Starting phenix.real_space_refine on Wed Mar 4 13:49:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ain_11799/03_2026/7ain_11799.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ain_11799/03_2026/7ain_11799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ain_11799/03_2026/7ain_11799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ain_11799/03_2026/7ain_11799.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ain_11799/03_2026/7ain_11799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ain_11799/03_2026/7ain_11799.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 94 5.16 5 C 9020 2.51 5 N 2300 2.21 5 O 2486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13904 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 6899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 6899 Classifications: {'peptide': 904} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 34, 'TRANS': 869} Chain breaks: 3 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'TPO:plan-1': 1, 'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 6899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 6899 Classifications: {'peptide': 904} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 34, 'TRANS': 869} Chain breaks: 3 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'TPO:plan-1': 1, 'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.98, per 1000 atoms: 0.21 Number of scatterers: 13904 At special positions: 0 Unit cell: (104.811, 92.442, 147.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 P 4 15.00 O 2486 8.00 N 2300 7.00 C 9020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 640 " distance=2.04 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 369 " distance=2.02 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 640 " distance=2.04 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 369 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A1101 " - " ASN A 377 " " NAG B1101 " - " ASN B 377 " " NAG C 1 " - " ASN B 328 " " NAG G 1 " - " ASN A 328 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 508.0 milliseconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3332 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 61.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.676A pdb=" N THR B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 131' Processing helix chain 'B' and resid 135 through 149 removed outlier: 5.151A pdb=" N LEU B 142 " --> pdb=" O MET B 138 " (cutoff:3.500A) Proline residue: B 143 - end of helix Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 156 through 193 removed outlier: 6.234A pdb=" N VAL B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N LEU B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 243 removed outlier: 3.529A pdb=" N MET B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 258 through 284 Processing helix chain 'B' and resid 285 through 314 removed outlier: 3.662A pdb=" N VAL B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 370 through 376 Processing helix chain 'B' and resid 390 through 394 removed outlier: 3.502A pdb=" N THR B 393 " --> pdb=" O GLY B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.695A pdb=" N GLY B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 445 No H-bonds generated for 'chain 'B' and resid 443 through 445' Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 460 through 491 Proline residue: B 466 - end of helix removed outlier: 3.672A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 517 through 550 removed outlier: 4.256A pdb=" N ILE B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Proline residue: B 541 - end of helix Processing helix chain 'B' and resid 554 through 561 removed outlier: 3.920A pdb=" N VAL B 558 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS B 561 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 584 removed outlier: 3.691A pdb=" N LEU B 572 " --> pdb=" O PRO B 568 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 616 Proline residue: B 593 - end of helix removed outlier: 3.659A pdb=" N CYS B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 648 removed outlier: 3.606A pdb=" N SER B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 675 removed outlier: 3.603A pdb=" N ILE B 653 " --> pdb=" O TRP B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 696 removed outlier: 3.599A pdb=" N GLU B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 734 removed outlier: 4.289A pdb=" N LEU B 726 " --> pdb=" O HIS B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 770 Processing helix chain 'B' and resid 783 through 795 removed outlier: 3.938A pdb=" N GLN B 793 " --> pdb=" O SER B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 835 removed outlier: 3.545A pdb=" N PHE B 825 " --> pdb=" O ALA B 821 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 826 " --> pdb=" O TRP B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 Processing helix chain 'B' and resid 868 through 881 removed outlier: 3.640A pdb=" N LEU B 872 " --> pdb=" O ASP B 868 " (cutoff:3.500A) Proline residue: B 876 - end of helix Processing helix chain 'B' and resid 904 through 917 Processing helix chain 'B' and resid 932 through 946 Processing helix chain 'B' and resid 1029 through 1048 removed outlier: 3.914A pdb=" N LYS B1038 " --> pdb=" O HIS B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1065 No H-bonds generated for 'chain 'B' and resid 1063 through 1065' Processing helix chain 'B' and resid 1066 through 1078 Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.676A pdb=" N THR A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 127 through 131' Processing