Starting phenix.real_space_refine on Sat Aug 23 14:46:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9khh_62340/08_2025/9khh_62340.cif Found real_map, /net/cci-nas-00/data/ceres_data/9khh_62340/08_2025/9khh_62340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9khh_62340/08_2025/9khh_62340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9khh_62340/08_2025/9khh_62340.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9khh_62340/08_2025/9khh_62340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9khh_62340/08_2025/9khh_62340.map" } resolution = 3.65 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= -0.000 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 7472 2.51 5 N 2342 2.21 5 O 2476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12354 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "E" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 778 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain breaks: 1 Chain: "F" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 776 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "B" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "C" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 4577 Classifications: {'peptide': 732} Incomplete info: {'backbone_only': 273, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 37, 'TRANS': 694} Chain breaks: 3 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1203 Unresolved non-hydrogen angles: 1753 Unresolved non-hydrogen dihedrals: 813 Unresolved non-hydrogen chiralities: 374 Planarities with less than four sites: {'ARG:plan': 8, 'TYR:plan': 8, 'HIS:plan': 4, 'PHE:plan': 32, 'GLU:plan': 9, 'TRP:plan': 7, 'ASN:plan1': 8, 'ASP:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 508 Chain: "D" Number of atoms: 4555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 4555 Classifications: {'peptide': 725} Incomplete info: {'backbone_only': 266, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 36, 'TRANS': 688} Chain breaks: 3 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1172 Unresolved non-hydrogen angles: 1708 Unresolved non-hydrogen dihedrals: 793 Unresolved non-hydrogen chiralities: 364 Planarities with less than four sites: {'TYR:plan': 8, 'PHE:plan': 32, 'GLU:plan': 9, 'TRP:plan': 7, 'ARG:plan': 7, 'ASN:plan1': 8, 'ASP:plan': 3, 'HIS:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 497 Time building chain proxies: 2.49, per 1000 atoms: 0.20 Number of scatterers: 12354 At special positions: 0 Unit cell: (190.638, 131.733, 151.011, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 2476 8.00 N 2342 7.00 C 7472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 428 " - pdb=" SG CYS A 501 " distance=2.04 Simple disulfide: pdb=" SG CYS E 39 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 110 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 69 " - pdb=" SG CYS E 128 " distance=2.03 Simple disulfide: pdb=" SG CYS E 93 " - pdb=" SG CYS F 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 95 " - pdb=" SG CYS F 93 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS F 131 " distance=2.03 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 110 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 69 " - pdb=" SG CYS F 128 " distance=2.03 Simple disulfide: pdb=" SG CYS B 428 " - pdb=" SG CYS B 501 " distance=2.04 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 43 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 364 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 43 " distance=2.03 Simple disulfide: pdb=" SG CYS D 339 " - pdb=" SG CYS D 364 " distance=2.03 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: 0.84 Conformation dependent library (CDL) restraints added in 481.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2454 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 21 sheets defined 29.4% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 467 through 470 Processing helix chain 'A' and resid 492 through 496 removed outlier: 3.989A pdb=" N THR A 496 " --> pdb=" O PRO A 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 113 No H-bonds generated for 'chain 'F' and resid 111 through 113' Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 492 through 496 removed outlier: 3.989A pdb=" N THR B 496 " --> pdb=" O PRO B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.704A pdb=" N ARG C 126 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 175 removed outlier: 3.812A pdb=" N ASN C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 247 removed outlier: 3.835A pdb=" N ILE C 244 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 245 " --> pdb=" O GLN C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.502A pdb=" N GLU C 341 " --> pdb=" O ASN C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.285A pdb=" N PHE C 409 " --> pdb=" O SER C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 567 removed outlier: 4.560A pdb=" N CYS C 567 " --> pdb=" O THR C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 601 removed outlier: 3.526A pdb=" N LEU C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE C 586 " --> pdb=" O VAL C 582 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET C 587 " --> pdb=" O SER C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 615 removed outlier: 3.733A pdb=" N PHE C 608 " --> pdb=" O ARG C 604 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP C 611 " --> pdb=" O GLU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 649 removed outlier: 4.480A pdb=" N LYS C 619 " --> pdb=" O GLY C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 683 removed