Starting phenix.real_space_refine on Fri Jul 3 12:08:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ain_11799/07_2026/7ain_11799.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ain_11799/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7ain_11799/07_2026/7ain_11799.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ain_11799/07_2026/7ain_11799.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ain_11799/07_2026/7ain_11799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ain_11799/07_2026/7ain_11799.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ain_11799/07_2026/7ain_11799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ain_11799/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 chiralities: 1 Time building chain proxies: 2.68, per 1000 atoms: 0.19 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 621.0 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: 0.50 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: 2.25 Time building geometry restraints manager: 1.64 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 - 15.67: 7562 15.67 - 31.33: 546 31.33 - 47.00: 118 47.00 - 62.66: 38 62.66 - 78.33: 10 Dihedral angle restraints: 8274 sinusoidal: 3092 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 8271 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: 0.03 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: 5.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.680 Find NCS groups from input model: 0.120 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 : 12.201 78.327 4924 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/Z covalent geometry : bond 0.01051 / 0.45 (14218) covalent geometry : angle 0.92736 / 0.50 (19342) SS BOND : bond 0.00632 / 0.32 ( 6) SS BOND : angle 4.02582 / 2.34 ( 12) hydrogen bonds : bond 0.10624 / 7.14 ( 812) hydrogen bonds : angle 5.51110 / 3.99 ( 2346) link_BETA1-4 : bond 0.00487 / 0.25 ( 4) link_BETA1-4 : angle 3.54117 / 1.83 ( 12) link_NAG-ASN : bond 0.00869 / 0.44 ( 4) link_NAG-ASN : angle 3.23398 / 1.83 ( 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 : 0.549 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: 0.1268 time to fit residues: 57.5272 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 : 0.444 ------------------------------------------------------------------------------- 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... 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 = 0.4054 r_free = 0.4054 target = 0.170319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123881 restraints weight = 16328.606| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.93 r_work: 0.3410 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14232 Z= 0.157 Angle : 0.646 10.177 19378 Z= 0.327 Chirality : 0.043 0.248 2288 Planarity : 0.004 0.046 2400 Dihedral : 4.908 69.109 1924 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.47 % Favored : 97.42 % Rotamer: Outliers : 2.08 % Allowed : 11.77 % Favored : 86.15 % 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: -0.43 (0.19), residues: 1780 helix: 0.61 (0.16), residues: 1006 sheet: -1.79 (0.45), residues: 92 loop : -1.36 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 497 TYR 0.031 0.002 TYR B 937 PHE 0.030 0.002 PHE A 877 TRP 0.018 0.002 TRP B 649 HIS 0.005 0.001 HIS A 790 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (14218) covalent geometry : angle 0.63844 / 0.32 (19342) SS BOND : bond 0.00287 / 0.14 ( 6) SS BOND : angle 1.91890 / 1.09 ( 12) hydrogen bonds : bond 0.04442 / 2.93 ( 812) hydrogen bonds : angle 4.60911 / 3.36 ( 2346) link_BETA1-4 : bond 0.00728 / 0.37 ( 4) link_BETA1-4 : angle 2.99191 / 1.51 ( 12) link_NAG-ASN : bond 0.00424 / 0.21 ( 4) link_NAG-ASN : angle 2.10077 / 1.20 ( 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 251 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: B 116 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6859 (mm-30) REVERT: B 353 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8371 (mtpp) REVERT: B 397 TRP cc_start: 0.7821 (m100) cc_final: 0.7566 (m100) REVERT: B 459 LYS cc_start: 0.8462 (mttt) cc_final: 0.8068 (mttp) REVERT: B 460 ASP cc_start: 0.7343 (t70) cc_final: 0.7140 (t0) REVERT: B 601 MET cc_start: 0.8459 (tpp) cc_final: 0.8170 (tpp) REVERT: B 673 LYS cc_start: 0.8619 (tppt) cc_final: 0.7869 (ttpp) REVERT: B 861 ASP cc_start: 0.7533 (m-30) cc_final: 0.7238 (m-30) REVERT: A 460 ASP cc_start: 0.7028 (t0) cc_final: 0.6806 (t0) REVERT: A 626 ARG cc_start: 0.7779 (ttt-90) cc_final: 0.6635 (tpt90) REVERT: A 627 TYR cc_start: 0.8055 (m-80) cc_final: 0.7719 (m-80) REVERT: A 677 ASP cc_start: 0.7802 (t70) cc_final: 0.7401 (t0) REVERT: A 861 ASP cc_start: 0.7107 (m-30) cc_final: 0.6890 (m-30) REVERT: A 1070 TYR cc_start: 0.8460 (t80) cc_final: 0.8221 (t80) outliers start: 30 outliers final: 9 residues processed: 242 average time/residue: 0.1134 time to fit residues: 40.9254 Evaluate side-chains 193 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 522 VAL 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: 0.5980 chunk 121 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 177 optimal weight: 0.0370 chunk 41 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 290 ASN A 844 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 = 0.4091 r_free = 0.4091 target = 0.174606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.127565 restraints weight = 16432.459| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.02 r_work: 0.3438 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2536 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= 0.127 Angle : 0.591 9.819 19378 Z= 0.298 Chirality : 0.043 0.451 2288 Planarity : 0.004 0.036 2400 Dihedral : 4.713 66.179 1924 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.09 % Favored : 96.80 % Rotamer: Outliers : 1.66 % Allowed : 13.71 % Favored : 84.63 % 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: 0.09 (0.20), residues: 1780 helix: 1.07 (0.16), residues: 1010 sheet: -1.54 (0.49), residues: 92 loop : -1.21 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 624 TYR 0.030 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/Z covalent geometry : bond 0.00285 / 0.13 (14218) covalent geometry : angle 0.58346 / 0.30 (19342) SS BOND : bond 0.00562 / 0.29 ( 6) SS BOND : angle 1.78672 / 1.04 ( 12) hydrogen bonds : bond 0.03987 / 2.63 ( 812) hydrogen bonds : angle 4.38439 / 3.19 ( 2346) link_BETA1-4 : bond 0.00631 / 0.32 ( 4) link_BETA1-4 : angle 2.78085 / 1.43 ( 12) link_NAG-ASN : bond 0.00339 / 0.17 ( 4) link_NAG-ASN : angle 1.87584 / 1.04 ( 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 221 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 138 MET cc_start: 0.8437 (ttp) cc_final: 0.8233 (ttt) REVERT: B 353 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8506 (mtpp) REVERT: B 459 LYS cc_start: 0.8435 (mttt) cc_final: 0.8050 (mttp) REVERT: B 460 ASP cc_start: 0.7335 (t70) cc_final: 0.7124 (t0) REVERT: B 601 MET cc_start: 0.8344 (tpp) cc_final: 0.8083 (tpp) REVERT: B 673 LYS cc_start: 0.8625 (tppt) cc_final: 0.7872 (ttpp) REVERT: B 847 PHE cc_start: 0.8733 (m-10) cc_final: 0.8498 (m-10) REVERT: B 861 ASP cc_start: 0.7453 (m-30) cc_final: 0.7213 (m-30) REVERT: B 923 GLU cc_start: 0.6083 (mp0) cc_final: 0.5872 (mp0) REVERT: A 116 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6962 (pt0) REVERT: A 287 ARG cc_start: 0.8331 (ptt-90) cc_final: 0.8042 (ptt-90) REVERT: A 460 ASP cc_start: 0.6999 (t0) cc_final: 0.6779 (t0) REVERT: A 627 TYR cc_start: 0.8079 (m-80) cc_final: 0.7765 (m-80) REVERT: A 677 ASP cc_start: 0.7854 (t70) cc_final: 0.7538 (t70) REVERT: A 861 ASP cc_start: 0.6906 (m-30) cc_final: 0.6637 (m-30) REVERT: A 871 MET cc_start: 0.7937 (tpt) cc_final: 0.7348 (tpt) REVERT: A 942 MET cc_start: 0.8032 (ppp) cc_final: 0.7817 (ptm) REVERT: A 1070 TYR cc_start: 0.8509 (t80) cc_final: 0.7959 (t80) outliers start: 24 outliers final: 14 residues processed: 211 average time/residue: 0.1101 time to fit residues: 35.5304 Evaluate side-chains 185 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 264 LEU 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 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: 2.9990 chunk 128 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 178 