helix chain 'A' and resid 135 through 149 removed outlier: 5.151A pdb=" N LEU A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 156 through 193 removed outlier: 6.234A pdb=" N VAL A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N LEU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 243 removed outlier: 3.530A pdb=" N MET A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 258 through 284 Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.661A pdb=" N VAL A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 370 through 376 Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.502A pdb=" N THR A 393 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.696A pdb=" N GLY A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 447 through 453 Processing helix chain 'A' and resid 460 through 491 Proline residue: A 466 - end of helix removed outlier: 3.673A pdb=" N VAL A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 517 through 550 removed outlier: 4.257A pdb=" N ILE A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Proline residue: A 541 - end of helix Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.919A pdb=" N VAL A 558 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS A 561 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 584 removed outlier: 3.691A pdb=" N LEU A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 616 Proline residue: A 593 - end of helix removed outlier: 3.659A pdb=" N CYS A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 648 removed outlier: 3.606A pdb=" N SER A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 675 removed outlier: 3.604A pdb=" N ILE A 653 " --> pdb=" O TRP A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 696 removed outlier: 3.599A pdb=" N GLU A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 4.289A pdb=" N LEU A 726 " --> pdb=" O HIS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 770 Processing helix chain 'A' and resid 783 through 795 removed outlier: 3.938A pdb=" N GLN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 835 removed outlier: 3.545A pdb=" N PHE A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 826 " --> pdb=" O TRP A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 868 through 881 removed outlier: 3.640A pdb=" N LEU A 872 " --> pdb=" O ASP A 868 " (cutoff:3.500A) Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 904 through 917 Processing helix chain 'A' and resid 932 through 946 Processing helix chain 'A' and resid 1029 through 1048 removed outlier: 3.914A pdb=" N LYS A1038 " --> pdb=" O HIS A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1066 through 1078 Processing sheet with id=AA1, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA2, first strand: chain 'B' and resid 342 through 345 removed outlier: 3.574A pdb=" N VAL B 350 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 775 through 781 removed outlier: 6.675A pdb=" N LEU B 708 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLY B 742 " --> pdb=" O LEU B 708 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL B 710 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL B 744 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY B 808 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 805 " --> pdb=" O LEU B 840 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA B 842 " --> pdb=" O VAL B 805 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET B 807 " --> pdb=" O ALA B 842 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B1053 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL B1087 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU B1055 " --> pdb=" O VAL B1087 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 859 through 860 removed outlier: 6.785A pdb=" N ILE B 890 " --> pdb=" O GLU B 921 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLU B 923 " --> pdb=" O ILE B 890 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE B 892 " --> pdb=" O GLU B 923 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 345 removed outlier: 3.575A pdb=" N VAL A 350 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 775 through 781 removed outlier: 6.674A pdb=" N LEU A 708 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLY A 742 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL A 710 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL A 744 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY A 808 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 805 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA A 842 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET A 807 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A1084 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A1053 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL A1087 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A1055 " --> pdb=" O VAL A1087 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 859 through 860 removed outlier: 6.784A pdb=" N ILE A 890 " --> pdb=" O GLU A 921 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N GLU A 923 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE A 892 " --> pdb=" O GLU A 923 " (cutoff:3.500A) 812 hydrogen bonds defined for protein. 