.405 77.204 1.00 48.93 S Time building chain proxies: 2.96, per 1000 atoms: 0.21 Number of scatterers: 13866 At special positions: 0 Unit cell: (118.988, 122.14, 128.444, 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) Zn 2 29.99 S 98 16.00 O 2549 8.00 N 2361 7.00 C 8856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 424.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 282 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 318 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 284 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 319 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 282 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 318 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 284 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 319 " Number of angles added : 6 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 18 sheets defined 45.9% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 34 through 55 Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 142 through 160 Processing helix chain 'A' and resid 179 through 193 Processing helix chain 'A' and resid 219 through 238 removed outlier: 3.985A pdb=" N ARG A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Proline residue: A 229 - end of helix Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 380 through 395 removed outlier: 3.941A pdb=" N HIS A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLU A 388 " --> pdb=" O HIS A 384 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ALA A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 417 Processing helix chain 'A' and resid 419 through 429 Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 480 through 499 Processing helix chain 'A' and resid 530 through 534 removed outlier: 3.753A pdb=" N ARG A 534 " --> pdb=" O ARG A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 554 removed outlier: 3.525A pdb=" N MET A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 580 Processing helix chain 'A' and resid 581 through 585 removed outlier: 3.623A pdb=" N GLN A 584 " --> pdb=" O GLU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 615 removed outlier: 3.708A pdb=" N LEU A 602 " --> pdb=" O ARG A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 645 through 651 Processing helix chain 'A' and resid 663 through 667 Processing helix chain 'A' and resid 673 through 683 removed outlier: 3.734A pdb=" N LYS A 677 " --> pdb=" O ASN A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 722 removed outlier: 3.538A pdb=" N GLN A 722 " --> pdb=" O PRO A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 752 Processing helix chain 'A' and resid 758 through 764 removed outlier: 3.927A pdb=" N LEU A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 778 Processing helix chain 'A' and resid 790 through 808 Processing helix chain 'A' and resid 811 through 813 No H-bonds generated for 'chain 'A' and resid 811 through 813' Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 824 through 840 Processing helix chain 'A' and resid 851 through 855 removed outlier: 3.770A pdb=" N VAL A 855 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 869 removed outlier: 3.546A pdb=" N SER A 869 " --> pdb=" O GLN A 866 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 866 through 869' Processing helix chain 'A' and resid 885 through 888 removed outlier: 3.505A pdb=" N GLU A 888 " --> pdb=" O GLN A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 885 through 888' Processing helix chain 'A' and resid 889 through 896 removed outlier: 4.207A pdb=" N CYS A 893 " --> pdb=" O PHE A 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 31 Processing helix chain 'B' and resid 34 through 55 Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 142 through 160 Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 219 through 238 removed outlier: 4.059A pdb=" N ARG B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) Proline residue: B 229 - end of helix Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 340 through 350 Processing helix chain 'B' and resid 380 through 395 removed outlier: 3.950A pdb=" N HIS B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU B 388 " --> pdb=" O HIS B 384 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ALA B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 417 Processing helix chain 'B' and resid 419 through 429 Processing helix chain 'B' and resid 441 through 446 Processing helix chain 'B' and resid 480 through 499 Processing helix chain 'B' and resid 530 through 534 Processing helix chain 'B' and resid 537 through 554 Processing helix chain 'B' and resid 557 through 580 Processing helix chain 'B' and resid 581 through 585 removed outlier: 3.648A pdb=" N GLN B 584 " --> pdb=" O GLU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 615 removed outlier: 3.628A pdb=" N LEU B 602 " --> pdb=" O ARG B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 627 through 638 Processing helix chain 'B' and resid 645 through 651 Processing helix chain 'B' and resid 663 through 667 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 718 through 722 Processing helix chain 'B' and resid 735 through 752 Processing helix chain 'B' and resid 758 through 764 removed outlier: 3.917A pdb=" N LEU B 764 " --> pdb=" O ASP B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 778 Processing helix chain 'B' and resid 790 through 808 Processing helix chain 'B' and resid 811 through 813 No H-bonds generated for 'chain 'B' and resid 811 through 813' Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 824 through 840 Processing helix chain 'B' and resid 866 through 869 removed outlier: 3.557A pdb=" N SER B 869 " --> pdb=" O GLN B 866 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 866 through 869' Processing helix chain 'B' and resid 885 through 888 removed outlier: 3.505A pdb=" N GLU B 888 " --> pdb=" O GLN B 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 885 through 888' Processing helix chain 'B' and resid 889 through 896 removed outlier: 4.152A pdb=" N CYS B 893 " --> pdb=" O PHE B 889 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 22 removed outlier: 6.290A pdb=" N VAL A 15 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LYS A 61 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 17 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLU A 63 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N VAL A 19 " --> pdb=" O