outlier: 3.703A pdb=" N PHE C 670 " --> pdb=" O ALA C 666 " (cutoff:3.500A) Proline residue: C 680 - end of helix removed outlier: 3.732A pdb=" N HIS C 683 " --> pdb=" O PHE C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 690 removed outlier: 4.062A pdb=" N SER C 690 " --> pdb=" O TYR C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 730 removed outlier: 3.885A pdb=" N PHE C 718 " --> pdb=" O ASN C 714 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU C 719 " --> pdb=" O SER C 715 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 720 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU C 728 " --> pdb=" O ILE C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 768 removed outlier: 3.842A pdb=" N VAL C 749 " --> pdb=" O MET C 745 " (cutoff:3.500A) Proline residue: C 762 - end of helix removed outlier: 3.887A pdb=" N PHE C 768 " --> pdb=" O ALA C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 790 Processing helix chain 'C' and resid 791 through 803 Proline residue: C 798 - end of helix Processing helix chain 'C' and resid 805 through 820 removed outlier: 3.906A pdb=" N LYS C 809 " --> pdb=" O ASN C 805 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG C 817 " --> pdb=" O LYS C 813 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG C 818 " --> pdb=" O LEU C 814 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL C 819 " --> pdb=" O LEU C 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.704A pdb=" N ARG D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 175 removed outlier: 3.812A pdb=" N ASN D 175 " --> pdb=" O HIS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 247 removed outlier: 3.835A pdb=" N ILE D 244 " --> pdb=" O PRO D 241 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS D 245 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 removed outlier: 3.503A pdb=" N GLU D 341 " --> pdb=" O ASN D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.285A pdb=" N PHE D 409 " --> pdb=" O SER D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 567 removed outlier: 4.561A pdb=" N CYS D 567 " --> pdb=" O THR D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 601 removed outlier: 3.526A pdb=" N LEU D 585 " --> pdb=" O SER D 581 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE D 586 " --> pdb=" O VAL D 582 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET D 587 " --> pdb=" O SER D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 615 removed outlier: 3.732A pdb=" N PHE D 608 " --> pdb=" O ARG D 604 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TRP D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 649 removed outlier: 4.481A pdb=" N LYS D 619 " --> pdb=" O GLY D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 683 removed outlier: 3.703A pdb=" N PHE D 670 " --> pdb=" O ALA D 666 " (cutoff:3.500A) Proline residue: D 680 - end of helix removed outlier: 3.732A pdb=" N HIS D 683 " --> pdb=" O PHE D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 690 removed outlier: 4.063A pdb=" N SER D 690 " --> pdb=" O TYR D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 730 removed outlier: 3.885A pdb=" N PHE D 718 " --> pdb=" O ASN D 714 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU D 719 " --> pdb=" O SER D 715 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 720 " --> pdb=" O LEU D 716 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU D 728 " --> pdb=" O ILE D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 768 removed outlier: 3.843A pdb=" N VAL D 749 " --> pdb=" O MET D 745 " (cutoff:3.500A) Proline residue: D 762 - end of helix removed outlier: 3.888A pdb=" N PHE D 768 " --> pdb=" O ALA D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 790 Processing helix chain 'D' and resid 791 through 803 Proline residue: D 798 - end of helix Processing helix chain 'D' and resid 805 through 820 removed outlier: 3.906A pdb=" N LYS D 809 " --> pdb=" O ASN D 805 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG D 817 " --> pdb=" O LYS D 813 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ARG D 818 " --> pdb=" O LEU D 814 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL D 819 " --> pdb=" O LEU D 815 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 424 through 426 Processing sheet with id=AA2, first strand: chain 'A' and resid 463 through 465 removed outlier: 5.430A pdb=" N GLY A 453 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ARG A 444 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 465 removed outlier: 5.430A pdb=" N GLY A 453 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ARG A 444 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 40 through 46 removed outlier: 3.593A pdb=" N GLU E 66 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ALA E 63 " --> pdb=" O PRO F 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 89 through 92 removed outlier: 7.685A pdb=" N ALA F 63 " --> pdb=" O PRO E 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 94 through 97 removed outlier: 3.592A pdb=" N HIS E 127 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 101 through 109 removed outlier: 3.522A pdb=" N LEU E 116 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR E 119 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 94 through 109 removed outlier: 6.750A pdb=" N HIS F 94 " --> pdb=" O GLU F 130 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU F 130 " --> pdb=" O HIS F 94 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS F 96 " --> pdb=" O CYS F 128 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS F 128 