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 844 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.167967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.120535 restraints weight = 16505.080| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.96 r_work: 0.3332 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 14232 Z= 0.236 Angle : 0.657 8.539 19378 Z= 0.332 Chirality : 0.046 0.320 2288 Planarity : 0.004 0.033 2400 Dihedral : 4.817 64.985 1924 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 2.70 % Allowed : 14.61 % Favored : 82.69 % 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: 1.11 (0.16), residues: 984 sheet: -1.88 (0.44), residues: 112 loop : -1.02 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 624 TYR 0.029 0.002 TYR B 937 PHE 0.021 0.002 PHE A 555 TRP 0.020 0.001 TRP A 704 HIS 0.003 0.001 HIS B 790 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.24 (14218) covalent geometry : angle 0.64925 / 0.33 (19342) SS BOND : bond 0.00550 / 0.28 ( 6) SS BOND : angle 2.34731 / 1.36 ( 12) hydrogen bonds : bond 0.04264 / 2.82 ( 812) hydrogen bonds : angle 4.46475 / 3.24 ( 2346) link_BETA1-4 : bond 0.00546 / 0.27 ( 4) link_BETA1-4 : angle 2.79887 / 1.41 ( 12) link_NAG-ASN : bond 0.00338 / 0.16 ( 4) link_NAG-ASN : angle 1.93988 / 1.10 ( 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 220 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.762 Fit side-chains REVERT: B 353 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8714 (mtpp) REVERT: B 397 TRP cc_start: 0.7949 (m100) cc_final: 0.7703 (m100) REVERT: B 459 LYS cc_start: 0.8501 (mttt) cc_final: 0.8095 (mttp) REVERT: B 460 ASP cc_start: 0.7465 (t70) cc_final: 0.7239 (t0) REVERT: B 601 MET cc_start: 0.8446 (tpp) cc_final: 0.7716 (tpp) REVERT: B 673 LYS cc_start: 0.8662 (tppt) cc_final: 0.7965 (tttm) REVERT: B 677 ASP cc_start: 0.8046 (t70) cc_final: 0.7706 (t70) REVERT: B 861 ASP cc_start: 0.7465 (m-30) cc_final: 0.6643 (m-30) REVERT: B 893 PHE cc_start: 0.7199 (m-80) cc_final: 0.6088 (m-80) REVERT: A 116 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6878 (pt0) REVERT: A 287 ARG cc_start: 0.8289 (ptt-90) cc_final: 0.8079 (ptt-90) REVERT: A 460 ASP cc_start: 0.7180 (t0) cc_final: 0.6902 (t0) REVERT: A 498 ASP cc_start: 0.7350 (t0) cc_final: 0.6923 (t70) REVERT: A 601 MET cc_start: 0.8263 (tpp) cc_final: 0.7993 (tpp) REVERT: A 626 ARG cc_start: 0.7920 (ttt-90) cc_final: 0.6796 (tpt90) REVERT: A 627 TYR cc_start: 0.8216 (m-80) cc_final: 0.7921 (m-80) REVERT: A 677 ASP cc_start: 0.7931 (t70) cc_final: 0.7560 (t70) REVERT: A 861 ASP cc_start: 0.7051 (m-30) cc_final: 0.6811 (m-30) REVERT: A 871 MET cc_start: 0.8199 (tpt) cc_final: 0.7802 (tpt) REVERT: A 942 MET cc_start: 0.8289 (ppp) cc_final: 0.8059 (ptm) REVERT: A 943 MET cc_start: 0.8883 (mmp) cc_final: 0.8683 (mmp) outliers start: 39 outliers final: 24 residues processed: 214 average time/residue: 0.1112 time to fit residues: 35.9798 Evaluate side-chains 191 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 264 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 522 VAL 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 180 THR Chi-restraints excluded: chain A residue 302 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 887 LYS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1039 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 26 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 134 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 146 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 382 GLN A 120 ASN A 915 HIS A1056 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.173055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126371 restraints weight = 16442.254| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.97 r_work: 0.3395 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14232 Z= 0.130 Angle : 0.574 8.751 19378 Z= 0.289 Chirality : 0.043 0.278 2288 Planarity : 0.004 0.049 2400 Dihedral : 4.635 63.670 1924 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer: Outliers : 1.66 % Allowed : 16.20 % Favored : 82.13 % 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: 0.49 (0.20), residues: 1780 helix: 1.40 (0.16), residues: 988 sheet: -1.67 (0.44), residues: 112 loop : -0.89 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 287 TYR 0.029 0.001 TYR B 937 PHE 0.018 0.001 PHE B 442 TRP 0.012 0.001 TRP B 649 HIS 0.003 0.000 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (14218) covalent geometry : angle 0.56634 / 0.29 (19342) SS BOND : bond 0.00282 / 0.14 ( 6) SS BOND : angle 2.17159 / 1.26 ( 12) hydrogen bonds : bond 0.03834 / 2.53 ( 812) hydrogen bonds : angle 4.31397 / 3.12 ( 2346) link_BETA1-4 : bond 0.00611 / 0.31 ( 4) link_BETA1-4 : angle 2.75719 / 1.41 ( 12) link_NAG-ASN : bond 0.00182 / 0.09 ( 4) link_NAG-ASN : angle 1.57604 / 0.90 ( 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 207 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.519 Fit side-chains REVERT: B 459 LYS cc_start: 0.8474 (mttt) cc_final: 0.8076 (mttp) REVERT: B 601 MET cc_start: 0.8314 (tpp) cc_final: 0.8028 (tpp) REVERT: B 673 LYS cc_start: 0.8633 (tppt) cc_final: 0.7941 (tttm) REVERT: B 677 ASP cc_start: 0.7992 (t70) cc_final: 0.7578 (t70) REVERT: B 861 ASP cc_start: 0.7291 (m-30) cc_final: 0.6497 (m-30) REVERT: B 893 PHE cc_start: 0.7152 (m-80) cc_final: 0.6107 (m-80) REVERT: B 923 GLU cc_start: 0.6299 (mp0) cc_final: 0.6093 (mp0) REVERT: A 116 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6820 (pt0) REVERT: A 287 ARG cc_start: 0.8284 (ptt-90) cc_final: 0.8044 (ptt-90) REVERT: A 460 ASP cc_start: 0.7128 (t0) cc_final: 0.6862 (t0) REVERT: A 601 MET cc_start: 0.8178 (tpp) cc_final: 0.7892 (tpp) REVERT: A 626 ARG cc_start: 0.7903 (ttt-90) cc_final: 0.6788 (tpt90) REVERT: A 627 TYR cc_start: 0.8133 (m-80) cc_final: 0.7834 (m-80) REVERT: A 656 MET cc_start: 0.8434 (mmm) cc_final: 0.8047 (mmm) REVERT: A 677 ASP cc_start: 0.7893 (t70) cc_final: 0.7420 (t70) REVERT: A 861 ASP cc_start: 0.6877 (m-30) cc_final: 0.6627 (m-30) REVERT: A 942 MET cc_start: 0.8336 (ppp) cc_final: 0.8001 (tpt) REVERT: A 943 MET cc_start: 0.8921 (mmp) cc_final: 0.8616 (mmp) outliers start: 24 outliers final: 17 residues processed: 201 average time/residue: 0.1087 time to fit residues: 33.5283 Evaluate side-chains 183 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 264 LEU Chi-restraints excluded: chain B residue 312 ILE 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 1039 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1056 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 128 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 320 HIS A 120 ASN A 915 HIS A1056 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.171033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124021 restraints weight = 16395.544| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.95 r_work: 0.3364 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 14232 Z= 0.172 Angle : 0.596 7.887 19378 Z= 0.299 Chirality : 0.044 0.405 2288 Planarity : 0.004 0.046 2400 Dihedral : 4.623 63.467 1924 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.60 % Favored : 96.29 % Rotamer: Outliers : 1.73 % Allowed : 17.31 % Favored : 80.96 % 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: 0.55 (0.20), residues: 1780 helix: 1.45 (0.16), residues: 982 sheet: -1.84 (0.48), residues: 92 loop : -0.84 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 287 TYR 0.030 0.001 TYR B 937 PHE 0.017 0.001 PHE A 555 TRP 0.010 0.001 TRP A 704 HIS 0.002 0.000 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (14218) covalent geometry : angle 0.58794 / 0.30 (19342) SS BOND : bond 0.00483 / 0.24 ( 6) SS BOND : angle 2.32593 / 1.36 ( 12) hydrogen bonds : bond 0.03883 / 2.56 ( 812) hydrogen bonds : angle 4.30691 / 3.12 ( 2346) link_BETA1-4 : bond 0.00552 / 0.28 ( 4) link_BETA1-4 : angle 2.74627 / 1.40 ( 12) link_NAG-ASN : bond 0.00194 / 0.09 ( 4) link_NAG-ASN : angle 1.60560 / 0.91 ( 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 199 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.532 Fit side-chains REVERT: B 324 CYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6509 (m) REVERT: B 325 MET cc_start: 0.7338 (mtm) cc_final: 0.7062 (mtp) REVERT: B 459 LYS cc_start: 0.8488 (mttt) cc_final: 0.8075 (mttp) REVERT: B 601 MET cc_start: 0.8357 (tpp) cc_final: 0.8033 (tpp) REVERT: B 673 LYS cc_start: 0.8651 (tppt) cc_final: 0.7941 (ttpp) REVERT: B 677 ASP cc_start: 0.8001 (t70) cc_final: 0.7577 (t70) REVERT: B 861 ASP cc_start: 0.7311 (m-30) cc_final: 0.6515 (m-30) REVERT: B 893 PHE cc_start: 0.7193 (m-80) cc_final: 0.6177 (m-80) REVERT: B 923 GLU cc_start: 0.6296 (mp0) cc_final: 0.6068 (mp0) REVERT: A 116 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6827 (pt0) REVERT: A 287 ARG cc_start: 0.8291 (ptt-90) cc_final: 0.8039 (ptt-90) REVERT: A 384 ILE cc_start: 0.7524 (tp) cc_final: 0.7152 (tp) REVERT: A 460 ASP cc_start: 0.7196 (t0) cc_final: 0.6848 (t0) REVERT: A 498 ASP cc_start: 0.7359 (t0) cc_final: 0.6907 (t70) REVERT: A 626 ARG cc_start: 0.7931 (ttt-90) cc_final: 0.6825 (tpt90) REVERT: A 627 TYR cc_start: 0.8177 (m-80) cc_final: 0.7894 (m-80) REVERT: A 677 ASP cc_start: 0.7916 (t70) cc_final: 0.7623 (t70) REVERT: A 861 ASP cc_start: 0.6949 (m-30) cc_final: 0.6695 (m-30) REVERT: A 942 MET cc_start: 0.8319 (ppp) cc_final: 0.7846 (tmm) outliers start: 25 outliers final: 19 residues processed: 194 average time/residue: 0.1152 time to fit residues: 33.9790 Evaluate side-chains 189 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 264 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 381 ILE 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 1039 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 284 ILE 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 913 LEU Chi-restraints excluded: chain A residue 1052 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: 3.9990 chunk 145 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 84 optimal weight: 0.0370 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 703 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 = 0.4067 r_free = 0.4067 target = 0.173721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127342 restraints weight = 16251.586| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.93 r_work: 0.3405 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 14232 Z= 0.126 Angle : 0.563 8.209 19378 Z= 0.284 Chirality : 0.043 0.364 2288 Planarity : 0.004 0.041 2400 Dihedral : 4.533 62.674 1924 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer: Outliers : 1.80 % Allowed : 17.11 % Favored : 81.09 % 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: 0.74 (0.20), residues: 1780 helix: 1.61 (0.16), residues: 982 sheet: -1.89 (0.48), residues: 92 loop : -0.74 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.030 0.001 TYR B 937 PHE 0.018 0.001 PHE B 442 TRP 0.010 0.001 TRP B 649 HIS 0.003 0.000 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (14218) covalent geometry : angle 0.55609 / 0.28 (19342) SS BOND : bond 0.00329 / 0.16 ( 6) SS BOND : angle 2.04237 / 1.20 ( 12) hydrogen bonds : bond 0.03714 / 2.44 ( 812) hydrogen bonds : angle 4.23619 / 3.07 ( 2346) link_BETA1-4 : bond 0.00514 / 0.26 ( 4) link_BETA1-4 : angle 2.71312 / 1.39 ( 12) link_NAG-ASN : bond 0.00153 / 0.08 ( 4) link_NAG-ASN : angle 1.44977 / 0.82 ( 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 208 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: B 459 LYS cc_start: 0.8428 (mttt) cc_final: 0.8017 (mttp) REVERT: B 601 MET cc_start: 0.8260 (tpp) cc_final: 0.7951 (tpp) REVERT: B 673 LYS cc_start: 0.8624 (tppt) cc_final: 0.7942 (tttm) REVERT: B 677 ASP cc_start: 0.7871 (t70) cc_final: 0.7421 (t70) REVERT: B 861 ASP cc_start: 0.7107 (m-30) cc_final: 0.6330 (m-30) REVERT: B 893 PHE cc_start: 0.7109 (m-80) cc_final: 0.6114 (m-80) REVERT: B 923 GLU cc_start: 0.6202 (mp0) cc_final: 0.5975 (mp0) REVERT: A 116 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6773 (pt0) REVERT: A 287 ARG cc_start: 0.8248 (ptt-90) cc_final: 0.7982 (ptt-90) REVERT: A 384 ILE cc_start: 0.7479 (tp) cc_final: 0.7191 (tp) REVERT: A 460 ASP cc_start: 0.7096 (t0) cc_final: 0.6740 (t0) REVERT: A 601 MET cc_start: 0.8125 (tpp) cc_final: 0.7857 (tpp) REVERT: A 626 ARG cc_start: 0.7883 (ttt-90) cc_final: 0.6771 (tpt90) REVERT: A 627 TYR cc_start: 0.8078 (m-80) cc_final: 0.7806 (m-80) REVERT: A 656 MET cc_start: 