GLU A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 134 Processing sheet with id=AA3, first strand: chain 'A' and resid 195 through 197 removed outlier: 3.739A pdb=" N GLY A 307 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN A 301 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 211 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 197 removed outlier: 3.739A pdb=" N GLY A 307 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN A 301 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 281 removed outlier: 3.696A pdb=" N VAL A 320 " --> pdb=" O PHE A 281 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 329 through 331 Processing sheet with id=AA7, first strand: chain 'A' and resid 403 through 405 removed outlier: 6.341A pdb=" N GLN A 403 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N PHE A 438 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS A 405 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS A 456 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL A 467 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ARG A 511 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU A 469 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE A 513 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N THR A 471 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 641 through 644 removed outlier: 6.297A pdb=" N ILE A 621 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 643 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR A 623 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 622 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 589 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU A 703 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE A 591 " --> pdb=" O LEU A 703 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 782 through 789 removed outlier: 6.322A pdb=" N THR A 874 " --> pdb=" O HIS A 901 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N TYR A 903 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A 876 " --> pdb=" O TYR A 903 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU A 905 " --> pdb=" O VAL A 876 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLY A 878 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLU A 907 " --> pdb=" O GLY A 878 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N SER A 880 " --> pdb=" O GLU A 907 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 15 through 22 removed outlier: 6.303A pdb=" N VAL B 15 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LYS B 61 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 17 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLU B 63 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL B 19 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 131 through 134 Processing sheet with id=AB3, first strand: chain 'B' and resid 195 through 197 removed outlier: 6.485A pdb=" N LEU B 196 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 307 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN B 301 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU B 305 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA B 211 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 195 through 197 removed outlier: 6.485A pdb=" N LEU B 196 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 307 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN B 301 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU B 305 " --> pdb=" O GLN B 301 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 280 through 281 removed outlier: 3.691A pdb=" N VAL B 320 " --> pdb=" O PHE B 281 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 329 through 331 Processing sheet with id=AB7, first strand: chain 'B' and resid 403 through 405 removed outlier: 6.322A pdb=" N GLN B 403 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N PHE B 438 " --> pdb=" O GLN B 403 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS B 405 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS B 456 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL B 467 " --> pdb=" O ILE B 509 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG B 511 " --> pdb=" O VAL B 467 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU B 469 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE B 513 " --> pdb=" O LEU B 469 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N THR B 471 " --> pdb=" O ILE B 513 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 641 through 644 removed outlier: 6.278A pdb=" N ILE B 621 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL B 643 " --> pdb=" O ILE B 621 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TYR B 623 " --> pdb=" O VAL B 643 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B 622 " --> pdb=" O VAL B 660 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 589 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU B 703 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE B 591 " --> pdb=" O LEU B 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 782 through 789 removed outlier: 6.372A pdb=" N THR B 874 " --> pdb=" O HIS B 901 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR B 903 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL B 876 " --> pdb=" O TYR B 903 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU B 905 " --> pdb=" O VAL B 876 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLY B 878 " --> pdb=" O LEU B 905 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLU B 907 " --> pdb=" O GLY B 878 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N SER B 880 " --> pdb=" O GLU B 907 " (cutoff:3.500A) 657 hydrogen bonds defined for protein. 