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N CYS F 126 " --> pdb=" O PRO F 98 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR F 100 " --> pdb=" O LEU F 124 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F 116 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 424 through 426 Processing sheet with id=AB1, first strand: chain 'B' and resid 463 through 465 removed outlier: 5.431A pdb=" N GLY B 453 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ARG B 444 " --> pdb=" O GLY B 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 463 through 465 removed outlier: 5.431A pdb=" N GLY B 453 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ARG B 444 " --> pdb=" O GLY B 453 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 40 through 42 removed outlier: 7.033A pdb=" N LEU C 110 " --> pdb=" O ARG C 135 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU C 134 " --> pdb=" O TRP C 159 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU C 206 " --> pdb=" O ASP C 231 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.713A pdb=" N ILE C 192 " --> pdb=" O SER C 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 262 through 263 removed outlier: 3.521A pdb=" N ILE C 263 " --> pdb=" O PHE C 286 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 300 through 304 removed outlier: 6.834A pdb=" N LEU C 348 " --> pdb=" O SER C 371 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU C 418 " --> pdb=" O LYS C 440 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 463 " --> pdb=" O LEU C 439 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 462 " --> pdb=" O HIS C 521 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 40 through 42 removed outlier: 7.033A pdb=" N LEU D 110 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU D 134 " --> pdb=" O TRP D 159 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU D 206 " --> pdb=" O ASP D 231 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 191 through 192 removed outlier: 3.713A pdb=" N ILE D 192 " --> pdb=" O SER D 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 262 through 263 removed outlier: 3.521A pdb=" N ILE D 263 " --> pdb=" O PHE D 286 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 300 through 304 removed outlier: 6.834A pdb=" N LEU D 348 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU D 418 " --> pdb=" O LYS D 440 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 463 " --> pdb=" O LEU D 439 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1470 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: 2.26 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4506 1.35 - 1.47: 2843 1.47 - 1.59: 5116 1.59 - 1.71: 0 1.71 - 1.83: 82 Bond restraints: 12547 Sorted by residual: bond pdb=" CB GLN F 71 " pdb=" CG GLN F 71 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" CB LYS A 449 " pdb=" CG LYS A 449 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CB LYS B 449 " pdb=" CG LYS B 449 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CA CYS F 39 " pdb=" CB CYS F 39 " ideal model delta sigma weight residual 1.524 1.537 -0.013 1.22e-02 6.72e+03 1.12e+00 bond pdb=" CB GLN B 523 " pdb=" CG GLN B 523 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.08e+00 ... (remaining 12542 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 16492 2.28 - 4.57: 242 4.57 - 6.85: 24 6.85 - 9.14: 1 9.14 - 11.42: 3 Bond angle restraints: 16762 Sorted by residual: angle pdb=" CB MET C 308 " pdb=" CG MET C 308 " pdb=" SD MET C 308 " ideal model delta sigma weight residual 112.70 124.12 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB MET D 308 " pdb=" CG MET D 308 " pdb=" SD MET D 308 " ideal model delta sigma weight residual 112.70 124.11 -11.41 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CA GLN F 71 " pdb=" CB GLN F 71 " pdb=" CG GLN F 71 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" N ARG D 460 " pdb=" CA ARG D 460 " pdb=" C ARG D 460 " ideal model delta sigma weight residual 111.71 107.33 4.38 1.34e+00 5.57e-01 1.07e+01 angle pdb=" N ARG C 460 " pdb=" CA ARG C 460 " pdb=" C ARG C 460 " ideal model delta sigma weight residual 111.71 107.33 4.38 1.34e+00 5.57e-01 1.07e+01 ... (remaining 16757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6189 17.97 - 35.93: 505 35.93 - 53.90: 122 53.90 - 71.86: 18 71.86 - 89.83: 7 Dihedral angle restraints: 6841 sinusoidal: 2497 harmonic: 4344 Sorted by residual: dihedral pdb=" CB CYS E 65 " pdb=" SG CYS E 65 " pdb=" SG CYS E 126 " pdb=" CB CYS E 126 " ideal model delta sinusoidal sigma weight residual 93.00 166.57 -73.57 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CB CYS E 93 " pdb=" SG CYS E 93 " pdb=" SG CYS F 95 " pdb=" CB CYS F 95 " ideal model delta sinusoidal sigma weight residual 93.00 39.74 53.26 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CB CYS D 33 " pdb=" SG CYS D 33 " pdb=" SG CYS D 43 " pdb=" CB CYS D 43 " ideal model delta sinusoidal sigma weight residual 93.00 48.61 44.39 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 6838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 909 0.031 - 0.061: 441 0.061 - 0.092: 148 0.092 - 0.123: 88 0.123 - 0.153: 17 Chirality restraints: 1603 Sorted by residual: chirality pdb=" CA ILE C 263 " pdb=" N ILE C 263 " pdb=" C ILE C 263 " pdb=" CB ILE C 263 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ILE D 263 " pdb=" N ILE D 263 " pdb=" C ILE D 263 " pdb=" CB ILE D 263 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA ILE C 64 " pdb=" N ILE C 64 " pdb=" C ILE C 64 " pdb=" CB ILE C 64 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 1600 not shown) Planarity restraints: 