2346 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 1.60 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: 4376 1.35 - 1.47: 3663 1.47 - 1.60: 6015 1.60 - 1.73: 14 1.73 - 1.86: 150 Bond restraints: 14218 Sorted by residual: bond pdb=" OG1 TPO B 727 " pdb=" P TPO B 727 " ideal model delta sigma weight residual 1.717 1.617 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" OG1 TPO A 727 " pdb=" P TPO A 727 " ideal model delta sigma weight residual 1.717 1.617 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" O1P TPO A 727 " pdb=" P TPO A 727 " ideal model delta sigma weight residual 1.525 1.614 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" O1P TPO B 727 " pdb=" P TPO B 727 " ideal model delta sigma weight residual 1.525 1.614 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" O2P TPO A 727 " pdb=" P TPO A 727 " ideal model delta sigma weight residual 1.528 1.605 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 14213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 18738 2.34 - 4.67: 526 4.67 - 7.01: 63 7.01 - 9.35: 13 9.35 - 11.69: 2 Bond angle restraints: 19342 Sorted by residual: angle pdb=" C VAL B 866 " pdb=" N HIS B 867 " pdb=" CA HIS B 867 " ideal model delta sigma weight residual 122.53 115.85 6.68 1.61e+00 3.86e-01 1.72e+01 angle pdb=" C VAL A 866 " pdb=" N HIS A 867 " pdb=" CA HIS A 867 " ideal model delta sigma weight residual 122.53 115.88 6.65 1.61e+00 3.86e-01 1.71e+01 angle pdb=" CA CYS B 640 " pdb=" CB CYS B 640 " pdb=" SG CYS B 640 " ideal model delta sigma weight residual 114.40 122.59 -8.19 2.30e+00 1.89e-01 1.27e+01 angle pdb=" CA CYS A 640 " pdb=" CB CYS A 640 " pdb=" SG CYS A 640 " ideal model delta sigma weight residual 114.40 122.58 -8.18 2.30e+00 1.89e-01 1.27e+01 angle pdb=" C ASP A 255 " pdb=" CA ASP A 255 " pdb=" CB ASP A 255 " ideal model delta sigma weight residual 116.63 112.53 4.10 1.16e+00 7.43e-01 1.25e+01 ... (remaining 19337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.88: 7986 20.88 - 41.76: 354 41.76 - 62.64: 68 62.64 - 83.52: 22 83.52 - 104.39: 8 Dihedral angle restraints: 8438 sinusoidal: 3256 harmonic: 5182 Sorted by residual: dihedral pdb=" CA CYS B 640 " pdb=" C CYS B 640 " pdb=" N LEU B 641 " pdb=" CA LEU B 641 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA CYS A 640 " pdb=" C CYS A 640 " pdb=" N LEU A 641 " pdb=" CA LEU A 641 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CB CYS A 179 " pdb=" SG CYS A 179 " pdb=" SG CYS A 640 " pdb=" CB CYS A 640 " ideal model delta sinusoidal sigma weight residual 93.00 60.81 32.19 1 1.00e+01 1.00e-02 1.48e+01 ... (remaining 8435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1924 0.079 - 0.157: 345 0.157 - 0.236: 15 0.236 - 0.314: 2 0.314 - 0.393: 2 Chirality restraints: 2288 Sorted by residual: chirality pdb=" CA CYS B 640 " pdb=" N CYS B 640 " pdb=" C CYS B 640 " pdb=" CB CYS B 640 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA CYS A 640 " pdb=" N CYS A 640 " pdb=" C CYS A 640 " pdb=" CB CYS A 640 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2285 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 497 " -0.094 9.50e-02 1.11e+02 5.58e-02 1.77e+01 pdb=" NE ARG B 497 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 497 " -0.069 2.00e-02 2.50e+03 pdb=" NH1 ARG B 497 " 0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG B 497 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 497 " 0.093 9.50e-02 1.11e+02 5.54e-02 1.76e+01 pdb=" NE ARG A 497 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 497 " 0.069 2.00e-02 2.50e+03 pdb=" NH1 ARG A 497 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG A 497 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 240 " 0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C PHE A 240 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE A 240 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU A 241 " 0.024 2.00e-02 2.50e+03 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4005 2.81 - 3.33: 14280 3.33 - 3.85: 23380 3.85 - 4.38: 27096 4.38 - 4.90: 46636 Nonbonded interactions: 115397 Sorted by model distance: nonbonded pdb=" OH TYR B 141 " pdb=" OG1 THR B 475 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 141 " pdb=" OG1 THR A 475 " model vdw 2.282 3.040 nonbonded pdb=" O SER B1092 " pdb=" OG SER B1092 " model vdw 2.291 3.040 nonbonded pdb=" ND2 ASN B1040 " pdb=" O VAL B1076 " model vdw 2.291 3.120 nonbonded pdb=" ND2 ASN A1040 " pdb=" O VAL A1076 " model vdw 2.292 3.120 ... (remaining 115392 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } ncs_group { reference = chain 'C' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 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: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.910 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 : 0.011 0.100 14232 Z= 0.449 Angle : 0.940 11.687 19378 Z= 0.503 Chirality : 0.057 0.393 2288 Planarity : 0.006 0.065 2400 Dihedral : 13.500 104.395 5088 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.81 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.18), residues: 1780 helix: -0.37 (0.15), residues: 980 sheet: -1.64 (0.47), residues: 78 loop : -1.81 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.071 0.002 ARG B 497 TYR 0.018 0.002 TYR A 663 PHE 0.034 0.003 PHE A 877 TRP 0.039 0.003 TRP A 809 HIS 0.013 0.001 HIS A 790 Details of bonding type rmsd covalent geometry : bond 0.01051 (14218) covalent geometry : angle 0.92736 (19342) SS BOND : bond 0.00632 ( 6) SS BOND : angle 4.02582 ( 12) hydrogen bonds : bond 0.10624 ( 812) hydrogen bonds : angle 5.51110 ( 2346) link_BETA1-4 : bond 0.00487 ( 4) link_BETA1-4 : angle 3.54117 ( 12) link_NAG-ASN : bond 0.00869 ( 4) link_NAG-ASN : angle 3.23398 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.396 Fit side-chains REVERT: B 397 TRP cc_start: 0.7722 (m100) cc_final: 0.7509 (m100) REVERT: B 459 LYS cc_start: 0.8010 (mttt) cc_final: 0.7785 (mttp) REVERT: B 597 MET cc_start: 0.7873 (tpp) cc_final: 0.7636 (tpp) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1275 