Starting phenix.real_space_refine on Wed Jul 30 21:23:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9khh_62340/07_2025/9khh_62340.cif Found real_map, /net/cci-nas-00/data/ceres_data/9khh_62340/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9khh_62340/07_2025/9khh_62340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9khh_62340/07_2025/9khh_62340.map" model { file = "/net/cci-nas-00/data/ceres_data/9khh_62340/07_2025/9khh_62340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9khh_62340/07_2025/9khh_62340.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 8, 'TRP:plan': 7, 'HIS:plan': 4, 'PHE:plan': 32, 'GLU:plan': 9, 'ARG:plan': 8} 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: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 8, 'TRP:plan': 7, 'ASP:plan': 3, 'PHE:plan': 32, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 497 Time building chain proxies: 10.22, per 1000 atoms: 0.83 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: 2.91 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.65 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: 4.49 Time building geometry restraints manager: 3.49 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: 9.320 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.570 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.240 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (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 TRP 0.011 0.002 TRP B 442 HIS 0.005 0.001 HIS E 50 PHE 0.015 0.001 PHE D 58 TYR 0.025 0.002 TYR E 44 ARG 0.005 0.001 ARG F 97 Details of bonding type rmsd hydrogen bonds : bond 0.14884 ( 496) hydrogen bonds : angle 5.59685 ( 1470) SS BOND : bond 0.00404 ( 17) SS BOND : angle 1.85681 ( 34) covalent geometry : bond 0.00255 (12547) covalent geometry : angle 0.66065 (16762) *********************** 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 : 1.344 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: 0.7264 (tmm) REVERT: C 394 LEU cc_start: 0.8310 (tp) cc_final: 0.7644 (tt) 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: 0.2469 time to fit residues: 84.6679 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 : 2.262 ------------------------------------------------------------------------------- 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 154 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 87 optimal weight: 40.0000 chunk 106 optimal weight: 10.0000 chunk 166 optimal weight: 50.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 GLN C 417 ASN ** C 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN D 417 ASN ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.058974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.043892 restraints weight = 90335.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.045074 restraints weight = 48993.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.045778 restraints weight = 34449.707| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12564 Z= 0.235 Angle : 0.720 7.775 16796 Z= 0.365 Chirality : 0.049 0.196 1603 Planarity : 0.005 0.045 2371 Dihedral : 5.294 32.936 1961 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.87 % Allowed : 18.80 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1845 helix: 3.32 (0.25), residues: 456 sheet: -1.49 (0.28), residues: 341 loop : -0.69 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 159 HIS 0.006 0.002 HIS C 140 PHE 0.024 0.002 PHE A 473 TYR 0.020 0.003 TYR E 44 ARG 0.008 0.001 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 496) hydrogen bonds : angle 4.21770 ( 1470) SS BOND : bond 0.00431 ( 17) SS BOND : angle 1.20562 ( 34) covalent geometry : bond 0.00495 (12547) covalent geometry : angle 0.71838 (16762) *********************** 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 161 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 GLU cc_start: 0.9362 (tp30) cc_final: 0.9020 (tm-30) REVERT: E 116 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7730 (pp) REVERT: B 426 LEU cc_start: 0.8490 (tp) cc_final: 0.8099 (tp) REVERT: C 83 LEU cc_start: 0.9579 (mt) cc_final: 0.9268 (mt) REVERT: C 451 LEU cc_start: 0.8191 (mt) cc_final: 0.7529 (tp) REVERT: C 456 PHE cc_start: 0.8251 (m-80) cc_final: 0.7905 (m-80) REVERT: D 315 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8660 (mm) REVERT: D 345 LEU cc_start: 0.8990 (tp) cc_final: 0.8694 (pp) REVERT: D 456 PHE cc_start: 0.8748 (m-80) cc_final: 0.8456 (m-10) outliers start: 44 outliers final: 22 residues processed: 153 average time/residue: 0.2375 time to fit residues: 57.4005 Evaluate side-chains 120 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 48 ILE 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 B residue 529 VAL Chi-restraints excluded: chain C residue 51 VAL 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 79 ASN 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 Chi-restraints excluded: chain D residue 433 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 53 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 131 optimal weight: 0.6980 chunk 168 optimal weight: 20.