2371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS F 50 " 0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO F 51 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO F 51 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 51 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 44 " 0.011 2.00e-02 2.50e+03 1.00e-02 2.02e+00 pdb=" CG TYR E 44 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR E 44 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR E 44 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 44 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 44 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 44 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 44 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 436 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO B 437 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 437 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 437 " 0.019 5.00e-02 4.00e+02 ... (remaining 2368 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 4 2.35 - 2.99: 6755 2.99 - 3.63: 17390 3.63 - 4.26: 25130 4.26 - 4.90: 43664 Nonbonded interactions: 92943 Sorted by model distance: nonbonded pdb=" SD MET E 59 " pdb=" CE2 TRP D 159 " model vdw 1.714 3.620 nonbonded pdb=" SD MET E 59 " pdb=" NE1 TRP D 159 " model vdw 1.733 3.480 nonbonded pdb=" SD MET E 59 " pdb=" CZ2 TRP D 159 " model vdw 1.985 3.700 nonbonded pdb=" SG CYS C 471 " pdb=" CA CYS C 532 " model vdw 2.262 3.830 nonbonded pdb=" NZ LYS E 54 " pdb=" CE2 TYR D 280 " model vdw 2.468 3.420 ... (remaining 92938 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' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 30 through 473 or resid 527 through 820)) selection = (chain 'D' and (resid 30 through 459 or (resid 460 and (name N or name CA or nam \ e C or name O or name CB )) or resid 461 through 820)) } ncs_group { reference = (chain 'E' and resid 35 through 132) selection = (chain 'F' and (resid 35 through 112 or resid 114 through 132)) } 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 group one per residue 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: 11.290 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.760 Find NCS groups from input model: 0.220 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12564 Z= 0.126 Angle : 0.665 11.422 16796 Z= 0.360 Chirality : 0.045 0.153 1603 Planarity : 0.004 0.045 2371 Dihedral : 13.838 89.825 4336 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.62 % Allowed : 17.40 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.21), residues: 1845 helix: 3.24 (0.26), residues: 458 sheet: -1.36 (0.29), residues: 332 loop : -0.55 (0.20), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 97 TYR 0.025 0.002 TYR E 44 PHE 0.015 0.001 PHE D 58 TRP 0.011 0.002 TRP B 442 HIS 0.005 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00255 (12547) covalent geometry : angle 0.66065 (16762) SS BOND : bond 0.00404 ( 17) SS BOND : angle 1.85681 ( 34) hydrogen bonds : bond 0.14884 ( 496) hydrogen bonds : angle 5.59685 ( 1470) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 233 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 GLU cc_start: 0.6042 (pm20) cc_final: 0.5819 (pm20) REVERT: F 114 MET cc_start: 0.7482 (tmm) cc_final: 0.7263 (tmm) REVERT: C 394 LEU cc_start: 0.8310 (tp) cc_final: 0.7885 (tp) REVERT: C 456 PHE cc_start: 0.6134 (m-80) cc_final: 0.5721 (m-80) outliers start: 7 outliers final: 3 residues processed: 238 average time/residue: 0.1053 time to fit residues: 36.4269 Evaluate side-chains 127 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.0060 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 417 ASN ** C 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 ASN ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.062140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.047884 restraints weight = 90626.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.049216 restraints weight = 47183.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.050010 restraints weight = 32241.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.050491 restraints weight = 25638.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.050787 restraints weight = 22383.008| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12564 Z= 0.124 Angle : 0.633 8.227 16796 Z= 0.313 Chirality : 0.046 0.189 1603 Planarity : 0.004 0.042 2371 Dihedral : 4.577 30.979 1961 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.28 % Allowed : 19.77 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.21), residues: 1845 helix: 3.50 (0.25), residues: 446 sheet: -1.29 (0.28), residues: 366 loop : -0.52 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 121 TYR 0.018 0.002 TYR E 44 PHE 0.019 0.001 PHE F 89 TRP 0.011 0.002 TRP C 159 HIS 0.005 0.001 HIS C 405 Details of bonding type rmsd covalent geometry : bond 0.00276 (12547) covalent geometry : angle 0.63214 (16762) SS BOND : bond 0.00272 ( 17) SS BOND : angle 1.11143 ( 34) hydrogen bonds : bond 0.03155 ( 496) hydrogen bonds : angle 4.03009 ( 1470) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 LYS cc_start: 0.8105 (pptt) cc_final: 0.7778 (pptt) REVERT: A 494 GLU cc_start: 0.9295 (tp30) cc_final: 0.8940 (tm-30) REVERT: A 518 PHE cc_start: 0.8030 (m-80) cc_final: 0.7785 (m-80) REVERT: B 426 LEU cc_start: 0.8363 (tp) cc_final: 0.7922 (tp) REVERT: C 367 LEU cc_start: 0.9173 (mt) cc_final: 0.8926 (mm) REVERT: C 451 LEU cc_start: 0.8093 (mt) cc_final: 0.7391 (tp) REVERT: C 456 PHE cc_start: 0.8061 (m-80) cc_final: 0.7798 (m-80) REVERT: D 315 