1896 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: 2.61 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4463 1.34 - 1.46: 2585 1.46 - 1.58: 6965 1.58 - 1.69: 1 1.69 - 1.81: 142 Bond restraints: 14156 Sorted by residual: bond pdb=" CG PRO B 430 " pdb=" CD PRO B 430 " ideal model delta sigma weight residual 1.512 1.417 0.095 2.70e-02 1.37e+03 1.24e+01 bond pdb=" CB PRO B 430 " pdb=" CG PRO B 430 " ideal model delta sigma weight residual 1.506 1.639 -0.133 3.90e-02 6.57e+02 1.15e+01 bond pdb=" N PRO B 430 " pdb=" CA PRO B 430 " ideal model delta sigma weight residual 1.468 1.423 0.045 1.70e-02 3.46e+03 6.88e+00 bond pdb=" N PRO B 430 " pdb=" CD PRO B 430 " ideal model delta sigma weight residual 1.474 1.502 -0.028 1.40e-02 5.10e+03 3.98e+00 bond pdb=" CB GLU A 81 " pdb=" CG GLU A 81 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.42e+00 ... (remaining 14151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 19034 3.57 - 7.14: 61 7.14 - 10.71: 5 10.71 - 14.28: 0 14.28 - 17.85: 1 Bond angle restraints: 19101 Sorted by residual: angle pdb=" CA PRO B 430 " pdb=" N PRO B 430 " pdb=" CD PRO B 430 " ideal model delta sigma weight residual 111.50 93.65 17.85 1.40e+00 5.10e-01 1.63e+02 angle pdb=" N PRO B 430 " pdb=" CD PRO B 430 " pdb=" CG PRO B 430 " ideal model delta sigma weight residual 103.80 94.90 8.90 1.20e+00 6.94e-01 5.50e+01 angle pdb=" N THR B 136 " pdb=" CA THR B 136 " pdb=" CB THR B 136 " ideal model delta sigma weight residual 114.17 109.30 4.87 1.14e+00 7.69e-01 1.83e+01 angle pdb=" N PRO B 430 " pdb=" CA PRO B 430 " pdb=" CB PRO B 430 " ideal model delta sigma weight residual 102.60 98.97 3.63 1.10e+00 8.26e-01 1.09e+01 angle pdb=" C ASN B 291 " pdb=" CA ASN B 291 " pdb=" CB ASN B 291 " ideal model delta sigma weight residual 109.48 114.88 -5.40 1.68e+00 3.54e-01 1.03e+01 ... (remaining 19096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7562 17.99 - 35.97: 841 35.97 - 53.96: 213 53.96 - 71.94: 30 71.94 - 89.93: 9 Dihedral angle restraints: 8655 sinusoidal: 3585 harmonic: 5070 Sorted by residual: dihedral pdb=" CA ARG B 133 " pdb=" C ARG B 133 " pdb=" N ASP B 134 " pdb=" CA ASP B 134 " ideal model delta harmonic sigma weight residual 180.00 154.02 25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ALA A 776 " pdb=" C ALA A 776 " pdb=" N GLN A 777 " pdb=" CA GLN A 777 " ideal model delta harmonic sigma weight residual -180.00 -161.41 -18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CG ARG A 820 " pdb=" CD ARG A 820 " pdb=" NE ARG A 820 " pdb=" CZ ARG A 820 " ideal model delta sinusoidal sigma weight residual -90.00 -37.40 -52.60 2 1.50e+01 4.44e-03 1.35e+01 ... (remaining 8652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1662 0.047 - 0.094: 371 0.094 - 0.141: 99 0.141 - 0.188: 2 0.188 - 0.235: 1 Chirality restraints: 2135 Sorted by residual: chirality pdb=" CA PRO B 430 " pdb=" N PRO B 430 " pdb=" C PRO B 430 " pdb=" CB PRO B 430 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CG LEU A 736 " pdb=" CB LEU A 736 " pdb=" CD1 LEU A 736 " pdb=" CD2 LEU A 736 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE B 245 " pdb=" N ILE B 245 " pdb=" C ILE B 245 " pdb=" CB ILE B 245 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 2132 not shown) Planarity restraints: 2426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 429 " -0.073 5.00e-02 4.00e+02 9.86e-02 1.56e+01 pdb=" N PRO B 430 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO B 430 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 430 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 617 " 0.042 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO B 618 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 618 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 618 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 850 " -0.033 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO B 851 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 851 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 851 " -0.028 5.00e-02 4.00e+02 ... (remaining 2423 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 242 2.68 - 3.24: 12898 3.24 - 3.79: 21390 3.79 - 4.35: 28649 4.35 - 4.90: 48380 Nonbonded interactions: 111559 Sorted by model distance: nonbonded pdb=" OE2 GLU A 588 " pdb=" OH TYR A 675 " model vdw 2.131 3.040 nonbonded pdb=" OG SER A 92 " pdb=" OD1 ASP B 134 " model vdw 2.158 3.040 nonbonded pdb=" OH TYR A 69 " pdb=" O GLY A 75 " model vdw 2.190 3.040 nonbonded pdb=" N GLU B 539 " pdb=" OE1 GLU B 539 " model vdw 2.192 3.120 nonbonded pdb=" OD2 ASP B 248 " pdb=" OG SER B 251 " model vdw 2.197 3.040 ... (remaining 111554 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 351 or resid 379 through 518 or resid 525 throug \ h 1001)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.180 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 14164 Z= 0.202 Angle : 0.614 17.854 19107 Z= 0.339 Chirality : 0.042 0.235 2135 Planarity : 0.005 0.099 2426 Dihedral : 15.770 89.926 5365 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.32 % Allowed : 17.84 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.20), residues: 1717 helix: 1.83 (0.19), residues: 712 sheet: 1.29 (0.32), residues: 280 loop : -0.47 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 820 TYR 0.020 0.001 TYR A 623 PHE 0.024 0.002 PHE A 317 TRP 0.012 0.002 TRP B 259 HIS 0.007 0.001 HIS A 890 Details of bonding type rmsd covalent geometry : bond 0.00472 (14156) covalent geometry : angle 0.61402 (19101) hydrogen bonds : bond 0.14688 ( 641) hydrogen bonds : angle 5.74334 ( 1896) metal coordination : bond 0.00425 ( 8) metal coordination : angle 1.37492 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 364 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8022 (t80) cc_final: 0.7820 (t80) REVERT: A 308 TYR cc_start: 0.7432 (p90) cc_final: 0.7133 (p90) REVERT: A 394 LEU cc_start: 0.8543 (mp) cc_final: 0.8273 (mp) REVERT: A 824 ASP cc_start: 0.7049 (m-30) cc_final: 0.6827 (m-30) REVERT: A 849 PHE cc_start: 0.8165 (m-80) cc_final: 0.7940 (m-80) REVERT: B 31 LYS cc_start: 0.7877 (ptmm) cc_final: 0.7609 (ttpp) REVERT: B 612 ASP cc_start: 0.7363 (m-30) cc_final: 0.7081 (m-30) REVERT: B 614 PHE cc_start: 0.8440 (m-80) cc_final: 0.8085 (m-80) outliers start: 5 outliers final: 1 residues processed: 366 average time/residue: 0.6335 time to fit residues: 250.5581 Evaluate side-chains 357 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 356 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 872 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.0030 overall best weight: 0.5288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN ** B 575 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 = 0.3760 r_free = 0.3760 target = 0.136234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114843 restraints weight = 18012.152| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.13 r_work: 0.3339 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14164 Z= 0.119 Angle : 0.515 8.542 19107 Z= 0.272 Chirality : 0.041 0.147 2135 Planarity : 0.004 0.054 2426 Dihedral : 4.017 22.809 1866 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.09 % Allowed : 18.09 