time to fit residues: 57.5592 Evaluate side-chains 181 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 629 HIS B 752 ASN B 882 HIS B1040 ASN A 629 HIS A 752 ASN A 882 HIS A1040 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.170523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124018 restraints weight = 16318.666| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.93 r_work: 0.3413 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14232 Z= 0.157 Angle : 0.659 10.222 19378 Z= 0.330 Chirality : 0.043 0.251 2288 Planarity : 0.004 0.046 2400 Dihedral : 7.127 68.958 2088 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.42 % Favored : 97.47 % Rotamer: Outliers : 2.01 % Allowed : 11.70 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 1780 helix: 0.63 (0.16), residues: 1006 sheet: -1.78 (0.45), residues: 92 loop : -1.36 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 497 TYR 0.031 0.002 TYR B 937 PHE 0.029 0.002 PHE A 877 TRP 0.017 0.002 TRP B 649 HIS 0.005 0.001 HIS A 790 Details of bonding type rmsd covalent geometry : bond 0.00359 (14218) covalent geometry : angle 0.64972 (19342) SS BOND : bond 0.00300 ( 6) SS BOND : angle 1.82099 ( 12) hydrogen bonds : bond 0.04408 ( 812) hydrogen bonds : angle 4.60864 ( 2346) link_BETA1-4 : bond 0.00540 ( 4) link_BETA1-4 : angle 3.52844 ( 12) link_NAG-ASN : bond 0.00452 ( 4) link_NAG-ASN : angle 2.14864 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: B 116 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6863 (mm-30) REVERT: B 353 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8382 (mtpp) REVERT: B 397 TRP cc_start: 0.7817 (m100) cc_final: 0.7562 (m100) REVERT: B 459 LYS cc_start: 0.8459 (mttt) cc_final: 0.8049 (mttp) REVERT: B 601 MET cc_start: 0.8444 (tpp) cc_final: 0.8161 (tpp) REVERT: B 673 LYS cc_start: 0.8619 (tppt) cc_final: 0.7867 (ttpp) REVERT: B 861 ASP cc_start: 0.7532 (m-30) cc_final: 0.7239 (m-30) REVERT: A 460 ASP cc_start: 0.7037 (t0) cc_final: 0.6801 (t0) REVERT: A 626 ARG cc_start: 0.7776 (ttt-90) cc_final: 0.6633 (tpt90) REVERT: A 627 TYR cc_start: 0.8058 (m-80) cc_final: 0.7724 (m-80) REVERT: A 677 ASP cc_start: 0.7804 (t70) cc_final: 0.7438 (t0) REVERT: A 767 MET cc_start: 0.8755 (mtm) cc_final: 0.8532 (mtp) REVERT: A 861 ASP cc_start: 0.7084 (m-30) cc_final: 0.6880 (m-30) REVERT: A 1070 TYR cc_start: 0.8477 (t80) cc_final: 0.8131 (t80) outliers start: 29 outliers final: 8 residues processed: 240 average time/residue: 0.1058 time to fit residues: 37.8244 Evaluate side-chains 194 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 185 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1039 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 84 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 164 optimal weight: 0.0050 chunk 87 optimal weight: 0.0770 chunk 132 optimal weight: 0.8980 chunk 177 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 overall best weight: 0.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN B 382 GLN A 836 HIS A 844 ASN A 915 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.175044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128158 restraints weight = 16415.777| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.02 r_work: 0.3442 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14232 Z= 0.124 Angle : 0.590 9.572 19378 Z= 0.297 Chirality : 0.043 0.468 2288 Planarity : 0.004 0.037 2400 Dihedral : 5.680 66.014 2088 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.03 % Favored : 96.85 % Rotamer: Outliers : 1.80 % Allowed : 13.85 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 1780 helix: 1.10 (0.16), residues: 1010 sheet: -1.48 (0.50), residues: 92 loop : -1.21 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 624 TYR 0.029 0.001 TYR B 937 PHE 0.019 0.001 PHE A 877 TRP 0.012 0.001 TRP B 649 HIS 0.003 0.001 HIS A 836 Details of bonding type rmsd covalent geometry : bond 0.00278 (14218) covalent geometry : angle 0.58119 (19342) SS BOND : bond 0.00380 ( 6) SS BOND : angle 2.10177 ( 12) hydrogen bonds : bond 0.03964 ( 812) hydrogen bonds : angle 4.36196 ( 2346) link_BETA1-4 : bond 0.00508 ( 4) link_BETA1-4 : angle 3.12354 ( 12) link_NAG-ASN : bond 0.00413 ( 4) link_NAG-ASN : angle 1.95573 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 138 MET cc_start: 0.8438 (ttp) cc_final: 0.8222 (ttt) REVERT: B 353 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8508 (mtpp) REVERT: B 459 LYS cc_start: 0.8427 (mttt) cc_final: 0.8033 (mttp) REVERT: B 601 MET cc_start: 0.8323 (tpp) cc_final: 0.8049 (tpp) REVERT: B 673 LYS cc_start: 0.8621 (tppt) cc_final: 0.7865 (ttpp) REVERT: B 847 PHE cc_start: 0.8716 (m-10) cc_final: 0.8475 (m-10) REVERT: B 861 ASP cc_start: 0.7451 (m-30) cc_final: 0.7208 (m-30) REVERT: B 923 GLU cc_start: 0.6065 (mp0) cc_final: 0.5858 (mp0) REVERT: B 938 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7709 (mm-30) REVERT: A 116 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6942 (pt0) REVERT: A 460 ASP cc_start: 0.6993 (t0) cc_final: 0.6774 (t0) REVERT: A 627 TYR cc_start: 0.8066 (m-80) cc_final: 0.7750 (m-80) REVERT: A 656 MET cc_start: 0.8464 (mmm) cc_final: 0.8080 (mmm) REVERT: A 677 ASP cc_start: 0.7850 (t70) cc_final: 0.7533 (t70) REVERT: A 861 ASP cc_start: 0.6871 (m-30) cc_final: 0.6598 (m-30) REVERT: A 871 MET cc_start: 0.7930 (tpt) cc_final: 0.7377 (tpt) REVERT: A 942 MET cc_start: 0.8042 (ppp) cc_final: 0.7832 (ptm) REVERT: A 1070 TYR cc_start: 0.8397 (t80) cc_final: 0.8059 (t80) outliers start: 26 outliers final: 13 residues processed: 213 average time/residue: 0.0976 time to fit residues: 