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8686 (mm) REVERT: D 345 LEU cc_start: 0.9019 (tp) cc_final: 0.8680 (pp) REVERT: D 456 PHE cc_start: 0.8478 (m-80) cc_final: 0.8264 (m-80) outliers start: 26 outliers final: 16 residues processed: 157 average time/residue: 0.1029 time to fit residues: 25.1034 Evaluate side-chains 131 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain E residue 43 HIS Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 132 ASN Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 372 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 120 optimal weight: 0.8980 chunk 101 optimal weight: 40.0000 chunk 63 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 GLN C 373 GLN ** C 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN ** D 423 ASN ** 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 = 0.3761 r_free = 0.3761 target = 0.058216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.042865 restraints weight = 92324.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.044028 restraints weight = 50056.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.044715 restraints weight = 35221.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.045119 restraints weight = 28751.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.045366 restraints weight = 25538.701| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12564 Z= 0.249 Angle : 0.707 7.820 16796 Z= 0.357 Chirality : 0.047 0.192 1603 Planarity : 0.005 0.055 2371 Dihedral : 5.292 31.220 1961 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.31 % Allowed : 18.45 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.21), residues: 1845 helix: 3.45 (0.25), residues: 460 sheet: -1.39 (0.28), residues: 346 loop : -0.66 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 451 TYR 0.018 0.002 TYR E 44 PHE 0.015 0.002 PHE A 473 TRP 0.018 0.002 TRP C 159 HIS 0.007 0.002 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00552 (12547) covalent geometry : angle 0.70558 (16762) SS BOND : bond 0.00716 ( 17) SS BOND : angle 1.28704 ( 34) hydrogen bonds : bond 0.03549 ( 496) hydrogen bonds : angle 4.06928 ( 1470) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 101 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 GLU cc_start: 0.9337 (tp30) cc_final: 0.9079 (tm-30) REVERT: B 426 LEU cc_start: 0.8355 (tp) cc_final: 0.8089 (tp) REVERT: B 523 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8250 (pm20) REVERT: C 83 LEU cc_start: 0.9557 (mt) cc_final: 0.9326 (mt) REVERT: C 91 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7985 (t0) REVERT: C 425 LEU cc_start: 0.9122 (mp) cc_final: 0.8590 (pt) REVERT: C 447 LEU cc_start: 0.8592 (tp) cc_final: 0.8223 (tp) outliers start: 49 outliers final: 31 residues processed: 138 average time/residue: 0.0902 time to fit residues: 20.0465 Evaluate side-chains 122 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 TYR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 433 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 30 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 151 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 147 optimal weight: 0.0020 chunk 108 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.058361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.043105 restraints weight = 91210.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.044284 restraints weight = 48920.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.044994 restraints weight = 34296.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.045415 restraints weight = 27800.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.045674 restraints weight = 24610.844| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12564 Z= 0.146 Angle : 0.601 8.133 16796 Z= 0.298 Chirality : 0.044 0.173 1603 Planarity : 0.004 0.048 2371 Dihedral : 4.711 31.462 1961 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.87 % Allowed : 19.24 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.21), residues: 1845 helix: 3.55 (0.25), residues: 461 sheet: -1.30 (0.28), residues: 347 loop : -0.54 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 444 TYR 0.009 0.001 TYR E 44 PHE 0.009 0.001 PHE D 286 TRP 0.009 0.001 TRP C 159 HIS 0.004 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00324 (12547) covalent geometry : angle 0.59946 (16762) SS BOND : bond 0.00230 ( 17) SS BOND : angle 1.13565 ( 34) hydrogen bonds : bond 0.02764 ( 496) hydrogen bonds : angle 3.66159 ( 1470) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 426 LEU cc_start: 0.8638 (tp) cc_final: 0.8382 (tp) REVERT: B 523 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8290 (pm20) REVERT: C 83 LEU cc_start: 0.9534 (mt) cc_final: 0.9310 (mt) REVERT: C 308 MET cc_start: 0.9024 (mtp) cc_final: 0.8740 (tpp) REVERT: C 396 LEU cc_start: 0.9831 (mm) cc_final: 0.9427 (pp) REVERT: C 456 PHE cc_start: 0.8108 (m-80) cc_final: 0.7892 (m-80) REVERT: D 315 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8687 (mm) REVERT: D 439 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9235 (tp) outliers start: 44 outliers final: 28 residues processed: 130 average time/residue: 0.0895 time to fit residues: 18.3056 Evaluate side-chains 123 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 TYR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 439 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 173 optimal weight: 30.0000 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN ** C 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN D 271 ASN ** D 423 ASN ** 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 = 0.3717 r_free = 0.3717 target = 0.056489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.040982 restraints weight = 94210.