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.20), residues: 1717 helix: 2.00 (0.19), residues: 718 sheet: 1.27 (0.31), residues: 280 loop : -0.37 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 21 TYR 0.016 0.001 TYR A 623 PHE 0.013 0.001 PHE A 283 TRP 0.008 0.001 TRP B 112 HIS 0.010 0.001 HIS B 890 Details of bonding type rmsd covalent geometry : bond 0.00262 (14156) covalent geometry : angle 0.51422 (19101) hydrogen bonds : bond 0.04263 ( 641) hydrogen bonds : angle 4.44296 ( 1896) metal coordination : bond 0.00656 ( 8) metal coordination : angle 2.07845 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 354 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8193 (ttpt) REVERT: A 308 TYR cc_start: 0.7931 (p90) cc_final: 0.7681 (p90) REVERT: A 394 LEU cc_start: 0.8774 (mp) cc_final: 0.8492 (mp) REVERT: A 534 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7885 (ptm-80) REVERT: A 537 ASP cc_start: 0.8009 (m-30) cc_final: 0.7694 (p0) REVERT: B 103 HIS cc_start: 0.7570 (p-80) cc_final: 0.7278 (m-70) REVERT: B 308 TYR cc_start: 0.8170 (p90) cc_final: 0.7757 (p90) REVERT: B 348 MET cc_start: 0.8762 (ttm) cc_final: 0.8492 (ttt) REVERT: B 401 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6757 (tm-30) REVERT: B 483 GLU cc_start: 0.7938 (mp0) cc_final: 0.7635 (mp0) REVERT: B 612 ASP cc_start: 0.8177 (m-30) cc_final: 0.7716 (m-30) REVERT: B 614 PHE cc_start: 0.8534 (m-80) cc_final: 0.8142 (m-80) REVERT: B 751 GLU cc_start: 0.7982 (tp30) cc_final: 0.7532 (tp30) REVERT: B 821 ARG cc_start: 0.8242 (mtp180) cc_final: 0.7908 (mtm180) outliers start: 48 outliers final: 20 residues processed: 376 average time/residue: 0.6601 time to fit residues: 267.9241 Evaluate side-chains 361 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 340 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 747 LYS Chi-restraints excluded: chain B residue 762 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 21 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN A 650 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.132867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111440 restraints weight = 18213.831| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.15 r_work: 0.3289 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 14164 Z= 0.282 Angle : 0.584 8.241 19107 Z= 0.305 Chirality : 0.045 0.182 2135 Planarity : 0.004 0.054 2426 Dihedral : 4.180 21.227 1863 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.31 % Allowed : 17.39 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.19), residues: 1717 helix: 1.75 (0.18), residues: 718 sheet: 1.23 (0.31), residues: 280 loop : -0.49 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 21 TYR 0.015 0.002 TYR A 529 PHE 0.027 0.002 PHE A 317 TRP 0.008 0.002 TRP A 344 HIS 0.007 0.001 HIS B 890 Details of bonding type rmsd covalent geometry : bond 0.00674 (14156) covalent geometry : angle 0.58361 (19101) hydrogen bonds : bond 0.05100 ( 641) hydrogen bonds : angle 4.32898 ( 1896) metal coordination : bond 0.00886 ( 8) metal coordination : angle 1.21921 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 373 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.6730 (mpp) REVERT: A 291 ASN cc_start: 0.8522 (p0) cc_final: 0.8269 (p0) REVERT: A 464 ASN cc_start: 0.8649 (m-40) cc_final: 0.8184 (m-40) REVERT: A 534 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7946 (ptm-80) REVERT: A 821 ARG cc_start: 0.8174 (mtp180) cc_final: 0.7501 (mtp85) REVERT: A 823 GLU cc_start: 0.7776 (pm20) cc_final: 0.7001 (pm20) REVERT: A 842 HIS cc_start: 0.5420 (OUTLIER) cc_final: 0.3995 (p90) REVERT: B 10 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7299 (mmm) REVERT: B 179 GLU cc_start: 0.3747 (OUTLIER) cc_final: 0.3061 (mm-30) REVERT: B 183 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6267 (mpp) REVERT: B 308 TYR cc_start: 0.8220 (p90) cc_final: 0.7833 (p90) REVERT: B 407 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7073 (mm-30) REVERT: B 411 LYS cc_start: 0.8557 (mttm) cc_final: 0.8293 (mttp) REVERT: B 483 GLU cc_start: 0.8011 (mp0) cc_final: 0.7634 (mp0) REVERT: B 612 ASP cc_start: 0.8219 (m-30) cc_final: 0.7792 (m-30) REVERT: B 614 PHE cc_start: 0.8677 (m-80) cc_final: 0.8215 (m-80) REVERT: B 821 ARG cc_start: 0.8198 (mtp180) cc_final: 0.7709 (mtp180) REVERT: B 823 GLU cc_start: 0.7758 (pm20) cc_final: 0.7276 (pm20) outliers start: 67 outliers final: 28 residues processed: 399 average time/residue: 0.6319 time to fit residues: 272.6193 Evaluate side-chains 392 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 358 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain B residue 10 MET Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 872 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 167 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN A 636 GLN A 650 GLN ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 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 = 0.3736 r_free = 0.3736 target = 0.134170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112827 restraints weight = 18078.636| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.13 r_work: 0.3310 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14164 Z= 0.171 Angle : 0.516 8.113 19107 Z= 0.271 Chirality : 0.042 0.180 2135 Planarity : 0.004 0.050 2426 Dihedral : 4.026 21.539 1863 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.06 % Allowed : 18.87 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.20), residues: 1717 helix: 1.86 (0.18), residues: 718 sheet: 1.05 (0.31), residues: 282 loop : -0.40 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 820 TYR 0.017 0.001 TYR A 623 PHE 0.022 0.001 PHE A 317 TRP 0.009 0.001 TRP A 112 HIS 0.006 0.001 HIS B 890 Details of bonding type rmsd covalent geometry : bond 0.00404 (14156) covalent geometry : angle 0.51511 (19101) hydrogen bonds : bond 0.04280 ( 641) hydrogen bonds : angle 4.19117 ( 1896) metal coordination : bond 0.00191 ( 8) metal coordination : angle 1.37384 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 361 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7476 (mm-30) REVERT: A 183 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6810 (mpp) REVERT: A 291 ASN cc_start: 0.8462 (p0) cc_final: 0.8171 (p0) REVERT: A 534 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7934 (ptm-80) REVERT: A 537 ASP cc_start: 0.8122 (m-30) cc_final: 0.7783 (p0) REVERT: A 646 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8150 (ttpp) REVERT: A 650 GLN cc_start: 0.8241 (mt0) cc_final: 0.7902 (mt0) REVERT: A 673 ASN cc_start: 0.8701 (t0) cc_final: 0.8452 (t0) REVERT: A 821 ARG cc_start: 0.8166 (mtp180) cc_final: 0.7540 (mtp85) REVERT: A 823 GLU cc_start: 0.7735 (pm20) cc_final: 0.7162 (pm20) REVERT: A 842 HIS cc_start: 0.5426 (OUTLIER) cc_final: 0.4008 (p90) REVERT: B 103 HIS cc_start: 0.7616 (p-80) cc_final: 0.7275 (m-70) REVERT: B 179 GLU cc_start: 0.3701 (OUTLIER) cc_final: 0.2871 (mm-30) REVERT: B 183 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.6400 (mpp) REVERT: B 308 TYR cc_start: 0.8215 (p90) cc_final: 0.7873 (p90) REVERT: B 348 MET cc_start: 0.8782 (ttm) cc_final: 0.8471 (ttt) REVERT: B 401 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7081 (tm-30) REVERT: B 407 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7329 (mm-30) REVERT: B 483 GLU cc_start: 0.8013 (mp0) cc_final: 0.7616 (mp0) REVERT: B 560 SER cc_start: 0.8340 (t) cc_final: 0.8047 (m) REVERT: B 612 ASP cc_start: 0.8183 (m-30) cc_final: 0.7738 (m-30) REVERT: B 614 PHE cc_start: 0.8648 (m-80) cc_final: 0.8123 (m-80) REVERT: B 821 ARG cc_start: 0.8145 (mtp180) cc_final: 0.7637 (mtp180) REVERT: B 823 GLU cc_start: 0.7703 (pm20) cc_final: 0.7245 (pm20) REVERT: B 833 LEU cc_start: 0.8468 (mp) cc_final: 0.8261 (mm) REVERT: B 865 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7145 (tp) outliers start: 63 outliers final: 29 residues processed: 398 average time/residue: 0.6424 time to fit residues: 276.9824 Evaluate side-chains 390 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 354 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 747 LYS Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 865 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 87 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** B 575 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 = 0.3732 r_free = 0.3732 target = 0.134010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.112708 restraints weight = 18095.867| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.14 r_work: 0.3305 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14164 Z= 0.197 Angle : 0.532 8.774 19107 Z= 0.277 Chirality : 0.043 0.180 2135 Planarity : 0.004 0.049 2426 Dihedral : 4.019 20.484 1863 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.73 % Allowed : 19.90 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.20), residues: 1717 helix: 1.85 (0.18), residues: 717 sheet: 1.03 (0.31), residues: 282 loop : -0.41 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 820 TYR 0.015 0.001 TYR B 198 PHE 0.021 0.001 PHE A 317 TRP 0.009 0.001 TRP A 344 HIS 0.007 0.001 HIS B 890 Details of bonding type rmsd covalent geometry : bond 0.00469 (14156) covalent geometry : angle 0.53211 (19101) hydrogen bonds : bond 0.04375 ( 641) hydrogen bonds : angle 4.16479 ( 1896) metal coordination : bond 0.00381 ( 8) metal coordination : angle 1.20981 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 365 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7547 (mm-30) REVERT: A 183 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.6781 (mpp) REVERT: A 291 ASN cc_start: 0.8429 (p0) cc_final: 0.8082 (p0) REVERT: A 295 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8174 (ttpt) REVERT: A 534 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7946 (ptm-80) REVERT: A 537 ASP cc_start: 0.8114 (m-30) cc_final: 0.7791 (p0) REVERT: A 646 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8148 (ttpp) REVERT: A 650 GLN cc_start: 0.8232 (mt0) cc_final: 0.7904 (mt0) REVERT: A 673 ASN cc_start: 0.8680 (t0) cc_final: 0.8400 (t0) REVERT: A 821 ARG cc_start: 0.8171 (mtp180) cc_final: 0.7529 (mtp85) REVERT: A 823 GLU cc_start: 0.7710 (pm20) cc_final: 0.7080 (pm20) REVERT: A 842 HIS cc_start: 0.5474 (OUTLIER) cc_final: 0.3990 (p90) REVERT: B 10 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.6710 (mpp) REVERT: B 103 HIS cc_start: 0.7668 (p-80) cc_final: 0.7304 (m-70) REVERT: B 135 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.7114 (p) REVERT: B 179 GLU cc_start: 0.3735 (OUTLIER) cc_final: 0.2875 (mm-30) REVERT: B 183 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.6457 (mpp) REVERT: B 308 TYR cc_start: 0.8192 (p90) cc_final: 0.7806 (p90) REVERT: B 348 MET cc_start: 0.8781 (ttm) cc_final: 0.8487 (ttt) REVERT: B 401 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7112 (tm-30) REVERT: B 407 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7326 (mm-30) REVERT: B 483 GLU cc_start: 0.8013 (mp0) cc_final: 0.7613 (mp0) REVERT: B 496 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8568 (mt) REVERT: B 560 SER cc_start: 0.8330 (t) cc_final: 0.8024 (m) REVERT: B 612 ASP cc_start: 0.8186 (m-30) cc_final: 0.7753 (m-30) REVERT: B 614 PHE cc_start: 0.8660 (m-80) cc_final: 0.8173 (m-80) REVERT: B 821 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7818 (mtp180) REVERT: B 823 GLU cc_start: 0.7673 (pm20) cc_final: 0.7301 (pm20) REVERT: B 833 LEU cc_start: 0.8461 (mp) cc_final: 0.8252 (mm) REVERT: B 865 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7174 (tp) outliers start: 58 outliers final: 32 residues processed: 396 average time/residue: 0.6348 time to fit residues: 272.5503 Evaluate side-chains 401 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 359 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain B residue 10 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 865 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 139 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN A 491 GLN A 636 GLN ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 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 = 0.3725 r_free = 0.3725 target = 0.133417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112223 restraints weight = 17992.420| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.13 r_work: 0.3302 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14164 Z= 0.212 Angle : 0.540 9.458 19107 Z= 0.281 Chirality : 0.043 0.181 2135 Planarity : 0.004 0.048 2426 Dihedral : 4.039 19.344 1863 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.25 % Allowed : 19.32 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.20), residues: 1717 helix: 1.80 (0.18), residues: 717 sheet: 1.00 (0.30), residues: 282 loop : -0.44 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 820 TYR 0.017 0.002 TYR A 623 PHE 0.023 0.001 PHE A 317 TRP 0.009 0.001 TRP A 344 HIS 0.006 0.001 