31.8457 Evaluate side-chains 187 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 915 HIS Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 887 LYS Chi-restraints excluded: chain A residue 1039 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 118 optimal weight: 0.0770 chunk 128 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 164 optimal weight: 0.0570 chunk 178 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 166 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN A 915 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.172305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126373 restraints weight = 16310.973| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.95 r_work: 0.3437 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 14232 Z= 0.124 Angle : 0.569 8.451 19378 Z= 0.285 Chirality : 0.043 0.338 2288 Planarity : 0.004 0.032 2400 Dihedral : 5.327 64.368 2088 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.03 % Favored : 96.85 % Rotamer: Outliers : 1.94 % Allowed : 14.06 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.20), residues: 1780 helix: 1.42 (0.16), residues: 998 sheet: -1.65 (0.45), residues: 112 loop : -1.04 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.029 0.001 TYR B 937 PHE 0.018 0.001 PHE A 442 TRP 0.011 0.001 TRP A 704 HIS 0.003 0.000 HIS B 802 Details of bonding type rmsd covalent geometry : bond 0.00289 (14218) covalent geometry : angle 0.56116 (19342) SS BOND : bond 0.00372 ( 6) SS BOND : angle 1.95980 ( 12) hydrogen bonds : bond 0.03763 ( 812) hydrogen bonds : angle 4.21940 ( 2346) link_BETA1-4 : bond 0.00521 ( 4) link_BETA1-4 : angle 2.95979 ( 12) link_NAG-ASN : bond 0.00289 ( 4) link_NAG-ASN : angle 1.79025 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 459 LYS cc_start: 0.8389 (mttt) cc_final: 0.8026 (mttp) REVERT: B 601 MET cc_start: 0.8303 (tpp) cc_final: 0.8047 (tpp) REVERT: B 673 LYS cc_start: 0.8659 (tppt) cc_final: 0.7968 (mppt) REVERT: B 677 ASP cc_start: 0.7957 (t70) cc_final: 0.7600 (t70) REVERT: B 861 ASP cc_start: 0.7347 (m-30) cc_final: 0.7136 (m-30) REVERT: B 938 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7711 (mm-30) REVERT: A 116 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6831 (pt0) REVERT: A 460 ASP cc_start: 0.7120 (t0) cc_final: 0.6900 (t0) REVERT: A 601 MET cc_start: 0.8171 (tpp) cc_final: 0.7969 (tpp) REVERT: A 626 ARG cc_start: 0.7847 (ttt-90) cc_final: 0.6746 (tpt90) REVERT: A 627 TYR cc_start: 0.8121 (m-80) cc_final: 0.7784 (m-80) REVERT: A 677 ASP cc_start: 0.7871 (t70) cc_final: 0.7630 (t70) REVERT: A 861 ASP cc_start: 0.6820 (m-30) cc_final: 0.6573 (m-30) REVERT: A 942 MET cc_start: 0.8269 (ppp) cc_final: 0.8011 (ptm) REVERT: A 1070 TYR cc_start: 0.8401 (t80) cc_final: 0.7952 (t80) outliers start: 28 outliers final: 16 residues processed: 216 average time/residue: 0.1029 time to fit residues: 33.6455 Evaluate side-chains 189 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 887 LYS Chi-restraints excluded: chain A residue 913 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 26 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 915 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.168815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121991 restraints weight = 16403.850| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.97 r_work: 0.3401 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 14232 Z= 0.164 Angle : 0.596 8.054 19378 Z= 0.299 Chirality : 0.044 0.381 2288 Planarity : 0.004 0.045 2400 Dihedral : 5.274 63.627 2088 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.52 % Rotamer: Outliers : 1.73 % Allowed : 15.51 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.20), residues: 1780 helix: 1.32 (0.16), residues: 1012 sheet: -1.56 (0.49), residues: 92 loop : -1.01 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 287 TYR 0.029 0.001 TYR B 937 PHE 0.018 0.001 PHE A 442 TRP 0.010 0.001 TRP A 809 HIS 0.002 0.001 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.00399 (14218) covalent geometry : angle 0.58882 (19342) SS BOND : bond 0.00641 ( 6) SS BOND : angle 2.06545 ( 12) hydrogen bonds : bond 0.03861 ( 812) hydrogen bonds : angle 4.25601 ( 2346) link_BETA1-4 : bond 0.00537 ( 4) link_BETA1-4 : angle 2.85609 ( 12) link_NAG-ASN : bond 0.00229 ( 4) link_NAG-ASN : angle 1.78536 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.479 Fit side-chains REVERT: B 459 LYS cc_start: 0.8475 (mttt) cc_final: 0.7981 (ptmt) REVERT: B 601 MET cc_start: 0.8358 (tpp) cc_final: 0.8049 (tpp) REVERT: B 673 LYS cc_start: 0.8691 (tppt) cc_final: 0.7969 (ttpp) REVERT: B 677 ASP cc_start: 0.8032 (t70) cc_final: 0.7631 (t70) REVERT: B 861 ASP cc_start: 0.7380 (m-30) cc_final: 0.6623 (m-30) REVERT: B 893 PHE cc_start: 0.7202 (m-80) cc_final: 0.6144 (m-80) REVERT: A 116 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6838 (pt0) REVERT: A 284 ILE cc_start: 0.7800 (mt) cc_final: 0.7460 (pt) REVERT: A 287 ARG cc_start: 0.8416 (ptt-90) cc_final: 0.8012 (ptt90) REVERT: A 384 ILE cc_start: 0.7534 (tp) cc_final: 0.7200 (tp) REVERT: A 460 ASP cc_start: 0.7222 (t0) cc_final: 0.6959 (t0) REVERT: A 626 ARG cc_start: 0.7917 (ttt-90) cc_final: 0.6811 (tpt90) REVERT: A 627 TYR cc_start: 0.8182 (m-80) cc_final: 0.7885 (m-80) REVERT: A 656 MET cc_start: 0.8546 (mmm) cc_final: 0.8223 (mmm) REVERT: A 677 ASP cc_start: 0.7951 (t70) cc_final: 0.7696 (t70) REVERT: A 861 ASP cc_start: 0.6961 (m-30) cc_final: 0.6718 (m-30) REVERT: A 942 MET cc_start: 0.8300 (ppp) cc_final: 0.8082 (ptt) REVERT: A 943 MET cc_start: 0.8859 (mmp) cc_final: 0.8653 (mmp) outliers start: 25 outliers final: 