0.8402 (mmm) cc_final: 0.8066 (mmm) REVERT: A 677 ASP cc_start: 0.7835 (t70) cc_final: 0.7510 (t70) REVERT: A 861 ASP cc_start: 0.6812 (m-30) cc_final: 0.6543 (m-30) outliers start: 26 outliers final: 19 residues processed: 202 average time/residue: 0.1109 time to fit residues: 34.3334 Evaluate side-chains 190 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 264 LEU Chi-restraints excluded: chain B residue 279 VAL 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 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 180 THR Chi-restraints excluded: chain A residue 284 ILE 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 913 LEU Chi-restraints excluded: chain A residue 1052 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 53 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 132 optimal weight: 3.9990 chunk 26 optimal weight: 0.0040 chunk 159 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4064 r_free = 0.4064 target = 0.174205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129735 restraints weight = 16389.592| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.73 r_work: 0.3431 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3343 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= 0.121 Angle : 0.576 10.158 19378 Z= 0.288 Chirality : 0.043 0.372 2288 Planarity : 0.004 0.037 2400 Dihedral : 4.469 62.177 1924 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.20 % Favored : 96.69 % Rotamer: Outliers : 1.66 % Allowed : 17.73 % Favored : 80.61 % 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: 0.91 (0.20), residues: 1780 helix: 1.72 (0.16), residues: 982 sheet: -1.81 (0.48), residues: 92 loop : -0.61 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 287 TYR 0.030 0.001 TYR B 937 PHE 0.018 0.001 PHE B 442 TRP 0.010 0.001 TRP B 649 HIS 0.003 0.000 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (14218) covalent geometry : angle 0.56916 / 0.29 (19342) SS BOND : bond 0.00312 / 0.15 ( 6) SS BOND : angle 1.92552 / 1.14 ( 12) hydrogen bonds : bond 0.03637 / 2.40 ( 812) hydrogen bonds : angle 4.18695 / 3.03 ( 2346) link_BETA1-4 : bond 0.00502 / 0.25 ( 4) link_BETA1-4 : angle 2.68197 / 1.38 ( 12) link_NAG-ASN : bond 0.00173 / 0.09 ( 4) link_NAG-ASN : angle 1.36672 / 0.78 ( 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: 24 poor density : 182 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: B 459 LYS cc_start: 0.8388 (mttt) cc_final: 0.8018 (mttp) REVERT: B 601 MET cc_start: 0.8463 (tpp) cc_final: 0.8240 (tpp) REVERT: B 673 LYS cc_start: 0.8789 (tppt) cc_final: 0.8113 (tttm) REVERT: B 677 ASP cc_start: 0.8118 (t70) cc_final: 0.7811 (t70) REVERT: B 861 ASP cc_start: 0.7279 (m-30) cc_final: 0.6535 (m-30) REVERT: B 893 PHE cc_start: 0.7333 (m-80) cc_final: 0.6373 (m-80) REVERT: B 923 GLU cc_start: 0.6528 (mp0) cc_final: 0.6279 (mp0) REVERT: A 284 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7594 (pt) REVERT: A 287 ARG cc_start: 0.8258 (ptt-90) cc_final: 0.7997 (ptt-90) REVERT: A 384 ILE cc_start: 0.7635 (tp) cc_final: 0.7354 (tp) REVERT: A 460 ASP cc_start: 0.7291 (t0) cc_final: 0.7037 (t0) REVERT: A 601 MET cc_start: 0.8303 (tpp) cc_final: 0.8090 (tpp) REVERT: A 626 ARG cc_start: 0.8098 (ttt-90) cc_final: 0.7043 (tpt90) REVERT: A 627 TYR cc_start: 0.8353 (m-80) cc_final: 0.8114 (m-80) REVERT: A 656 MET cc_start: 0.8599 (mmm) cc_final: 0.8366 (mmm) REVERT: A 677 ASP cc_start: 0.8099 (t70) cc_final: 0.7873 (t70) REVERT: A 861 ASP cc_start: 0.6910 (m-30) cc_final: 0.6707 (m-30) REVERT: A 905 MET cc_start: 0.6257 (tpp) cc_final: 0.5749 (ptt) REVERT: A 942 MET cc_start: 0.7994 (ppp) cc_final: 0.7492 (ptt) REVERT: A 1079 GLU cc_start: 0.7932 (tp30) cc_final: 0.7445 (tp30) outliers start: 24 outliers final: 14 residues processed: 201 average time/residue: 0.1118 time to fit residues: 33.7947 Evaluate side-chains 185 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 264 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 661 MET Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 913 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 146 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.172944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128224 