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.057333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.041925 restraints weight = 93172.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.043059 restraints weight = 50280.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.043730 restraints weight = 35548.640| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12564 Z= 0.295 Angle : 0.739 6.966 16796 Z= 0.373 Chirality : 0.047 0.178 1603 Planarity : 0.005 0.063 2371 Dihedral : 5.447 30.934 1961 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.04 % Favored : 94.85 % Rotamer: Outliers : 4.39 % Allowed : 18.10 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1845 helix: 3.27 (0.25), residues: 468 sheet: -1.54 (0.27), residues: 350 loop : -0.71 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 159 HIS 0.007 0.002 HIS C 320 PHE 0.015 0.002 PHE C 409 TYR 0.020 0.002 TYR B 499 ARG 0.009 0.001 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 496) hydrogen bonds : angle 4.12596 ( 1470) SS BOND : bond 0.00740 ( 17) SS BOND : angle 1.44561 ( 34) covalent geometry : bond 0.00648 (12547) covalent geometry : angle 0.73686 (16762) *********************** 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 147 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 97 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 GLU cc_start: 0.9320 (tp30) cc_final: 0.9036 (tm-30) REVERT: E 116 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7627 (pp) REVERT: B 426 LEU cc_start: 0.8563 (tp) cc_final: 0.8269 (tp) REVERT: B 523 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8375 (pm20) REVERT: C 83 LEU cc_start: 0.9616 (mt) cc_final: 0.9238 (mt) REVERT: C 91 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8164 (t0) REVERT: D 447 LEU cc_start: 0.8882 (tp) cc_final: 0.7942 (mt) outliers start: 50 outliers final: 36 residues processed: 136 average time/residue: 0.2546 time to fit residues: 55.0469 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 : 1.887 ------------------------------------------------------------------------------- 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 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 48 ILE 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 501 CYS Chi-restraints excluded: chain B residue 527 VAL 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 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 345 LEU Chi-restraints excluded: chain C residue 372 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 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 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.0670 chunk 182 optimal weight: 6.9990 chunk 4 optimal weight: 0.0980 chunk 117 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 178 optimal weight: 0.0050 chunk 149 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.3132 ------------------------------------------------------------------------------- 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 207 HIS D 210 ASN D 271 ASN ** D 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.058669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.043570 restraints weight = 90267.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.044757 restraints weight = 48005.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.045475 restraints weight = 33450.380| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12564 Z= 0.097 Angle : 0.586 8.839 16796 Z= 0.286 Chirality : 0.044 0.160 1603 Planarity : 0.004 0.041 2371 Dihedral : 4.592 31.227 1961 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.99 % Allowed : 19.95 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1845 helix: 3.58 (0.25), residues: 459 sheet: -1.30 (0.28), residues: 357 loop : -0.52 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 515 HIS 0.003 0.001 HIS E 50 PHE 0.011 0.001 PHE C 385 TYR 0.010 0.001 TYR B 465 ARG 0.004 0.000 ARG F 121 Details of bonding type rmsd hydrogen bonds : bond 0.02596 ( 496) hydrogen bonds : angle 3.58064 ( 1470) SS BOND : bond 0.00172 ( 17) SS BOND : angle 1.02615 ( 34) covalent geometry : bond 0.00214 (12547) covalent geometry : angle 0.58506 (16762) *********************** 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 137 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 59 MET cc_start: 0.8746 (ttt) cc_final: 0.8511 (ttm) REVERT: E 116 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7385 (pp) REVERT: B 426 LEU cc_start: 0.8735 (tp) cc_final: 0.8490 (tp) REVERT: C 83 LEU cc_start: 0.9590 (mt) cc_final: 0.9195 (mt) REVERT: C 250 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8679 (mt) REVERT: C 344 MET cc_start: 0.8132 (pmm) cc_final: 0.7904 (pmm) REVERT: C 425 LEU cc_start: 0.9130 (mp) cc_final: 0.8649 (pt) REVERT: C 456 PHE cc_start: 0.8230 (m-80) cc_final: 0.7992 (m-80) REVERT: D 447 LEU cc_start: 0.8774 (tp) cc_final: 0.7874 (mt) outliers start: 34 outliers final: 23 residues processed: 128 average time/residue: 0.2799 time to fit residues: 56.6463 Evaluate side-chains 115 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 454 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 527 VAL 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 345 LEU Chi-restraints excluded: chain C residue 372 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 315 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 133 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 166 optimal weight: 50.0000 chunk 93 optimal weight: 20.0000 chunk 176 optimal weight: 40.0000 chunk 169 optimal weight: 40.0000 chunk 25 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 ASN ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3721 r_free = 0.3721 target = 0.056505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.041071 restraints weight = 91320.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.042189 restraints weight = 49474.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.042836 restraints weight = 35026.306| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12564 Z= 0.283 Angle : 0.698 7.106 16796 Z= 0.351 Chirality : 0.046 0.152 1603 Planarity : 0.004 0.038 2371 Dihedral : 5.286 31.281 1961 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.31 % Favored : 94.58 % Rotamer: Outliers : 4.04 % Allowed : 19.86 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1845 helix: 3.48 (0.24), residues: 470 sheet: -1.43 (0.27), residues: 371 loop : -0.58 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 159 HIS 0.009 0.002 HIS F 94 PHE 0.018 0.002 PHE E 89 TYR 0.013 0.002 TYR F 122 ARG 0.006 0.001 ARG F 74 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 496) hydrogen bonds : angle 3.89694 ( 1470) SS BOND : bond 0.00349 ( 17) SS BOND : angle 1.23447 ( 34) covalent geometry : bond 0.00619 (12547) covalent geometry : angle 0.69629 (16762) *********************** 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 133 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 87 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 GLU cc_start: 0.9314 (tp30) cc_final: 0.9064 (tm-30) REVERT: E 52 LEU cc_start: 0.9179 (mp) cc_final: 0.8870 (tt) REVERT: B 523 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8434 (pm20) REVERT: C 83 LEU cc_start: 0.9614 (mt) cc_final: 0.9254 (mt) REVERT: C 308 MET cc_start: 0.9100 (mtp) cc_final: 0.8897 (tpp) REVERT: D 447 LEU cc_start: 0.8994 (tp) cc_final: 0.8669 (mt) outliers start: 46 outliers final: 33 residues processed: 124 average time/residue: 0.2960 time to fit residues: 56.7365 Evaluate side-chains 118 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 489 ASN 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 F residue 48 ILE 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 491 LEU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 51 VAL 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 358 LEU 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 4 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 150 optimal weight: 0.9990 chunk 105 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 181 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 64 optimal weight: 0.0980 chunk 40 optimal weight: 0.0770 chunk 6 optimal weight: 1.9990 overall best weight: 0.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 ASN C 405 HIS 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 = 0.3748 r_free = 0.3748 target = 0.057871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.042147 restraints weight = 89851.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.043384 restraints weight = 46392.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.044131 restraints weight = 31861.166| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12564 Z= 0.100 Angle : 0.564 8.263 16796 Z= 0.277 Chirality : 0.043 0.163 1603 Planarity : 0.003 0.039 2371 Dihedral : 4.478 31.242 1961 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.34 % Allowed : 21.