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.042104 restraints weight = 50452.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.042747 restraints weight = 35636.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.043150 restraints weight = 29216.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.043373 restraints weight = 26046.360| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 12564 Z= 0.307 Angle : 0.734 7.492 16796 Z= 0.369 Chirality : 0.047 0.153 1603 Planarity : 0.004 0.038 2371 Dihedral : 5.414 30.671 1961 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.64 % Favored : 94.25 % Rotamer: Outliers : 4.31 % Allowed : 19.24 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.21), residues: 1845 helix: 3.45 (0.24), residues: 469 sheet: -1.43 (0.27), residues: 359 loop : -0.67 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 115 TYR 0.014 0.002 TYR F 122 PHE 0.020 0.002 PHE E 89 TRP 0.015 0.002 TRP D 159 HIS 0.008 0.002 HIS D 402 Details of bonding type rmsd covalent geometry : bond 0.00672 (12547) covalent geometry : angle 0.73211 (16762) SS BOND : bond 0.00384 ( 17) SS BOND : angle 1.28436 ( 34) hydrogen bonds : bond 0.03380 ( 496) hydrogen bonds : angle 3.96804 ( 1470) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 89 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 116 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7808 (pp) REVERT: B 426 LEU cc_start: 0.8639 (tp) cc_final: 0.8322 (tp) REVERT: B 523 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8438 (pm20) REVERT: C 83 LEU cc_start: 0.9562 (mt) cc_final: 0.9293 (mt) REVERT: C 99 LYS cc_start: 0.9174 (tmtt) cc_final: 0.8886 (tttm) REVERT: D 344 MET cc_start: 0.8260 (pmm) cc_final: 0.7992 (pmm) outliers start: 49 outliers final: 37 residues processed: 128 average time/residue: 0.1026 time to fit residues: 19.8819 Evaluate side-chains 123 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 85 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 TYR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 441 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 ASN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN ** C 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN ** D 423 ASN ** 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 = 0.3741 r_free = 0.3741 target = 0.057751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.041959 restraints weight = 90618.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.043211 restraints weight = 46734.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.043980 restraints weight = 32013.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.044459 restraints weight = 25568.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.044740 restraints weight = 22301.352| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12564 Z= 0.116 Angle : 0.586 8.141 16796 Z= 0.290 Chirality : 0.044 0.165 1603 Planarity : 0.003 0.039 2371 Dihedral : 4.612 31.067 1961 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.04 % Allowed : 20.47 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.21), residues: 1845 helix: 3.62 (0.24), residues: 470 sheet: -1.28 (0.27), residues: 363 loop : -0.54 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 37 TYR 0.010 0.001 TYR B 465 PHE 0.007 0.001 PHE D 240 TRP 0.008 0.001 TRP C 159 HIS 0.004 0.001 HIS F 68 Details of bonding type rmsd covalent geometry : bond 0.00262 (12547) covalent geometry : angle 0.58489 (16762) SS BOND : bond 0.00179 ( 17) SS BOND : angle 0.92192 ( 34) hydrogen bonds : bond 0.02590 ( 496) hydrogen bonds : angle 3.46288 ( 1470) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 93 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 GLU cc_start: 0.9333 (tp30) cc_final: 0.9111 (tm-30) REVERT: E 52 LEU cc_start: 0.9180 (mp) cc_final: 0.8877 (tt) REVERT: E 116 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7594 (pp) REVERT: B 426 LEU cc_start: 0.8595 (tp) cc_final: 0.8350 (tp) REVERT: B 523 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8316 (pm20) REVERT: C 83 LEU cc_start: 0.9494 (mt) cc_final: 0.9210 (mt) REVERT: C 250 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8613 (mt) REVERT: C 344 MET cc_start: 0.8222 (pmm) cc_final: 0.8000 (pmm) REVERT: C 394 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8679 (tp) REVERT: C 425 LEU cc_start: 0.9334 (mp) cc_final: 0.9015 (pt) REVERT: D 250 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8704 (mt) outliers start: 46 outliers final: 30 residues processed: 125 average time/residue: 0.1076 time to fit residues: 20.4727 Evaluate side-chains 120 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 TYR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain F residue 39 CYS Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 441 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 178 optimal weight: 30.0000 chunk 77 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 chunk 90 optimal weight: 20.0000 chunk 171 optimal weight: 0.0470 chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 ASN ** C 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.056773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.040993 restraints weight = 90578.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.042124 restraints weight = 48255.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.042838 restraints weight = 33765.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.043276 restraints weight = 27284.