17 residues processed: 199 average time/residue: 0.1057 time to fit residues: 31.6875 Evaluate side-chains 187 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 887 LYS Chi-restraints excluded: chain A residue 913 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 128 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 26 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 62 optimal weight: 0.6980 chunk 61 optimal weight: 0.0050 chunk 143 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 915 HIS A1056 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.171583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.125417 restraints weight = 16295.363| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.97 r_work: 0.3446 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14232 Z= 0.118 Angle : 0.559 8.307 19378 Z= 0.279 Chirality : 0.043 0.371 2288 Planarity : 0.003 0.038 2400 Dihedral : 5.137 62.787 2088 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer: Outliers : 1.52 % Allowed : 16.41 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1780 helix: 1.53 (0.16), residues: 1008 sheet: -1.43 (0.50), residues: 92 loop : -0.83 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 287 TYR 0.029 0.001 TYR B 937 PHE 0.019 0.001 PHE A 728 TRP 0.011 0.001 TRP A 704 HIS 0.003 0.000 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00272 (14218) covalent geometry : angle 0.55025 (19342) SS BOND : bond 0.00454 ( 6) SS BOND : angle 2.43732 ( 12) hydrogen bonds : bond 0.03684 ( 812) hydrogen bonds : angle 4.16809 ( 2346) link_BETA1-4 : bond 0.00486 ( 4) link_BETA1-4 : angle 2.81017 ( 12) link_NAG-ASN : bond 0.00231 ( 4) link_NAG-ASN : angle 1.59036 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: B 324 CYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6631 (m) REVERT: B 325 MET cc_start: 0.7073 (mtm) cc_final: 0.6803 (mtp) REVERT: B 459 LYS cc_start: 0.8441 (mttt) cc_final: 0.7905 (ptmm) REVERT: B 601 MET cc_start: 0.8277 (tpp) cc_final: 0.8045 (tpp) REVERT: B 673 LYS cc_start: 0.8687 (tppt) cc_final: 0.7971 (ttpp) REVERT: B 677 ASP cc_start: 0.7985 (t70) cc_final: 0.7554 (t70) REVERT: B 861 ASP cc_start: 0.7296 (m-30) cc_final: 0.6536 (m-30) REVERT: B 893 PHE cc_start: 0.7151 (m-80) cc_final: 0.6114 (m-80) REVERT: A 116 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6848 (pt0) REVERT: A 384 ILE cc_start: 0.7517 (tp) cc_final: 0.7258 (tp) REVERT: A 460 ASP cc_start: 0.7181 (t0) cc_final: 0.6849 (t70) REVERT: A 626 ARG cc_start: 0.7925 (ttt-90) cc_final: 0.6833 (tpt90) REVERT: A 627 TYR cc_start: 0.8152 (m-80) cc_final: 0.7861 (m-80) REVERT: A 656 MET cc_start: 0.8497 (mmm) cc_final: 0.8152 (mmm) REVERT: A 677 ASP cc_start: 0.7960 (t70) cc_final: 0.7652 (t70) REVERT: A 861 ASP cc_start: 0.6776 (m-30) cc_final: 0.6532 (m-30) REVERT: A 871 MET cc_start: 0.7961 (tpt) cc_final: 0.7701 (mmm) REVERT: A 942 MET cc_start: 0.8283 (ppp) cc_final: 0.7934 (tpt) REVERT: A 943 MET cc_start: 0.8908 (mmp) cc_final: 0.8603 (mmp) REVERT: A 1070 TYR cc_start: 0.8511 (t80) cc_final: 0.8284 (t80) outliers start: 22 outliers final: 15 residues processed: 202 average time/residue: 0.1002 time to fit residues: 30.8061 Evaluate side-chains 189 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 887 LYS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1056 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 35 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.171240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124869 restraints weight = 16206.627| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.96 r_work: 0.3423 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14232 Z= 0.125 Angle : 0.562 8.936 19378 Z= 0.279 Chirality : 0.043 0.379 2288 Planarity : 0.004 0.048 2400 Dihedral : 5.087 62.327 2088 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.26 % Favored : 96.63 % Rotamer: Outliers : 1.80 % Allowed : 16.76 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1780 helix: 1.58 (0.16), residues: 1008 sheet: -1.45 (0.49), residues: 92 loop : -0.76 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 287 TYR 0.029 0.001 TYR B 937 PHE 0.016 0.001 PHE A 442 TRP 0.009 0.001 TRP A 704 HIS 0.003 0.000 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00293 (14218) covalent geometry : angle 0.55443 (19342) SS BOND : bond 0.00381 ( 6) SS BOND : angle 2.15355 ( 12) hydrogen bonds : bond 0.03630 ( 812) hydrogen bonds : angle 4.13533 ( 2346) link_BETA1-4 : bond 0.00493 ( 4) link_BETA1-4 : angle 2.77447 ( 12) link_NAG-ASN : bond 0.00195 ( 4) link_NAG-ASN : angle 1.57065 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: B 187 MET cc_start: 0.6858 (tpp) cc_final: 0.6609 (tpt) REVERT: B 324 CYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6583 (m) REVERT: B 325 MET cc_start: 0.7256 (mtm) cc_final: 0.6942 (mtp) REVERT: B 459 LYS cc_start: 0.8454 (mttt) cc_final: 0.7918 (ptmm) REVERT: B 601 MET cc_start: 0.8301 (tpp) cc_final: 0.8034 (tpp) REVERT: B 673 LYS cc_start: 0.8701 (tppt) cc_final: 0.7977 (ttpp) REVERT: B 677 ASP cc_start: 0.8010 (t70) cc_final: 0.7583 (t70) REVERT: B 861 ASP cc_start: 0.7316 (m-30) cc_final: 0.6555 (m-30) REVERT: B 893 PHE cc_start: 0.7166 (m-80) cc_final: 0.6178 (m-80) REVERT: A 116 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6809 (pt0) REVERT: A 283 PHE cc_start: 0.8278 (t80) cc_final: 0.7869 (t80) REVERT: A 284 ILE cc_start: 0.7769 (mt) cc_final: 0.7456 (pt) REVERT: A 287 ARG cc_start: 0.8455 (ptt90) cc_final: 0.8005 (ptt90) REVERT: A 384 ILE cc_start: 0.7517 (tp) cc_final: 0.7281 (tp) REVERT: A 460 ASP cc_start: 0.7189 (t0) cc_final: 0.6847 (t70) REVERT: A 626 ARG cc_start: 0.7915 (ttt-90) cc_final: 0.6804 (tpt90) REVERT: A 627 TYR cc_start: 0.8142 (m-80) cc_final: 0.7859 (m-80) REVERT: A 656 MET cc_start: 0.8485 (mmm) cc_final: 0.8165 (mmm) REVERT: A 677 ASP cc_start: 0.7968 (t70) cc_final: 0.7655 (t70) REVERT: A 861 ASP cc_start: 0.6739 (m-30) cc_final: 0.6493 (m-30) REVERT: A 871 MET cc_start: 0.7954 (tpt) cc_final: 0.7725 (mmm) REVERT: A 942 MET cc_start: 0.8281 (ppp) cc_final: 0.7917 (tpt) REVERT: A 943 MET cc_start: 0.8952 (mmp) cc_final: 0.8662 (mmp) REVERT: A 1070 TYR cc_start: 0.8544 (t80) cc_final: 0.8311 (t80) outliers start: 26 outliers final: 20 residues processed: 200 average time/residue: 0.0968 time to fit residues: 29.4486 Evaluate side-chains 197 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 913 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 26 optimal weight: 30.0000 chunk 159 optimal weight: 3.9990 chunk 83 optimal weight: 40.0000 chunk 65 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 HIS A 120 ASN A 915 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.171252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.123107 restraints weight = 16425.695| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.97 r_work: 0.3324 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.135 14232 Z= 0.240 Angle : 0.662 9.665 19378 Z= 0.332 Chirality : 0.047 0.330 2288 Planarity : 0.004 0.043 2400 Dihedral : 5.336 62.331 2088 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.99 % Favored : 95.90 % Rotamer: Outliers : 2.01 % Allowed : 17.31 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1780 helix: 1.33 (0.17), residues: 990 sheet: -1.76 (0.48), residues: 92 loop : -0.78 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 287 TYR 0.029 0.002 TYR B 937 PHE 0.022 0.002 PHE A 555 TRP 0.015 0.001 TRP A 809 HIS 0.003 0.001 HIS B 790 Details of bonding type rmsd covalent geometry : bond 0.00595 (14218) covalent geometry : angle 0.65483 (19342) SS BOND : bond 0.00465 ( 6) SS BOND : angle 2.55923 ( 12) hydrogen bonds : bond 0.04116 ( 812) hydrogen bonds : angle 4.40166 ( 2346) link_BETA1-4 : bond 0.00448 ( 4) link_BETA1-4 : angle 2.73396 ( 12) link_NAG-ASN : bond 0.00220 ( 4) link_NAG-ASN : angle 1.74365 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.564 Fit side-chains REVERT: B 105 TYR cc_start: 0.7746 (OUTLIER) cc_final: 0.7394 (p90) REVERT: B 324 CYS cc_start: 0.6707 (OUTLIER) cc_final: 0.6409 (m) REVERT: B 459 LYS cc_start: 0.8568 (mttt) cc_final: 0.8017 (ptmm) REVERT: B 601 MET cc_start: 0.8296 (tpp) cc_final: 0.7981 (tpp) REVERT: B 673 LYS cc_start: 0.8670 (tppt) cc_final: 0.7964 (ttpp) REVERT: B 677 ASP cc_start: 0.8018 (t70) cc_final: 0.7574 (t70) REVERT: B 861 ASP cc_start: 0.7358 (m-30) cc_final: 0.6538 (m-30) REVERT: B 893 PHE cc_start: 0.7200 (m-80) cc_final: 0.6264 (m-80) REVERT: A 105 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7395 (p90) REVERT: A 116 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6785 (pt0) REVERT: A 287 ARG cc_start: 0.8509 (ptt90) cc_final: 0.8007 (ptt90) REVERT: A 459 LYS cc_start: 0.8593 (mttt) cc_final: 0.8129 (mttp) REVERT: A 460 ASP cc_start: 0.7282 (t0) cc_final: 0.6973 (t0) REVERT: A 498 ASP cc_start: 0.7460 (t0) cc_final: 0.7016 (t70) REVERT: A 626 ARG cc_start: 0.7953 (ttt-90) cc_final: 0.7730 (ttt-90) REVERT: A 627 TYR cc_start: 0.8208 (m-80) cc_final: 0.7964 (m-80) REVERT: A 677 ASP cc_start: 0.7976 (t70) cc_final: 0.7655 (t70) REVERT: A 861 ASP cc_start: 0.7050 (m-30) cc_final: 0.6763 (m-30) REVERT: A 942 MET cc_start: 0.8284 (ppp) cc_final: 0.7920 (tpt) REVERT: A 943 MET cc_start: 0.8985 (mmp) cc_final: 0.8723 (mmp) REVERT: A 1070 TYR cc_start: 0.8529 (t80) cc_final: 0.8324 (t80) outliers start: 29 outliers final: 23 residues processed: 199 average time/residue: 0.1007 time to fit residues: 30.5811 Evaluate side-chains 192 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1039 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 146 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN A 915 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.171018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124260 restraints weight = 16309.738| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.00 r_work: 0.3381 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14232 Z= 0.135 Angle : 0.590 10.027 19378 Z= 0.293 Chirality : 0.044 0.368 2288 Planarity : 0.004 0.040 2400 Dihedral : 5.140 61.635 2088 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.03 % Favored : 96.85 % Rotamer: Outliers : 1.59 % Allowed : 18.14 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.20), residues: 1780 helix: 1.51 (0.16), residues: 992 sheet: -1.89 (0.47), residues: 92 loop : -0.65 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.029 0.001 TYR B 937 PHE 0.019 0.001 PHE A 442 TRP 0.012 0.001 TRP B 649 HIS 0.004 0.000 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.00321 (14218) covalent geometry : angle 0.58283 (19342) SS BOND : bond 0.00337 ( 6) SS BOND : angle 2.09055 ( 12) hydrogen bonds : bond 0.03721 ( 812) hydrogen bonds : angle 4.25035 ( 2346) link_BETA1-4 : bond 0.00498 ( 4) link_BETA1-4 : angle 2.74406 ( 12) link_NAG-ASN : bond 0.00197 ( 4) link_NAG-ASN : angle 1.55489 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.432 Fit side-chains REVERT: B 324 CYS cc_start: 0.6444 (OUTLIER) cc_final: 0.6220 (m) REVERT: B 459 LYS cc_start: 0.8505 (mttt) cc_final: 0.7960 (ptmm) REVERT: B 601 MET cc_start: 0.8205 (tpp) cc_final: 0.7920 (tpp) REVERT: B 673 LYS cc_start: 0.8654 (tppt) cc_final: 0.7965 (tttm) REVERT: B 677 ASP cc_start: 0.7939 (t70) cc_final: 