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1845 helix: 3.63 (0.24), residues: 470 sheet: -1.23 (0.27), residues: 379 loop : -0.49 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 159 HIS 0.003 0.001 HIS F 50 PHE 0.006 0.001 PHE F 89 TYR 0.012 0.001 TYR B 465 ARG 0.003 0.000 ARG C 398 Details of bonding type rmsd hydrogen bonds : bond 0.02483 ( 496) hydrogen bonds : angle 3.38800 ( 1470) SS BOND : bond 0.00169 ( 17) SS BOND : angle 0.90788 ( 34) covalent geometry : bond 0.00222 (12547) covalent geometry : angle 0.56317 (16762) *********************** 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 131 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 1.531 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: E 52 LEU cc_start: 0.9175 (mp) cc_final: 0.8877 (tt) REVERT: B 523 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8283 (pm20) REVERT: C 83 LEU cc_start: 0.9605 (mt) cc_final: 0.9280 (mt) REVERT: C 99 LYS cc_start: 0.9196 (tmtt) cc_final: 0.8898 (tmtt) REVERT: C 250 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8750 (mt) REVERT: C 308 MET cc_start: 0.9069 (mtp) cc_final: 0.8821 (tpp) REVERT: C 344 MET cc_start: 0.7983 (pmm) cc_final: 0.7755 (pmm) REVERT: C 345 LEU cc_start: 0.9272 (mt) cc_final: 0.8976 (mt) REVERT: C 394 LEU cc_start: 0.9228 (tp) cc_final: 0.8802 (tp) REVERT: C 400 LEU cc_start: 0.9527 (mp) cc_final: 0.9275 (pt) REVERT: C 424 GLU cc_start: 0.9566 (mp0) cc_final: 0.9355 (pm20) REVERT: C 425 LEU cc_start: 0.9343 (mp) cc_final: 0.8988 (pt) REVERT: D 250 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8667 (mt) outliers start: 38 outliers final: 26 residues processed: 123 average time/residue: 0.2194 time to fit residues: 41.6552 Evaluate side-chains 119 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 501 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain B residue 474 THR 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 527 VAL 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 372 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 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 67 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 134 optimal weight: 0.0030 chunk 121 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 ASN 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 = 0.3716 r_free = 0.3716 target = 0.056871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.041100 restraints weight = 90523.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.042275 restraints weight = 48057.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.043009 restraints weight = 33582.857| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12564 Z= 0.199 Angle : 0.628 7.384 16796 Z= 0.311 Chirality : 0.044 0.151 1603 Planarity : 0.004 0.038 2371 Dihedral : 4.817 31.408 1961 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.82 % Favored : 95.07 % Rotamer: Outliers : 3.51 % Allowed : 21.44 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.21), residues: 1845 helix: 3.68 (0.24), residues: 476 sheet: -1.23 (0.27), residues: 371 loop : -0.51 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 159 HIS 0.006 0.001 HIS F 68 PHE 0.012 0.001 PHE E 89 TYR 0.009 0.001 TYR F 122 ARG 0.008 0.001 ARG F 37 Details of bonding type rmsd hydrogen bonds : bond 0.02882 ( 496) hydrogen bonds : angle 3.53284 ( 1470) SS BOND : bond 0.00272 ( 17) SS BOND : angle 1.11572 ( 34) covalent geometry : bond 0.00441 (12547) covalent geometry : angle 0.62653 (16762) *********************** 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 130 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 90 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 MET cc_start: 0.6840 (mtm) cc_final: 0.6164 (mtm) REVERT: E 52 LEU cc_start: 0.9196 (mp) cc_final: 0.8930 (tt) REVERT: B 523 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8452 (pm20) REVERT: C 250 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8789 (mt) REVERT: C 345 LEU cc_start: 0.9043 (mt) cc_final: 0.8836 (mt) REVERT: C 425 LEU cc_start: 0.9348 (mp) cc_final: 0.8955 (pt) outliers start: 40 outliers final: 31 residues processed: 119 average time/residue: 0.2190 time to fit residues: 40.4778 Evaluate side-chains 115 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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 501 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 129 GLU 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 527 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 372 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 441 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 181 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 170 optimal weight: 0.3980 chunk 174 optimal weight: 40.0000 chunk 72 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 68 HIS C 210 ASN C 271 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.057163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.041586 restraints weight = 88916.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.042769 restraints weight = 46806.