Starting phenix.real_space_refine on Tue Nov 18 12:14:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aio_11800/11_2025/7aio_11800.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aio_11800/11_2025/7aio_11800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7aio_11800/11_2025/7aio_11800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aio_11800/11_2025/7aio_11800.map" model { file = "/net/cci-nas-00/data/ceres_data/7aio_11800/11_2025/7aio_11800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aio_11800/11_2025/7aio_11800.cif" } resolution = 3.31 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 94 5.16 5 C 9028 2.51 5 N 2308 2.21 5 O 2485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13915 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 6918 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 34, 'TRANS': 875} Chain breaks: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 3, 'GLU:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 3, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 6891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 909, 6891 Classifications: {'peptide': 909} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 34, 'TRANS': 874} Chain breaks: 3 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'HIS:plan': 3, 'ASP:plan': 3, 'GLU:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 3, 'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.67, per 1000 atoms: 0.26 Number of scatterers: 13915 At special positions: 0 Unit cell: (104.811, 93.093, 147.777, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 94 16.00 O 2485 8.00 N 2308 7.00 C 9028 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 640 " distance=2.02 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: 1.40 Conformation dependent library (CDL) restraints added in 928.4 milliseconds 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3354 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 61.8% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.659A 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: 5.137A 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: 6.320A pdb=" N VAL B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N LEU B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 243 removed outlier: 3.559A 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: 3.685A pdb=" N VAL B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.838A 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: 3.521A pdb=" N THR B 393 " --> pdb=" O GLY B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.742A 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: 3.704A 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: 4.229A pdb=" N ILE B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.668A 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: 3.943A pdb=" N VAL B 558 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 561 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 584 removed outlier: 3.760A pdb=" N LEU B 572 " --> pdb=" O PRO B 568 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.847A 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: 3.679A pdb=" N CYS B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 648 removed outlier: 3.663A pdb=" N SER B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 675 removed outlier: 3.616A pdb=" N ILE B 653 " --> pdb=" O TRP B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 696 Processing helix chain 'B' and resid 722 through 734 removed outlier: 4.216A 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: 3.538A pdb=" N PHE B 825 " --> pdb=" O ALA B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 Processing helix chain 'B' and resid 868 through 881 removed outlier: 3.547A 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 899 through 917 removed outlier: 4.067A pdb=" N GLN B 904 " --> pdb=" O ASP B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 946 Processing helix chain 'B' and resid 1029 through 1048 removed outlier: 3.931A 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: 3.710A 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: 5.246A 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: 6.327A pdb=" N VAL A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N LEU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 243 removed outlier: 3.570A 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 256 through 284 removed outlier: 3.606A pdb=" N MET A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.724A pdb=" N VAL A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N SER A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.942A 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: 3.523A pdb=" N THR A 393 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.704A 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: 3.662A 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: 4.253A pdb=" N ILE A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.575A 