HIS B 890 Details of bonding type rmsd covalent geometry : bond 0.00507 (14156) covalent geometry : angle 0.53951 (19101) hydrogen bonds : bond 0.04425 ( 641) hydrogen bonds : angle 4.15581 ( 1896) metal coordination : bond 0.00460 ( 8) metal coordination : angle 1.31938 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 365 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.6817 (mpp) REVERT: A 291 ASN cc_start: 0.8433 (p0) cc_final: 0.8034 (p0) REVERT: A 449 ARG cc_start: 0.8538 (ttp80) cc_final: 0.8191 (ttt90) REVERT: A 464 ASN cc_start: 0.8635 (m-40) cc_final: 0.8386 (m-40) REVERT: A 537 ASP cc_start: 0.8130 (m-30) cc_final: 0.7812 (p0) REVERT: A 611 LYS cc_start: 0.8731 (ttpp) cc_final: 0.8494 (ttpt) REVERT: A 646 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8147 (ttpp) REVERT: A 650 GLN cc_start: 0.8235 (mt0) cc_final: 0.7904 (mt0) REVERT: A 673 ASN cc_start: 0.8698 (t0) cc_final: 0.8435 (t0) REVERT: A 762 LEU cc_start: 0.8118 (mm) cc_final: 0.7878 (mm) REVERT: A 821 ARG cc_start: 0.8176 (mtp180) cc_final: 0.7506 (mtp85) REVERT: A 823 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7039 (pm20) REVERT: A 842 HIS cc_start: 0.5443 (OUTLIER) cc_final: 0.3969 (p90) REVERT: B 103 HIS cc_start: 0.7672 (p-80) cc_final: 0.7341 (m-70) REVERT: B 179 GLU cc_start: 0.3726 (OUTLIER) cc_final: 0.2864 (mm-30) REVERT: B 183 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.6460 (mpp) REVERT: B 261 LYS cc_start: 0.8364 (mmtt) cc_final: 0.7986 (mmmm) REVERT: B 295 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8409 (ttmt) REVERT: B 308 TYR cc_start: 0.8205 (p90) cc_final: 0.7775 (p90) REVERT: B 348 MET cc_start: 0.8781 (ttm) cc_final: 0.8488 (ttt) REVERT: B 401 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7164 (tm-30) REVERT: B 407 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7303 (mm-30) REVERT: B 483 GLU cc_start: 0.8031 (mp0) cc_final: 0.7617 (mp0) REVERT: B 496 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8576 (mt) REVERT: B 560 SER cc_start: 0.8344 (t) cc_final: 0.8044 (m) REVERT: B 612 ASP cc_start: 0.8194 (m-30) cc_final: 0.7754 (m-30) REVERT: B 614 PHE cc_start: 0.8676 (m-80) cc_final: 0.8183 (m-80) REVERT: B 790 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8203 (p) REVERT: B 821 ARG cc_start: 0.8259 (mtp180) cc_final: 0.7822 (mtp180) REVERT: B 823 GLU cc_start: 0.7716 (pm20) cc_final: 0.7279 (pm20) REVERT: B 833 LEU cc_start: 0.8471 (mp) cc_final: 0.8262 (mm) REVERT: B 865 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7198 (tp) outliers start: 66 outliers final: 34 residues processed: 397 average time/residue: 0.6829 time to fit residues: 293.4369 Evaluate side-chains 402 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 359 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 865 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 114 optimal weight: 0.0770 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN A 491 GLN ** A 777 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 = 0.3746 r_free = 0.3746 target = 0.135307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.114010 restraints weight = 17906.275| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.14 r_work: 0.3316 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14164 Z= 0.145 Angle : 0.518 9.647 19107 Z= 0.268 Chirality : 0.042 0.169 2135 Planarity : 0.004 0.049 2426 Dihedral : 3.937 19.401 1863 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.28 % Allowed : 20.99 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.20), residues: 1717 helix: 1.92 (0.19), residues: 717 sheet: 0.98 (0.30), residues: 282 loop : -0.37 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 21 TYR 0.016 0.001 TYR B 623 PHE 0.020 0.001 PHE A 317 TRP 0.009 0.001 TRP A 344 HIS 0.005 0.001 HIS A 890 Details of bonding type rmsd covalent geometry : bond 0.00341 (14156) covalent geometry : angle 0.51756 (19101) hydrogen bonds : bond 0.03951 ( 641) hydrogen bonds : angle 4.10106 ( 1896) metal coordination : bond 0.00323 ( 8) metal coordination : angle 1.30814 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 358 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.6812 (mpp) REVERT: A 291 ASN cc_start: 0.8391 (p0) cc_final: 0.8020 (p0) REVERT: A 534 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7618 (ptm-80) REVERT: A 537 ASP cc_start: 0.8103 (m-30) cc_final: 0.7748 (p0) REVERT: A 646 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8172 (ttpp) REVERT: A 650 GLN cc_start: 0.8202 (mt0) cc_final: 0.7846 (mt0) REVERT: A 673 ASN cc_start: 0.8642 (t0) cc_final: 0.8325 (t0) REVERT: A 762 LEU cc_start: 0.8067 (mm) cc_final: 0.7837 (mm) REVERT: A 821 ARG cc_start: 0.8179 (mtp180) cc_final: 0.7509 (mtp85) REVERT: A 823 GLU cc_start: 0.7716 (pm20) cc_final: 0.6950 (pm20) REVERT: A 842 HIS cc_start: 0.5411 (OUTLIER) cc_final: 0.3972 (p90) REVERT: B 103 HIS cc_start: 0.7684 (p-80) cc_final: 0.7319 (m-70) REVERT: B 179 GLU cc_start: 0.3671 (OUTLIER) cc_final: 0.3099 (mm-30) REVERT: B 261 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7960 (mmmm) REVERT: B 308 TYR cc_start: 0.8173 (p90) cc_final: 0.7767 (p90) REVERT: B 348 MET cc_start: 0.8762 (ttm) cc_final: 0.8452 (ttt) REVERT: B 401 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7078 (tm-30) REVERT: B 407 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7314 (mm-30) REVERT: B 483 GLU cc_start: 0.8020 (mp0) cc_final: 0.7611 (mp0) REVERT: B 496 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8566 (mt) REVERT: B 560 SER cc_start: 0.8285 (t) cc_final: 0.7977 (m) REVERT: B 612 ASP cc_start: 0.8199 (m-30) cc_final: 0.7757 (m-30) REVERT: B 637 GLN cc_start: 0.8515 (mt0) cc_final: 0.8285 (mt0) REVERT: B 790 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8233 (p) REVERT: B 821 ARG cc_start: 0.8290 (mtp180) cc_final: 0.7748 (mtp180) REVERT: B 823 GLU cc_start: 0.7711 (pm20) cc_final: 0.7206 (pm20) REVERT: B 833 LEU cc_start: 0.8453 (mp) cc_final: 0.8233 (mm) REVERT: B 837 GLU cc_start: 0.7581 (pp20) cc_final: 0.7240 (pp20) REVERT: B 865 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7188 (tp) outliers start: 51 outliers final: 32 residues processed: 388 average time/residue: 0.6859 time to fit residues: 288.3672 Evaluate side-chains 402 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 362 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 865 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.7980 chunk 159 