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.043512 restraints weight = 32358.741| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.6438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12564 Z= 0.134 Angle : 0.600 8.530 16796 Z= 0.294 Chirality : 0.044 0.176 1603 Planarity : 0.003 0.038 2371 Dihedral : 4.550 31.195 1961 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.01 % Favored : 95.93 % Rotamer: Outliers : 3.34 % Allowed : 22.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.21), residues: 1845 helix: 3.74 (0.23), residues: 478 sheet: -1.20 (0.27), residues: 374 loop : -0.49 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 159 HIS 0.004 0.001 HIS F 50 PHE 0.007 0.001 PHE D 240 TYR 0.011 0.001 TYR B 500 ARG 0.004 0.000 ARG F 37 Details of bonding type rmsd hydrogen bonds : bond 0.02563 ( 496) hydrogen bonds : angle 3.37273 ( 1470) SS BOND : bond 0.00178 ( 17) SS BOND : angle 0.98816 ( 34) covalent geometry : bond 0.00302 (12547) covalent geometry : angle 0.59905 (16762) *********************** 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 125 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 GLU cc_start: 0.8811 (pm20) cc_final: 0.8548 (pm20) REVERT: A 494 GLU cc_start: 0.9345 (tp30) cc_final: 0.9119 (tm-30) REVERT: E 52 LEU cc_start: 0.9089 (mp) cc_final: 0.8836 (tt) REVERT: E 106 LEU cc_start: 0.9180 (tp) cc_final: 0.8976 (tt) REVERT: B 523 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8345 (pm20) REVERT: C 250 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8754 (mt) REVERT: C 345 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8871 (mt) REVERT: C 394 LEU cc_start: 0.9218 (tp) cc_final: 0.9006 (tp) REVERT: C 400 LEU cc_start: 0.9499 (mp) cc_final: 0.9286 (pp) REVERT: C 425 LEU cc_start: 0.9338 (mp) cc_final: 0.8917 (pt) outliers start: 38 outliers final: 30 residues processed: 112 average time/residue: 0.2235 time to fit residues: 38.5806 Evaluate side-chains 115 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 1.523 ------------------------------------------------------------------------------- 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 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 114 MET 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 F residue 129 GLU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 527 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 260 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 345 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 198 THR Chi-restraints excluded: chain D residue 260 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 182 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 101 optimal weight: 40.0000 chunk 127 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 161 optimal weight: 30.0000 chunk 55 optimal weight: 0.8980 chunk 95 optimal weight: 50.0000 chunk 69 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 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 = 0.3693 r_free = 0.3693 target = 0.056181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.040231 restraints weight = 91116.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.041429 restraints weight = 47404.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.042163 restraints weight = 32826.109| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.6837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12564 Z= 0.225 Angle : 0.678 10.078 16796 Z= 0.332 Chirality : 0.045 0.168 1603 Planarity : 0.004 0.038 2371 Dihedral : 4.952 31.012 1961 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.80 % Favored : 94.09 % Rotamer: Outliers : 3.25 % Allowed : 22.76 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1845 helix: 3.75 (0.23), residues: 484 sheet: -1.35 (0.27), residues: 373 loop : -0.52 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 159 HIS 0.005 0.001 HIS D 256 PHE 0.012 0.001 PHE E 89 TYR 0.011 0.001 TYR A 500 ARG 0.006 0.001 ARG A 425 Details of bonding type rmsd hydrogen bonds : bond 0.02993 ( 496) hydrogen bonds : angle 3.58580 ( 1470) SS BOND : bond 0.00285 ( 17) SS BOND : angle 1.14471 ( 34) covalent geometry : bond 0.00493 (12547) covalent geometry : angle 0.67708 (16762) *********************** 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 119 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 53 TYR cc_start: 0.9145 (m-80) cc_final: 0.8663 (m-80) REVERT: B 523 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8486 (pm20) REVERT: C 345 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8811 (mt) REVERT: C 400 LEU cc_start: 0.9568 (mp) cc_final: 0.9346 (pp) REVERT: C 425 LEU cc_start: 0.9429 (mp) cc_final: 0.8987 (pt) REVERT: D 418 LEU cc_start: 0.9523 (tp) cc_final: 0.8936 (pp) outliers start: 37 outliers final: 33 residues processed: 108 average time/residue: 0.2227 time to fit residues: 37.6076 Evaluate side-chains 116 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 