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: 3.925A pdb=" N VAL A 558 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 561 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 584 removed outlier: 3.648A pdb=" N LEU A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 3.702A 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: 3.625A pdb=" N CYS A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 648 removed outlier: 3.679A pdb=" N SER A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 675 removed outlier: 3.566A pdb=" N ILE A 653 " --> pdb=" O TRP A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 696 removed outlier: 3.598A pdb=" N GLU A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 4.244A 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: 3.886A pdb=" N GLN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 835 removed outlier: 3.585A pdb=" N PHE A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 868 through 881 removed outlier: 3.652A 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 902 through 917 Processing helix chain 'A' and resid 932 through 949 Processing helix chain 'A' and resid 1029 through 1048 removed outlier: 3.928A 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: 3.594A 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: 6.633A pdb=" N LEU B 708 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLY B 742 " --> pdb=" O LEU B 708 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL B 710 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL B 744 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY B 808 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL B 805 " --> pdb=" O LEU B 840 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA B 842 " --> pdb=" O VAL B 805 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N MET B 807 " --> pdb=" O ALA B 842 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B1053 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B1087 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU B1055 " --> pdb=" O VAL B1087 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 858 through 860 removed outlier: 9.716A pdb=" N GLU B 921 " --> pdb=" O CYS B 888 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 890 " --> pdb=" O GLU B 921 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N GLU B 923 " --> pdb=" O ILE B 890 " (cutoff:3.500A) removed outlier: 5.825A 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: 3.554A 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: 6.646A pdb=" N LEU A 708 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLY A 742 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL A 710 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL A 744 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY A 808 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL A 805 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ALA A 842 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N MET A 807 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1084 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A1053 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL A1087 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.042A 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: 6.860A pdb=" N ILE A 890 " --> pdb=" O GLU A 921 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N GLU A 923 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE A 892 " --> pdb=" O GLU A 923 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2382 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: 2.78 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3310 1.33 - 1.45: 2891 1.45 - 1.57: 7877 1.57 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 14228 Sorted by residual: bond pdb=" N ILE A 250 " pdb=" CA ILE A 250 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.20e+00 bond pdb=" N ILE B 250 " pdb=" CA ILE B 250 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.17e+00 bond pdb=" N GLU B1093 " pdb=" CA GLU B1093 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.22e-02 6.72e+03 6.93e+00 bond pdb=" N GLN B 897 " pdb=" CA GLN B 897 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.73e+00 bond pdb=" N ARG B 334 " pdb=" CA ARG B 334 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.33e-02 5.65e+03 6.69e+00 ... (remaining 14223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 18954 2.38 - 4.76: 371 4.76 - 7.14: 25 7.14 - 9.52: 5 9.52 - 11.89: 1 Bond angle restraints: 19356 Sorted by residual: angle pdb=" C ILE B 639 " pdb=" N CYS B 640 " pdb=" CA CYS B 640 " ideal model delta sigma weight residual 122.38 113.67 8.71 1.81e+00 3.05e-01 2.32e+01 angle pdb=" C ASP A 255 " pdb=" CA ASP A 255 " pdb=" CB ASP A 255 " ideal model delta sigma weight residual 116.63 111.60 5.03 1.16e+00 7.43e-01 1.88e+01 angle pdb=" N ASN B 266 " pdb=" CA ASN B 266 " pdb=" C ASN B 266 " ideal model delta sigma weight residual 111.28 107.13 4.15 1.09e+00 8.42e-01 1.45e+01 