0.7446 (t70) REVERT: B 861 ASP cc_start: 0.7184 (m-30) cc_final: 0.6329 (m-30) REVERT: B 893 PHE cc_start: 0.7189 (m-80) cc_final: 0.6248 (m-80) REVERT: A 105 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.7305 (p90) REVERT: A 287 ARG cc_start: 0.8450 (ptt90) cc_final: 0.7972 (ptt90) REVERT: A 459 LYS cc_start: 0.8533 (mttt) cc_final: 0.8069 (mttp) REVERT: A 460 ASP cc_start: 0.7180 (t0) cc_final: 0.6780 (t70) REVERT: A 498 ASP cc_start: 0.7391 (t0) cc_final: 0.6920 (t70) REVERT: A 626 ARG cc_start: 0.7922 (ttt-90) cc_final: 0.6807 (tpt90) REVERT: A 627 TYR cc_start: 0.8126 (m-80) cc_final: 0.7872 (m-80) REVERT: A 656 MET cc_start: 0.8436 (mmm) cc_final: 0.8123 (mmm) REVERT: A 677 ASP cc_start: 0.7912 (t70) cc_final: 0.7566 (t70) REVERT: A 861 ASP cc_start: 0.6866 (m-30) cc_final: 0.6585 (m-30) REVERT: A 942 MET cc_start: 0.8311 (ppp) cc_final: 0.8035 (ptm) REVERT: A 1070 TYR cc_start: 0.8441 (t80) cc_final: 0.8231 (t80) REVERT: A 1079 GLU cc_start: 0.7738 (tp30) cc_final: 0.7201 (tp30) outliers start: 23 outliers final: 18 residues processed: 190 average time/residue: 0.1036 time to fit residues: 30.0680 Evaluate side-chains 187 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 423 HIS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1039 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 94 optimal weight: 0.9980 chunk 121 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.171089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124366 restraints weight = 16275.566| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.00 r_work: 0.3390 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14232 Z= 0.136 Angle : 0.593 10.098 19378 Z= 0.294 Chirality : 0.044 0.336 2288 Planarity : 0.004 0.039 2400 Dihedral : 5.092 61.218 2088 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.31 % Favored : 96.57 % Rotamer: Outliers : 1.52 % Allowed : 18.14 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.20), residues: 1780 helix: 1.63 (0.17), residues: 992 sheet: -1.88 (0.48), residues: 92 loop : -0.60 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 680 TYR 0.029 0.001 TYR B 937 PHE 0.017 0.001 PHE A 442 TRP 0.010 0.001 TRP B 649 HIS 0.003 0.000 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.00325 (14218) covalent geometry : angle 0.58622 (19342) SS BOND : bond 0.00324 ( 6) SS BOND : angle 2.06603 ( 12) hydrogen bonds : bond 0.03679 ( 812) hydrogen bonds : angle 4.20462 ( 2346) link_BETA1-4 : bond 0.00608 ( 4) link_BETA1-4 : angle 2.73891 ( 12) link_NAG-ASN : bond 0.00143 ( 4) link_NAG-ASN : angle 1.51620 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.516 Fit side-chains REVERT: B 324 CYS cc_start: 0.6657 (OUTLIER) cc_final: 0.6328 (m) REVERT: B 459 LYS cc_start: 0.8513 (mttt) cc_final: 0.7972 (ptmm) REVERT: B 601 MET cc_start: 0.8199 (tpp) cc_final: 0.7915 (tpp) REVERT: B 673 LYS cc_start: 0.8653 (tppt) cc_final: 0.7957 (ttpp) REVERT: B 677 ASP cc_start: 0.7957 (t70) cc_final: 0.7466 (t70) REVERT: B 713 LYS cc_start: 0.8500 (tttt) cc_final: 0.7958 (tptp) REVERT: B 861 ASP cc_start: 0.7205 (m-30) cc_final: 0.6387 (m-30) REVERT: B 893 PHE cc_start: 0.7164 (m-80) cc_final: 0.6274 (m-80) REVERT: A 105 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7211 (p90) REVERT: A 287 ARG cc_start: 0.8440 (ptt90) cc_final: 0.7919 (ptt90) REVERT: A 384 ILE cc_start: 0.7511 (tp) cc_final: 0.7110 (tp) REVERT: A 459 LYS cc_start: 0.8527 (mttt) cc_final: 0.8067 (mttp) REVERT: A 460 ASP cc_start: 0.7201 (t0) cc_final: 0.6806 (t70) REVERT: A 498 ASP cc_start: 0.7400 (t0) cc_final: 0.6910 (t70) REVERT: A 626 ARG cc_start: 0.7941 (ttt-90) cc_final: 0.6819 (tpt90) REVERT: A 627 TYR cc_start: 0.8137 (m-80) cc_final: 0.7896 (m-80) REVERT: A 656 MET cc_start: 0.8468 (mmm) cc_final: 0.8193 (mmm) REVERT: A 677 ASP cc_start: 0.7931 (t70) cc_final: 0.7576 (t70) REVERT: A 861 ASP cc_start: 0.6888 (m-30) cc_final: 0.6615 (m-30) REVERT: A 1079 GLU cc_start: 0.7705 (tp30) cc_final: 0.7165 (tp30) outliers start: 22 outliers final: 18 residues processed: 190 average time/residue: 0.1034 time to fit residues: 29.6663 Evaluate side-chains 190 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 423 HIS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 1039 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 170 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.168106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.120896 restraints weight = 16527.380| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.95 r_work: 0.3319 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 14232 Z= 0.249 Angle : 0.681 10.365 19378 Z= 0.339 Chirality : 0.048 0.320 2288 Planarity : 0.004 0.038 2400 Dihedral : 5.284 61.226 2088 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.93 % Favored : 95.96 % Rotamer: Outliers : 1.87 % Allowed : 18.14 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1780 helix: 1.39 (0.17), residues: 980 sheet: -2.03 (0.47), residues: 92 loop : -0.69 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 680 TYR 0.028 0.002 TYR B 937 PHE 0.021 0.002 PHE A 555 TRP 0.014 0.001 TRP A 809 HIS 0.004 0.001 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.00614 (14218) covalent geometry : angle 0.67448 (19342) SS BOND : bond 0.00502 ( 6) SS BOND : angle 2.45782 ( 12) hydrogen bonds : bond 0.04062 ( 812) hydrogen bonds : angle 4.40530 ( 2346) link_BETA1-4 : bond 0.00419 ( 4) link_BETA1-4 : angle 2.66196 ( 12) link_NAG-ASN : bond 0.00171 ( 4) link_NAG-ASN : angle 1.67554 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3110.29 seconds wall clock time: 54 minutes 4.27 seconds (3244.27 seconds total)