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN A 491 GLN ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** B 575 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 = 0.3739 r_free = 0.3739 target = 0.134236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.113033 restraints weight = 18057.212| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.13 r_work: 0.3315 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14164 Z= 0.165 Angle : 0.524 9.993 19107 Z= 0.271 Chirality : 0.042 0.191 2135 Planarity : 0.004 0.046 2426 Dihedral : 3.942 19.507 1863 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.28 % Allowed : 20.93 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.20), residues: 1717 helix: 1.87 (0.19), residues: 718 sheet: 1.01 (0.30), residues: 282 loop : -0.39 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 820 TYR 0.018 0.001 TYR A 623 PHE 0.023 0.001 PHE B 317 TRP 0.007 0.001 TRP A 344 HIS 0.008 0.001 HIS A 890 Details of bonding type rmsd covalent geometry : bond 0.00391 (14156) covalent geometry : angle 0.52376 (19101) hydrogen bonds : bond 0.04077 ( 641) hydrogen bonds : angle 4.10896 ( 1896) metal coordination : bond 0.00204 ( 8) metal coordination : angle 1.17812 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 357 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ILE cc_start: 0.8830 (mt) cc_final: 0.8587 (mm) REVERT: A 183 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6827 (mpp) REVERT: A 286 GLU cc_start: 0.8120 (mp0) cc_final: 0.7793 (mp0) REVERT: A 291 ASN cc_start: 0.8370 (p0) cc_final: 0.7985 (p0) REVERT: A 534 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7606 (ptm-80) REVERT: A 537 ASP cc_start: 0.8109 (m-30) cc_final: 0.7762 (p0) REVERT: A 614 PHE cc_start: 0.8581 (m-80) cc_final: 0.8249 (m-80) REVERT: A 646 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8189 (ttpp) REVERT: A 650 GLN cc_start: 0.8202 (mt0) cc_final: 0.7843 (mt0) REVERT: A 673 ASN cc_start: 0.8642 (t0) cc_final: 0.8346 (t0) REVERT: A 762 LEU cc_start: 0.8065 (mm) cc_final: 0.7831 (mm) REVERT: A 823 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: A 842 HIS cc_start: 0.5411 (OUTLIER) cc_final: 0.3933 (p90) REVERT: B 103 HIS cc_start: 0.7678 (p-80) cc_final: 0.7336 (m-70) REVERT: B 179 GLU cc_start: 0.3707 (OUTLIER) cc_final: 0.3152 (mm-30) REVERT: B 261 LYS cc_start: 0.8335 (mmtt) cc_final: 0.7972 (mmmm) REVERT: B 308 TYR cc_start: 0.8165 (p90) cc_final: 0.7764 (p90) REVERT: B 348 MET cc_start: 0.8765 (ttm) cc_final: 0.8464 (ttt) REVERT: B 401 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7218 (tm-30) REVERT: B 407 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7069 (mm-30) REVERT: B 411 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8256 (mttp) REVERT: B 483 GLU cc_start: 0.8010 (mp0) cc_final: 0.7599 (mp0) REVERT: B 496 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8579 (mt) REVERT: B 560 SER cc_start: 0.8307 (t) cc_final: 0.8016 (m) REVERT: B 612 ASP cc_start: 0.8225 (m-30) cc_final: 0.7812 (m-30) REVERT: B 637 GLN cc_start: 0.8505 (mt0) cc_final: 0.8261 (mt0) REVERT: B 790 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8247 (p) REVERT: B 821 ARG cc_start: 0.8303 (mtp180) cc_final: 0.7739 (mtp180) REVERT: B 823 GLU cc_start: 0.7680 (pm20) cc_final: 0.7175 (pm20) REVERT: B 833 LEU cc_start: 0.8485 (mp) cc_final: 0.8253 (mm) REVERT: B 837 GLU cc_start: 0.7553 (pp20) cc_final: 0.7202 (pp20) REVERT: B 838 LEU cc_start: 0.7709 (tt) cc_final: 0.7496 (tt) REVERT: B 842 HIS cc_start: 0.6305 (OUTLIER) cc_final: 0.4571 (p90) REVERT: B 865 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7224 (tp) outliers start: 51 outliers final: 32 residues processed: 384 average time/residue: 0.6923 time to fit residues: 287.5615 Evaluate side-chains 392 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 349 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 747 LYS Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 865 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 122 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 133 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN A 491 GLN ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.135185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114030 restraints weight = 18111.709| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.14 r_work: 0.3328 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14164 Z= 0.124 Angle : 0.532 10.539 19107 Z= 0.272 Chirality : 0.041 0.196 2135 Planarity : 0.004 0.046 2426 Dihedral : 3.886 19.519 1863 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.96 % Allowed : 21.83 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.20), residues: 1717 helix: 1.95 (0.19), residues: 718 sheet: 1.02 (0.30), residues: 282 loop : -0.34 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 820 TYR 0.023 0.001 TYR B 623 PHE 0.023 0.001 PHE B 317 TRP 0.008 0.001 TRP A 112 HIS 0.009 0.001 HIS A 890 Details of bonding type rmsd covalent geometry : bond 0.00289 (14156) covalent geometry : angle 0.53125 (19101) hydrogen bonds : bond 0.03775 ( 641) hydrogen bonds : angle 4.07448 ( 1896) metal coordination : bond 0.00369 ( 8) metal coordination : angle 1.32229 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 356 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ILE cc_start: 0.8820 (mt) cc_final: 0.8568 (mm) REVERT: A 148 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7635 (tp30) REVERT: A 183 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.6798 (mpp) REVERT: A 286 GLU cc_start: 0.8111 (mp0) cc_final: 0.7826 (mp0) REVERT: A 291 ASN cc_start: 0.8348 (p0) cc_final: 0.7966 (p0) REVERT: A 537 ASP cc_start: 0.8084 (m-30) cc_final: 0.7747 (p0) REVERT: A 614 PHE cc_start: 0.8558 (m-80) cc_final: 0.8228 (m-80) REVERT: A 646 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8190 (ttpp) REVERT: A 650 GLN cc_start: 0.8193 (mt0) cc_final: 0.7850 (mt0) REVERT: A 673 ASN cc_start: 0.8633 (t0) cc_final: 0.8326 (t0) REVERT: A 762 LEU cc_start: 0.8064 (mm) cc_final: 0.7822 (mm) REVERT: A 823 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7460 (pm20) REVERT: A 833 LEU cc_start: 0.8576 (mm) cc_final: 0.8262 (mt) REVERT: A 842 HIS cc_start: 0.5414 (OUTLIER) cc_final: 0.3930 (p90) REVERT: B 103 HIS cc_start: 0.7641 (p-80) cc_final: 0.7304 (m-70) REVERT: B 179 GLU cc_start: 0.3703 (OUTLIER) cc_final: 0.3132 (mm-30) REVERT: B 261 LYS cc_start: 0.8311 (mmtt) cc_final: 