angle pdb=" C VAL A 866 " pdb=" N HIS A 867 " pdb=" CA HIS A 867 " ideal model delta sigma weight residual 122.53 116.43 6.10 1.61e+00 3.86e-01 1.44e+01 angle pdb=" CA ILE A 250 " pdb=" C ILE A 250 " pdb=" O ILE A 250 " ideal model delta sigma weight residual 120.95 117.02 3.93 1.04e+00 9.25e-01 1.43e+01 ... (remaining 19351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.84: 7984 20.84 - 41.68: 362 41.68 - 62.51: 78 62.51 - 83.35: 18 83.35 - 104.19: 9 Dihedral angle restraints: 8451 sinusoidal: 3235 harmonic: 5216 Sorted by residual: 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 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 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 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" C ASN B 265 " pdb=" N ASN B 265 " pdb=" CA ASN B 265 " pdb=" CB ASN B 265 " ideal model delta harmonic sigma weight residual -122.60 -131.98 9.38 0 2.50e+00 1.60e-01 1.41e+01 ... (remaining 8448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.960: 2294 0.960 - 1.920: 0 1.920 - 2.880: 0 2.880 - 3.840: 0 3.840 - 4.800: 1 Chirality restraints: 2295 Sorted by residual: chirality pdb=" C1 NAG B1101 " pdb=" ND2 ASN B 377 " pdb=" C2 NAG B1101 " pdb=" O5 NAG B1101 " both_signs ideal model delta sigma weight residual False -2.40 2.40 -4.80 2.00e-01 2.50e+01 5.76e+02 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 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA ASN B 265 " pdb=" N ASN B 265 " pdb=" C ASN B 265 " pdb=" CB ASN B 265 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 2292 not shown) Planarity restraints: 2414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1101 " 0.202 2.00e-02 2.50e+03 1.72e-01 3.69e+02 pdb=" C7 NAG B1101 " -0.042 2.00e-02 2.50e+03 pdb=" C8 NAG B1101 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG B1101 " -0.282 2.00e-02 2.50e+03 pdb=" O7 NAG B1101 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 497 " -0.090 9.50e-02 1.11e+02 5.47e-02 1.79e+01 pdb=" NE ARG B 497 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 497 " -0.070 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 " 0.098 9.50e-02 1.11e+02 5.64e-02 1.70e+01 pdb=" NE ARG A 497 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 497 " 0.068 2.00e-02 2.50e+03 pdb=" NH1 ARG A 497 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG A 497 " -0.019 2.00e-02 2.50e+03 ... (remaining 2411 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1710 2.74 - 3.28: 14723 3.28 - 3.82: 23398 3.82 - 4.36: 27386 4.36 - 4.90: 47358 Nonbonded interactions: 114575 Sorted by model distance: nonbonded pdb=" ND2 ASN A1040 " pdb=" O VAL A1076 " model vdw 2.205 3.120 nonbonded pdb=" O PRO A1058 " pdb=" OH TYR A1070 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASN A 376 " pdb=" N SER A 415 " model vdw 2.285 3.120 nonbonded pdb=" NH1 ARG B 680 " pdb=" O PRO A 698 " model vdw 2.286 3.120 nonbonded pdb=" ND2 ASN B1040 " pdb=" O VAL B1076 " model vdw 2.286 3.120 ... (remaining 114570 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 102 through 947 or resid 1029 through 1101)) selection = (chain 'B' and (resid 102 through 896 or (resid 901 and (name N or name CA or na \ me C or name O or name CB )) or resid 902 through 907 or (resid 908 through 915 \ and (name N or name CA or name C or name O or name CB )) or resid 916 through 94 \ 6 or (resid 1028 and (name N or name CA or name C or name O or name CB )) or res \ id 1029 through 1101)) } 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: 6.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.850 Find NCS groups from input model: 0.440 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: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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 : 0.006 0.054 14242 Z= 0.288 Angle : 0.808 11.895 19392 Z= 0.472 Chirality : 0.112 4.800 2295 Planarity : 0.007 0.172 2410 Dihedral : 13.631 104.188 5079 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.88 % Favored : 97.01 % Rotamer: Outliers : 0.83 % Allowed : 5.76 % Favored : 93.41 % 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: 1805 helix: -0.33 (0.15), residues: 1001 sheet: -1.74 (0.43), residues: 102 loop : -1.84 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.071 0.002 ARG B 497 TYR 0.017 0.002 TYR A 937 PHE 0.018 0.002 PHE A 877 TRP 0.036 0.002 TRP A 649 HIS 0.009 0.001 HIS B 790 Details of bonding type rmsd covalent geometry : bond 0.00577 (14228) covalent geometry : angle 0.78984 (19356) SS BOND : bond 0.00467 ( 6) SS BOND : angle 2.30562 ( 12) hydrogen bonds : bond 0.11399 ( 824) hydrogen bonds : angle 5.37143 ( 2382) link_BETA1-4 : bond 0.00178 ( 4) link_BETA1-4 : angle 4.28027 ( 12) link_NAG-ASN : bond 0.00509 ( 4) link_NAG-ASN : angle 5.01432 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 313 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4020 (tpt) cc_final: 0.3652 (tpt) outliers start: 12 outliers final: 1 residues processed: 322 average time/residue: 0.1372 