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.043544 restraints weight = 23976.884| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.6394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12564 Z= 0.218 Angle : 0.647 7.590 16796 Z= 0.323 Chirality : 0.044 0.153 1603 Planarity : 0.004 0.038 2371 Dihedral : 4.922 31.272 1961 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.37 % Favored : 94.53 % Rotamer: Outliers : 4.22 % Allowed : 21.53 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.21), residues: 1845 helix: 3.70 (0.24), residues: 474 sheet: -1.31 (0.27), residues: 365 loop : -0.56 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 407 TYR 0.011 0.001 TYR F 122 PHE 0.012 0.001 PHE E 89 TRP 0.017 0.002 TRP D 159 HIS 0.005 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00479 (12547) covalent geometry : angle 0.64575 (16762) SS BOND : bond 0.00324 ( 17) SS BOND : angle 1.13549 ( 34) hydrogen bonds : bond 0.02925 ( 496) hydrogen bonds : angle 3.60845 ( 1470) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 86 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 MET cc_start: 0.6811 (mtm) cc_final: 0.6467 (mtm) REVERT: E 52 LEU cc_start: 0.9101 (mp) cc_final: 0.8850 (tt) REVERT: E 116 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7656 (pp) REVERT: B 426 LEU cc_start: 0.8677 (tp) cc_final: 0.8395 (tp) REVERT: B 523 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8431 (pm20) REVERT: C 83 LEU cc_start: 0.9542 (mt) cc_final: 0.9285 (mt) REVERT: C 425 LEU cc_start: 0.9393 (mp) cc_final: 0.8672 (tp) REVERT: D 250 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8765 (tt) outliers start: 48 outliers final: 37 residues processed: 121 average time/residue: 0.0946 time to fit residues: 18.0894 Evaluate side-chains 121 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 TYR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain F residue 39 CYS Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 TYR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 441 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 110 optimal weight: 7.9990 chunk 76 optimal weight: 0.0870 chunk 61 optimal weight: 0.7980 chunk 165 optimal weight: 30.0000 chunk 78 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 175 optimal weight: 6.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 ASN ** C 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.057245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.041553 restraints weight = 90484.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.042712 restraints weight = 47967.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.043433 restraints weight = 33429.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.043891 restraints weight = 26896.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.044162 restraints weight = 23623.648| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12564 Z= 0.138 Angle : 0.595 8.397 16796 Z= 0.294 Chirality : 0.043 0.159 1603 Planarity : 0.003 0.038 2371 Dihedral : 4.603 31.160 1961 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.95 % Allowed : 21.70 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.21), residues: 1845 helix: 3.77 (0.24), residues: 474 sheet: -1.25 (0.27), residues: 364 loop : -0.54 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 37 TYR 0.009 0.001 TYR B 500 PHE 0.008 0.001 PHE D 240 TRP 0.011 0.001 TRP D 159 HIS 0.003 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00311 (12547) covalent geometry : angle 0.59417 (16762) SS BOND : bond 0.00186 ( 17) SS BOND : angle 1.00621 ( 34) hydrogen bonds : bond 0.02551 ( 496) hydrogen bonds : angle 3.43655 ( 1470) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 85 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 52 LEU cc_start: 0.9090 (mp) cc_final: 0.8825 (tt) REVERT: E 116 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7640 (pp) REVERT: B 426 LEU cc_start: 0.8622 (tp) cc_final: 0.8361 (tp) REVERT: B 523 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8343 (pm20) REVERT: C 83 LEU cc_start: 0.9513 (mt) cc_final: 0.9264 (mt) REVERT: C 250 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8722 (mt) REVERT: C 394 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8716 (tp) REVERT: C 425 LEU cc_start: 0.9354 (mp) cc_final: 0.8705 (tp) REVERT: D 250 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8690 (tt) outliers start: 45 outliers final: 32 residues processed: 116 average time/residue: 0.1071 time to fit residues: 18.9760 Evaluate side-chains 118 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 TYR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain E residue 114 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain F residue 39 CYS Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 441 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 64 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 180 optimal weight: 30.0000 chunk 24 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 68 HIS ** C 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.057569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.041954 restraints weight = 89461.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.043152 restraints weight = 47447.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.043896 restraints weight = 32815.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.044347 restraints weight = 26196.