0.7954 (mmmm) REVERT: B 308 TYR cc_start: 0.8144 (p90) cc_final: 0.7789 (p90) REVERT: B 348 MET cc_start: 0.8757 (ttm) cc_final: 0.8526 (ttt) REVERT: B 401 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7021 (tm-30) REVERT: B 407 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7364 (mm-30) REVERT: B 483 GLU cc_start: 0.8014 (mp0) cc_final: 0.7606 (mp0) REVERT: B 612 ASP cc_start: 0.8203 (m-30) cc_final: 0.7789 (m-30) REVERT: B 637 GLN cc_start: 0.8482 (mt0) cc_final: 0.8271 (mt0) REVERT: B 790 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8244 (p) REVERT: B 821 ARG cc_start: 0.8278 (mtp180) cc_final: 0.7607 (mtp180) REVERT: B 823 GLU cc_start: 0.7652 (pm20) cc_final: 0.7096 (pm20) REVERT: B 833 LEU cc_start: 0.8469 (mp) cc_final: 0.8244 (mm) REVERT: B 837 GLU cc_start: 0.7528 (pp20) cc_final: 0.7156 (pp20) REVERT: B 838 LEU cc_start: 0.7671 (tt) cc_final: 0.7433 (tt) REVERT: B 842 HIS cc_start: 0.6285 (OUTLIER) cc_final: 0.4552 (p90) REVERT: B 865 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7210 (tp) outliers start: 46 outliers final: 26 residues processed: 379 average time/residue: 0.6888 time to fit residues: 282.7199 Evaluate side-chains 383 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 348 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 514 HIS Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 865 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN A 491 GLN ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 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 = 0.3748 r_free = 0.3748 target = 0.134984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113792 restraints weight = 18056.968| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.14 r_work: 0.3324 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14164 Z= 0.146 Angle : 0.535 9.735 19107 Z= 0.273 Chirality : 0.042 0.199 2135 Planarity : 0.004 0.045 2426 Dihedral : 3.892 19.381 1863 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.77 % Allowed : 22.22 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.20), residues: 1717 helix: 1.91 (0.19), residues: 718 sheet: 1.00 (0.30), residues: 282 loop : -0.36 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 820 TYR 0.021 0.001 TYR A 623 PHE 0.024 0.001 PHE B 317 TRP 0.007 0.001 TRP A 112 HIS 0.009 0.001 HIS A 890 Details of bonding type rmsd covalent geometry : bond 0.00346 (14156) covalent geometry : angle 0.53496 (19101) hydrogen bonds : bond 0.03886 ( 641) hydrogen bonds : angle 4.08935 ( 1896) metal coordination : bond 0.00211 ( 8) metal coordination : angle 1.22437 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 349 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ILE cc_start: 0.8830 (mt) cc_final: 0.8583 (mm) REVERT: A 183 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.6799 (mpp) REVERT: A 286 GLU cc_start: 0.8117 (mp0) cc_final: 0.7847 (mp0) REVERT: A 291 ASN cc_start: 0.8340 (p0) cc_final: 0.7923 (p0) REVERT: A 537 ASP cc_start: 0.8063 (m-30) cc_final: 0.7749 (p0) REVERT: A 614 PHE cc_start: 0.8561 (m-80) cc_final: 0.8233 (m-80) REVERT: A 646 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8192 (ttpp) REVERT: A 650 GLN cc_start: 0.8188 (mt0) cc_final: 0.7841 (mt0) REVERT: A 673 ASN cc_start: 0.8626 (t0) cc_final: 0.8321 (t0) REVERT: A 762 LEU cc_start: 0.8055 (mm) cc_final: 0.7797 (mm) REVERT: A 823 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7459 (pm20) REVERT: A 842 HIS cc_start: 0.5394 (OUTLIER) cc_final: 0.3925 (p90) REVERT: B 103 HIS cc_start: 0.7673 (p-80) cc_final: 0.7308 (m-70) REVERT: B 179 GLU cc_start: 0.3598 (OUTLIER) cc_final: 0.3046 (mm-30) REVERT: B 261 LYS cc_start: 0.8316 (mmtt) cc_final: 0.7957 (mmmm) REVERT: B 308 TYR cc_start: 0.8146 (p90) cc_final: 0.7799 (p90) REVERT: B 348 MET cc_start: 0.8753 (ttm) cc_final: 0.8516 (ttt) REVERT: B 401 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7023 (tm-30) REVERT: B 407 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7330 (mm-30) REVERT: B 483 GLU cc_start: 0.8009 (mp0) cc_final: 0.7596 (mp0) REVERT: B 612 ASP cc_start: 0.8189 (m-30) cc_final: 0.7784 (m-30) REVERT: B 637 GLN cc_start: 0.8480 (mt0) cc_final: 0.8260 (mt0) REVERT: B 790 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8254 (p) REVERT: B 821 ARG cc_start: 0.8285 (mtp180) cc_final: 0.7672 (mtp180) REVERT: B 823 GLU cc_start: 0.7656 (pm20) cc_final: 0.7113 (pm20) REVERT: B 833 LEU cc_start: 0.8471 (mp) cc_final: 0.8247 (mm) REVERT: B 837 GLU cc_start: 0.7506 (pp20) cc_final: 0.7154 (pp20) REVERT: B 838 LEU cc_start: 0.7699 (tt) cc_final: 0.7466 (tt) REVERT: B 842 HIS cc_start: 0.6321 (OUTLIER) cc_final: 0.4588 (p90) REVERT: B 865 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7194 (tp) outliers start: 43 outliers final: 26 residues processed: 371 average time/residue: 0.6750 time to fit residues: 270.4060 Evaluate side-chains 377 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 343 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 646 LYS Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 842 HIS Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 842 HIS Chi-restraints excluded: chain B residue 865 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 17 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 477 ASN A 491 GLN A 637 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112614 restraints weight = 17976.673| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.12 r_work: 0.3298 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14164 Z= 0.259 Angle : 0.602 10.993 19107 Z= 0.307 Chirality : 0.045 0.227 2135 Planarity : 0.004 0.047 2426 Dihedral : 4.119 18.710 1863 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.70 % Allowed : 22.67 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.20), residues: 1717 helix: 1.69 (0.19), residues: 718 sheet: 1.02 (0.30), residues: 282 loop : -0.45 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 820 TYR 0.021 0.002 TYR A 623 PHE 0.027 0.002 PHE A 317 TRP 0.007 0.002 TRP B 259 HIS 0.011 0.001 HIS A 890 Details of bonding type rmsd covalent geometry : bond 0.00624 (14156) covalent geometry : angle 0.60234 (19101) hydrogen bonds : bond 0.04697 ( 641) hydrogen bonds : angle 4.21618 ( 1896) metal coordination : bond 0.00890 ( 8) metal coordination : angle 0.97660 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6076.39 seconds wall clock time: 104 minutes 9.85 seconds (6249.85 seconds total)