restraints weight = 16518.079| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.74 r_work: 0.3413 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14232 Z= 0.140 Angle : 0.587 9.051 19378 Z= 0.293 Chirality : 0.044 0.353 2288 Planarity : 0.004 0.036 2400 Dihedral : 4.481 61.606 1924 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer: Outliers : 1.66 % Allowed : 18.14 % Favored : 80.19 % 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: 0.84 (0.20), residues: 1780 helix: 1.64 (0.16), residues: 992 sheet: -1.88 (0.48), residues: 92 loop : -0.64 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 680 TYR 0.030 0.002 TYR B 937 PHE 0.016 0.001 PHE A 442 TRP 0.009 0.001 TRP B 649 HIS 0.003 0.000 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (14218) covalent geometry : angle 0.58018 / 0.29 (19342) SS BOND : bond 0.00493 / 0.25 ( 6) SS BOND : angle 2.03187 / 1.20 ( 12) hydrogen bonds : bond 0.03693 / 2.43 ( 812) hydrogen bonds : angle 4.20628 / 3.04 ( 2346) link_BETA1-4 : bond 0.00517 / 0.26 ( 4) link_BETA1-4 : angle 2.67269 / 1.37 ( 12) link_NAG-ASN : bond 0.00108 / 0.05 ( 4) link_NAG-ASN : angle 1.38505 / 0.78 ( 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 201 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: B 459 LYS cc_start: 0.8429 (mttt) cc_final: 0.7984 (ptmt) REVERT: B 601 MET cc_start: 0.8449 (tpp) cc_final: 0.8206 (tpp) REVERT: B 673 LYS cc_start: 0.8801 (tppt) cc_final: 0.8117 (ttpp) REVERT: B 677 ASP cc_start: 0.8149 (t70) cc_final: 0.7832 (t70) REVERT: B 861 ASP cc_start: 0.7316 (m-30) cc_final: 0.6585 (m-30) REVERT: B 893 PHE cc_start: 0.7342 (m-80) cc_final: 0.6468 (m-80) REVERT: B 923 GLU cc_start: 0.6537 (mp0) cc_final: 0.6266 (mp0) REVERT: A 283 PHE cc_start: 0.8375 (t80) cc_final: 0.7976 (t80) REVERT: A 284 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7578 (pt) REVERT: A 287 ARG cc_start: 0.8260 (ptt-90) cc_final: 0.7989 (ptt-90) REVERT: A 384 ILE cc_start: 0.7637 (tp) cc_final: 0.7367 (tp) REVERT: A 459 LYS cc_start: 0.8451 (mttt) cc_final: 0.8052 (mttp) REVERT: A 460 ASP cc_start: 0.7316 (t0) cc_final: 0.7039 (t0) REVERT: A 498 ASP cc_start: 0.7400 (t0) cc_final: 0.7057 (t70) REVERT: A 601 MET cc_start: 0.8281 (tpp) cc_final: 0.8067 (tpp) REVERT: A 627 TYR cc_start: 0.8362 (m-80) cc_final: 0.8159 (m-80) REVERT: A 656 MET cc_start: 0.8610 (mmm) cc_final: 0.8376 (mmm) REVERT: A 677 ASP cc_start: 0.8118 (t70) cc_final: 0.7882 (t70) REVERT: A 861 ASP cc_start: 0.6971 (m-30) cc_final: 0.6763 (m-30) REVERT: A 938 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7990 (mm-30) REVERT: A 942 MET cc_start: 0.8039 (ppp) cc_final: 0.7555 (ptt) REVERT: A 1079 GLU cc_start: 0.7883 (tp30) cc_final: 0.7426 (tp30) outliers start: 24 outliers final: 18 residues processed: 195 average time/residue: 0.1142 time to fit residues: 33.7459 Evaluate side-chains 189 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 279 VAL 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 423 HIS Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 661 MET 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 180 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1052 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 94 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 chunk 154 optimal weight: 0.1980 chunk 146 optimal weight: 0.9990 chunk 156 optimal weight: 0.0870 chunk 79 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.175360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131006 restraints weight = 16449.379| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.75 r_work: 0.3447 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14232 Z= 0.118 Angle : 0.577 11.067 19378 Z= 0.288 Chirality : 0.044 0.355 2288 Planarity : 0.004 0.035 2400 Dihedral : 4.405 60.847 1924 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer: Outliers : 1.59 % Allowed : 18.21 % Favored : 80.19 % 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: 1.05 (0.20), residues: 1780 helix: 1.80 (0.16), residues: 982 sheet: -1.83 (0.48), residues: 92 loop : -0.49 