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.044651 restraints weight = 22962.507| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.6583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12564 Z= 0.113 Angle : 0.595 9.782 16796 Z= 0.290 Chirality : 0.043 0.156 1603 Planarity : 0.003 0.040 2371 Dihedral : 4.417 30.983 1961 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.51 % Allowed : 22.85 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.21), residues: 1845 helix: 3.81 (0.23), residues: 478 sheet: -1.24 (0.28), residues: 345 loop : -0.54 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 107 TYR 0.009 0.001 TYR A 500 PHE 0.008 0.001 PHE A 443 TRP 0.010 0.001 TRP D 159 HIS 0.003 0.001 HIS D 256 Details of bonding type rmsd covalent geometry : bond 0.00258 (12547) covalent geometry : angle 0.59451 (16762) SS BOND : bond 0.00159 ( 17) SS BOND : angle 0.94359 ( 34) hydrogen bonds : bond 0.02418 ( 496) hydrogen bonds : angle 3.36209 ( 1470) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 87 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 52 LEU cc_start: 0.9028 (mp) cc_final: 0.8772 (tt) REVERT: E 116 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7382 (pp) REVERT: B 426 LEU cc_start: 0.8620 (tp) cc_final: 0.8343 (mt) REVERT: B 523 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8270 (pm20) REVERT: C 83 LEU cc_start: 0.9475 (mt) cc_final: 0.9223 (mt) REVERT: C 394 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8880 (tp) REVERT: C 425 LEU cc_start: 0.9322 (mp) cc_final: 0.8681 (tp) REVERT: D 250 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8748 (mt) outliers start: 40 outliers final: 29 residues processed: 112 average time/residue: 0.0939 time to fit residues: 16.9594 Evaluate side-chains 116 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 TYR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain E residue 114 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain F residue 39 CYS Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 64 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 174 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 ASN ** C 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.056057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.040084 restraints weight = 91409.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.041243 restraints weight = 47879.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.041991 restraints weight = 33314.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.042418 restraints weight = 26795.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.042693 restraints weight = 23518.483| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12564 Z= 0.257 Angle : 0.709 9.022 16796 Z= 0.349 Chirality : 0.046 0.232 1603 Planarity : 0.004 0.039 2371 Dihedral : 5.048 30.922 1961 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.18 % Favored : 93.71 % Rotamer: Outliers : 3.25 % Allowed : 23.37 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.21), residues: 1845 helix: 3.78 (0.23), residues: 484 sheet: -1.29 (0.28), residues: 344 loop : -0.66 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 346 TYR 0.015 0.002 TYR B 500 PHE 0.011 0.002 PHE C 240 TRP 0.015 0.002 TRP D 159 HIS 0.005 0.001 HIS D 256 Details of bonding type rmsd covalent geometry : bond 0.00564 (12547) covalent geometry : angle 0.70776 (16762) SS BOND : bond 0.00288 ( 17) SS BOND : angle 1.10892 ( 34) hydrogen bonds : bond 0.03005 ( 496) hydrogen bonds : angle 3.74474 ( 1470) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 83 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 116 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7527 (pp) REVERT: B 523 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8511 (pm20) REVERT: C 425 LEU cc_start: 0.9417 (mp) cc_final: 0.8787 (tp) outliers start: 37 outliers final: 31 residues processed: 108 average time/residue: 0.1025 time to fit residues: 17.1635 Evaluate side-chains 114 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain F residue 39 CYS Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 161 optimal weight: 30.0000 chunk 160 optimal weight: 5.9990 chunk 103 optimal weight: 50.0000 chunk 129 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.056372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.040529 restraints weight = 90864.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.041706 restraints weight = 47492.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.042447 restraints weight = 32802.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.042892 restraints weight = 26288.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.043151 restraints weight = 23079.684| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.7139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12564 Z= 0.188 Angle : 0.650 8.742 16796 Z= 0.318 Chirality : 0.045 0.190 1603 Planarity : 0.003 0.039 2371 Dihedral : 4.830 30.891 1961 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.88 % Favored : 95.01 % Rotamer: Outliers : 3.25 % Allowed : 23.11 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.21), residues: 1845 helix: 3.74 (0.23), residues: 492 sheet: -1.21 (0.28), residues: 336 loop : -0.71 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 425 TYR 0.012 0.001 TYR B 499 PHE 0.010 0.001 PHE D 240 TRP 0.013 0.002 TRP D 159 HIS 0.004 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00417 (12547) covalent geometry : angle 0.64943 (16762) SS BOND : bond 0.00222 ( 17) SS BOND : angle 1.04148 ( 34) hydrogen bonds : bond 0.02715 ( 496) hydrogen bonds : angle 3.56872 ( 1470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3143.34 seconds wall clock time: 54 minutes 50.14 seconds (3290.14 seconds total)