time to fit residues: 62.6015 Evaluate side-chains 175 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1093 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 GLN ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 ASN B 752 ASN B 882 HIS A 133 GLN A 629 HIS A 752 ASN A 882 HIS A1045 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.132329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.100928 restraints weight = 25598.854| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.49 r_work: 0.3384 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14242 Z= 0.152 Angle : 0.718 23.446 19392 Z= 0.349 Chirality : 0.048 0.942 2295 Planarity : 0.004 0.045 2410 Dihedral : 7.406 58.840 2095 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.60 % Favored : 97.29 % Rotamer: Outliers : 1.73 % Allowed : 13.31 % Favored : 84.95 % 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: -0.30 (0.19), residues: 1805 helix: 0.79 (0.16), residues: 1010 sheet: -1.61 (0.43), residues: 112 loop : -1.41 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 785 TYR 0.020 0.001 TYR B 937 PHE 0.021 0.002 PHE B 634 TRP 0.018 0.002 TRP A 649 HIS 0.004 0.001 HIS A 790 Details of bonding type rmsd covalent geometry : bond 0.00337 (14228) covalent geometry : angle 0.67747 (19356) SS BOND : bond 0.01058 ( 6) SS BOND : angle 1.82713 ( 12) hydrogen bonds : bond 0.04512 ( 824) hydrogen bonds : angle 4.57137 ( 2382) link_BETA1-4 : bond 0.00485 ( 4) link_BETA1-4 : angle 3.68071 ( 12) link_NAG-ASN : bond 0.01021 ( 4) link_NAG-ASN : angle 8.75933 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4320 (tpt) cc_final: 0.3735 (tpt) REVERT: B 107 ASN cc_start: 0.7474 (p0) cc_final: 0.7257 (p0) REVERT: B 381 ILE cc_start: 0.6502 (OUTLIER) cc_final: 0.6213 (mt) REVERT: B 431 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.7522 (t) REVERT: B 601 MET cc_start: 0.8865 (tpp) cc_final: 0.8647 (tpp) REVERT: B 661 MET cc_start: 0.7341 (tmm) cc_final: 0.7057 (ttm) REVERT: B 703 ASN cc_start: 0.7432 (m-40) cc_final: 0.7096 (t0) REVERT: B 1040 ASN cc_start: 0.8894 (m-40) cc_final: 0.8249 (m110) REVERT: B 1046 LYS cc_start: 0.9240 (mmtt) cc_final: 0.8976 (mmtm) REVERT: A 117 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7676 (mm-30) REVERT: A 329 ARG cc_start: 0.7562 (mmt90) cc_final: 0.7098 (mtt90) REVERT: A 353 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8413 (mtmm) REVERT: A 453 ASN cc_start: 0.7602 (OUTLIER) cc_final: 0.7388 (t0) REVERT: A 580 GLU cc_start: 0.7992 (tp30) cc_final: 0.7650 (tp30) outliers start: 25 outliers final: 12 residues processed: 238 average time/residue: 0.1092 time to fit residues: 39.8907 Evaluate side-chains 186 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 453 ASN Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 1 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 0.0670 chunk 81 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN A1040 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.130539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.099988 restraints weight = 26091.794| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.45 r_work: 0.3377 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14242 Z= 0.144 Angle : 0.658 22.369 19392 Z= 0.316 Chirality : 0.045 0.627 2295 Planarity : 0.004 0.035 2410 Dihedral : 5.908 57.556 2092 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.27 % Favored : 96.62 % Rotamer: Outliers : 2.08 % Allowed : 13.87 % Favored : 84.05 % 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: 0.16 (0.20), residues: 1805 helix: 1.14 (0.16), residues: 1014 sheet: -1.39 (0.44), residues: 117 loop : -1.18 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 939 TYR 0.016 0.001 TYR B 937 PHE 0.017 0.001 PHE B 645 TRP 0.013 0.001 TRP B 649 HIS 0.004 0.001 HIS B 802 Details of bonding type rmsd covalent geometry : bond 0.00328 (14228) covalent geometry : angle 0.61929 (19356) SS BOND : bond 0.01195 ( 6) SS BOND : angle 1.66075 ( 12) hydrogen bonds : bond 0.04165 ( 824) hydrogen bonds : angle 4.37312 ( 2382) link_BETA1-4 : bond 0.00533 ( 4) link_BETA1-4 : angle 3.49080 ( 12) link_NAG-ASN : bond 0.01128 ( 4) link_NAG-ASN : angle 8.17616 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4601 (tpt) cc_final: 0.3943 (tpt) REVERT: B 116 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7799 (pt0) REVERT: B 138 MET cc_start: 0.8272 (tpp) cc_final: 0.7965 (tpp) REVERT: B 381 ILE cc_start: 0.6622 (OUTLIER) cc_final: 0.6403 (mt) REVERT: B 499 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7907 (mttp) REVERT: B 703 ASN cc_start: 0.7441 (m-40) cc_final: 0.7235 (t0) REVERT: B 1046 LYS cc_start: 0.9213 (mmtt) cc_final: 0.8955 (mmtm) REVERT: A 329 ARG cc_start: 0.7613 (mmt90) cc_final: 0.7154 (mtt90) REVERT: A 353 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8484 (mtmm) REVERT: A 580 GLU cc_start: 0.8008 (tp30) cc_final: 0.7681 (tp30) REVERT: A 815 GLN cc_start: 0.8581 (mp10) cc_final: 0.8377 (mp10) REVERT: A 942 MET cc_start: 0.8635 (ptt) cc_final: 0.8328 (ptt) outliers start: 30 outliers final: 14 residues processed: 206 average time/residue: 0.1079 time to fit residues: 34.3311 Evaluate side-chains 181 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 662 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 135 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 93 optimal weight: 0.0060 chunk 176 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.132198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.101693 restraints weight = 25945.386| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.47 r_work: 0.3398 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14242 Z= 0.124 Angle : 0.623 21.385 19392 Z= 0.300 Chirality : 0.044 0.497 2295 Planarity : 0.004 0.033 2410 Dihedral : 5.447 55.284 2092 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.21 % Favored : 96.68 % Rotamer: Outliers : 2.64 % Allowed : 14.56 % Favored : 82.80 % 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: 0.44 (0.20), residues: 1805 helix: 1.37 (0.16), residues: 1016 sheet: -1.18 (0.45), residues: 121 loop : -1.09 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 820 TYR 0.015 0.001 TYR B 937 PHE 0.015 0.001 PHE A 442 TRP 0.011 0.001 TRP B 649 HIS 0.005 0.001 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.00276 (14228) covalent geometry : angle 0.58645 (19356) SS BOND : bond 0.00263 ( 6) SS BOND : angle 1.74020 ( 12) hydrogen bonds : bond 0.03928 ( 824) hydrogen bonds : angle 4.24263 ( 2382) link_BETA1-4 : bond 0.00630 ( 4) link_BETA1-4 : angle 3.09253 ( 12) link_NAG-ASN : bond 0.01363 ( 4) link_NAG-ASN : angle 7.74637 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4611 (tpt) cc_final: 0.3949 (tpt) REVERT: B 116 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7786 (pt0) REVERT: B 381 ILE cc_start: 0.6571 (OUTLIER) cc_final: 0.6360 (mt) REVERT: B 431 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.7527 (t) REVERT: B 499 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7854 (mttp) REVERT: B 661 MET cc_start: 0.7376 (tmm) cc_final: 0.7090 (ttm) REVERT: B 689 PHE cc_start: 0.8673 (t80) cc_final: 0.8412 (t80) REVERT: B 760 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8251 (tp30) REVERT: B 1046 LYS cc_start: 0.9204 (mmtt) cc_final: 0.8969 (mmtm) REVERT: A 120 ASN cc_start: 0.8286 (t0) cc_final: 0.8078 (m-40) REVERT: A 329 ARG cc_start: 0.7655 (mmt90) cc_final: 0.7363 (mpt-90) REVERT: A 353 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8559 (mtmm) REVERT: A 580 GLU cc_start: 0.7984 (tp30) cc_final: 0.7738 (tp30) outliers start: 38 outliers final: 16 residues processed: 218 average time/residue: 0.1061 time to fit residues: 35.4798 Evaluate side-chains 188 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 760 GLU Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.7374 > 50: distance: 70 - 74: 6.492 distance: 74 - 75: 11.059 distance: 75 - 76: 4.205 distance: 75 - 78: 12.367 distance: 76 - 77: 26.763 distance: 76 - 83: 8.666 distance: 78 - 79: 28.700 distance: 79 - 80: 13.962 distance: 80 - 81: 18.429 distance: 81 - 82: 13.559 distance: 83 - 84: 24.694 distance: 84 - 85: 25.485 distance: 84 - 87: 38.966 distance: 85 - 86: 35.041 distance: 85 - 88: 14.545 distance: 88 - 89: 22.441 distance: 89 - 90: 19.973 distance: 89 - 92: 14.829 distance: 90 - 91: 19.619 distance: 90 - 96: 22.763 distance: 92 - 93: 16.529 distance: 93 - 94: 17.861 distance: 93 - 95: 6.547 distance: 96 - 97: 31.069 distance: 97 - 98: 27.594 distance: 98 - 99: 25.634 distance: 98 - 100: 8.453 distance: 100 - 101: 10.676 distance: 101 - 102: 43.998 distance: 101 - 104: 51.932 distance: 102 - 103: 29.164 distance: 102 - 109: 25.371 distance: 104 - 105: 33.205 distance: 105 - 106: 12.186 distance: 106 - 107: 12.649 distance: 106 - 108: 9.883 distance: 109 - 110: 6.119 distance: 109 - 115: 7.709 distance: 110 - 111: 12.479 distance: 110 - 113: 17.907 distance: 111 - 112: 21.722 distance: 111 - 116: 14.547 distance: 113 - 114: 13.686 distance: 114 - 115: 11.968 distance: 116 - 117: 6.507 distance: 117 - 118: 15.719 distance: 117 - 120: 9.661 distance: 118 - 119: 14.677 distance: 118 - 123: 13.367 distance: 120 - 121: 15.005 distance: 120 - 122: 17.258 distance: 123 - 124: 15.076 distance: 124 - 125: 8.237 distance: 124 - 127: 12.250 distance: 125 - 126: 10.146 distance: 125 - 137: 19.904 distance: 127 - 128: 13.438 distance: 128 - 129: 7.257 distance: 128 - 130: 3.926 distance: 129 - 131: 4.345 distance: 130 - 132: 8.077 distance: 132 - 134: 8.170 distance: 133 - 135: 7.982 distance: 134 - 136: 3.197 distance: 135 - 136: 8.854 distance: 137 - 138: 18.904 distance: 138 - 139: 11.175 distance: 138 - 141: 16.872 distance: 139 - 140: 12.048 distance: 139 - 142: 16.709 distance: 140 - 162: 23.715 distance: 142 - 143: 9.808 distance: 143 - 144: 8.867 distance: 143 - 146: 25.804 distance: 144 - 145: 12.081 distance: 144 - 150: 20.484 distance: 145 - 169: 11.814 distance: 146 - 147: 26.389 distance: 147 - 148: 37.667 distance: 147 - 149: 16.624