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 917 TYR 0.029 0.001 TYR B 937 PHE 0.016 0.001 PHE B 442 TRP 0.012 0.001 TRP A 649 HIS 0.003 0.000 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (14218) covalent geometry : angle 0.57038 / 0.29 (19342) SS BOND : bond 0.00346 / 0.17 ( 6) SS BOND : angle 1.97065 / 1.16 ( 12) hydrogen bonds : bond 0.03540 / 2.33 ( 812) hydrogen bonds : angle 4.16144 / 3.01 ( 2346) link_BETA1-4 : bond 0.00575 / 0.29 ( 4) link_BETA1-4 : angle 2.64754 / 1.36 ( 12) link_NAG-ASN : bond 0.00143 / 0.07 ( 4) link_NAG-ASN : angle 1.27419 / 0.72 ( 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 202 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 284 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7574 (pt) REVERT: B 459 LYS cc_start: 0.8398 (mttt) cc_final: 0.7976 (ptmt) REVERT: B 601 MET cc_start: 0.8402 (tpp) cc_final: 0.7972 (tpp) REVERT: B 673 LYS cc_start: 0.8809 (tppt) cc_final: 0.8108 (ttpp) REVERT: B 677 ASP cc_start: 0.8158 (t70) cc_final: 0.7828 (t70) REVERT: B 853 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7309 (tm-30) REVERT: B 861 ASP cc_start: 0.7275 (m-30) cc_final: 0.6528 (m-30) REVERT: B 893 PHE cc_start: 0.7324 (m-80) cc_final: 0.6477 (m-80) REVERT: B 923 GLU cc_start: 0.6547 (mp0) cc_final: 0.6288 (mp0) REVERT: A 283 PHE cc_start: 0.8388 (t80) cc_final: 0.8002 (t80) REVERT: A 284 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7581 (pt) REVERT: A 287 ARG cc_start: 0.8248 (ptt-90) cc_final: 0.7976 (ptt-90) REVERT: A 384 ILE cc_start: 0.7611 (tp) cc_final: 0.7351 (tp) REVERT: A 459 LYS cc_start: 0.8426 (mttt) cc_final: 0.8034 (mttp) REVERT: A 460 ASP cc_start: 0.7321 (t0) cc_final: 0.7020 (t70) REVERT: A 677 ASP cc_start: 0.8118 (t70) cc_final: 0.7885 (t70) REVERT: A 861 ASP cc_start: 0.6919 (m-30) cc_final: 0.6715 (m-30) REVERT: A 905 MET cc_start: 0.6242 (tpp) cc_final: 0.5525 (ptt) REVERT: A 938 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7949 (mm-30) REVERT: A 942 MET cc_start: 0.8043 (ppp) cc_final: 0.7558 (ptt) REVERT: A 1079 GLU cc_start: 0.7852 (tp30) cc_final: 0.7362 (tp30) outliers start: 23 outliers final: 15 residues processed: 195 average time/residue: 0.1167 time to fit residues: 34.5310 Evaluate side-chains 191 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 279 VAL 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 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 1039 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 913 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 2 optimal weight: 0.4980 chunk 116 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 170 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 703 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 = 0.4062 r_free = 0.4062 target = 0.174140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.129621 restraints weight = 16488.003| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.74 r_work: 0.3429 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14232 Z= 0.130 Angle : 0.588 10.351 19378 Z= 0.293 Chirality : 0.044 0.350 2288 Planarity : 0.004 0.035 2400 Dihedral : 4.401 60.338 1924 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.26 % Favored : 96.63 % Rotamer: Outliers : 1.80 % Allowed : 18.01 % Favored : 80.19 % 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: 1.04 (0.20), residues: 1780 helix: 1.79 (0.17), residues: 982 sheet: -1.86 (0.48), residues: 92 loop : -0.48 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1062 TYR 0.029 0.002 TYR B 937 PHE 0.015 0.001 PHE B 442 TRP 0.009 0.001 TRP B 649 HIS 0.003 0.000 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (14218) covalent geometry : angle 0.58139 / 0.29 (19342) SS BOND : bond 0.00386 / 0.19 ( 6) SS BOND : angle 2.25292 / 1.34 ( 12) hydrogen bonds : bond 0.03580 / 2.35 ( 812) hydrogen bonds : angle 4.18001 / 3.02 ( 2346) link_BETA1-4 : bond 0.00543 / 0.27 ( 4) link_BETA1-4 : angle 2.61070 / 1.34 ( 12) link_NAG-ASN : bond 0.00095 / 0.05 ( 4) link_NAG-ASN : angle 1.29838 / 0.73 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3200.16 seconds wall clock time: 55 minutes 59.50 seconds (3359.50 seconds total)