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 62 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 39 CYS Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 527 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 260 ILE 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 345 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 198 THR Chi-restraints excluded: chain D residue 260 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 110 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 150 optimal weight: 8.9990 chunk 122 optimal weight: 0.0470 chunk 108 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 78 optimal weight: 0.0570 chunk 114 optimal weight: 0.7980 chunk 95 optimal weight: 50.0000 chunk 46 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.057508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.041860 restraints weight = 88387.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.043096 restraints weight = 46444.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.043859 restraints weight = 31886.502| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.6813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12564 Z= 0.099 Angle : 0.611 9.899 16796 Z= 0.292 Chirality : 0.044 0.165 1603 Planarity : 0.003 0.040 2371 Dihedral : 4.385 31.049 1961 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.55 % Allowed : 23.55 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.21), residues: 1845 helix: 3.78 (0.23), residues: 485 sheet: -1.21 (0.27), residues: 382 loop : -0.42 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 159 HIS 0.003 0.001 HIS E 50 PHE 0.006 0.001 PHE A 518 TYR 0.010 0.001 TYR A 485 ARG 0.002 0.000 ARG F 37 Details of bonding type rmsd hydrogen bonds : bond 0.02409 ( 496) hydrogen bonds : angle 3.26437 ( 1470) SS BOND : bond 0.00151 ( 17) SS BOND : angle 0.97854 ( 34) covalent geometry : bond 0.00227 (12547) covalent geometry : angle 0.60971 (16762) ********************** 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 115 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 1.371 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: B 523 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8347 (pm20) REVERT: C 345 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8832 (mt) REVERT: C 394 LEU cc_start: 0.9246 (tp) cc_final: 0.8844 (tp) REVERT: C 400 LEU cc_start: 0.9534 (mp) cc_final: 0.9333 (pp) REVERT: C 425 LEU cc_start: 0.9326 (mp) cc_final: 0.8942 (pt) REVERT: C 462 LEU cc_start: 0.9531 (tp) cc_final: 0.9186 (tp) REVERT: D 418 LEU cc_start: 0.9511 (tp) cc_final: 0.8904 (pp) outliers start: 29 outliers final: 26 residues processed: 107 average time/residue: 0.2085 time to fit residues: 34.8632 Evaluate side-chains 110 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 527 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 MET 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 F residue 129 GLU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 527 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 260 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 260 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 94 optimal weight: 50.0000 chunk 21 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 82 optimal weight: 0.0670 chunk 138 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 163 optimal weight: 30.0000 chunk 113 optimal weight: 4.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3730 r_free = 0.3730 target = 0.057360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.041691 restraints weight = 89604.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.042906 restraints weight = 47050.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.043668 restraints weight = 32405.738| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.6924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12564 Z= 0.116 Angle : 0.609 9.512 16796 Z= 0.291 Chirality : 0.043 0.168 1603 Planarity : 0.003 0.042 2371 Dihedral : 4.338 31.160 1961 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.46 % Allowed : 23.55 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.21), residues: 1845 helix: 3.84 (0.23), residues: 485 sheet: -1.15 (0.28), residues: 358 loop : -0.47 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 159 HIS 0.003 0.001 HIS D 256 PHE 0.008 0.001 PHE B 443 TYR 0.012 0.001 TYR A 485 ARG 0.002 0.000 ARG F 37 Details of bonding type rmsd hydrogen bonds : bond 0.02420 ( 496) hydrogen bonds : angle 3.19169 ( 1470) SS BOND : bond 0.00163 ( 17) SS BOND : angle 0.95323 ( 34) covalent geometry : bond 0.00266 (12547) covalent geometry : angle 0.60835 (16762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5905.52 seconds wall clock time: 109 minutes 35.54 seconds (6575.54 seconds total)