Starting phenix.real_space_refine on Tue Aug 26 07:20:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kds_37144/08_2025/8kds_37144.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kds_37144/08_2025/8kds_37144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kds_37144/08_2025/8kds_37144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kds_37144/08_2025/8kds_37144.map" model { file = "/net/cci-nas-00/data/ceres_data/8kds_37144/08_2025/8kds_37144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kds_37144/08_2025/8kds_37144.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 165 5.16 5 C 21849 2.51 5 N 5730 2.21 5 O 6609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34353 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1630 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 10, 'TRANS': 206} Chain: "D" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "G" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1630 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 10, 'TRANS': 206} Chain: "F" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "I" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1630 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 10, 'TRANS': 206} Chain: "H" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "B" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8190 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 998} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8190 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 998} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 8190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8190 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 998} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.91, per 1000 atoms: 0.20 Number of scatterers: 34353 At special positions: 0 Unit cell: (173.74, 191.59, 208.25, 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 165 16.00 O 6609 8.00 N 5730 7.00 C 21849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 203 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 147 " - pdb=" SG CYS I 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS H 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 389 " distance=2.03 Simple disulfide: pdb=" SG CYS B 407 " - pdb=" SG CYS B 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 552 " distance=2.03 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 515 " distance=2.03 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 617 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 676 " distance=2.03 Simple disulfide: pdb=" SG CYS B 689 " - pdb=" SG CYS B 698 " distance=2.03 Simple disulfide: pdb=" SG CYS B 761 " - pdb=" SG CYS B 783 " distance=2.03 Simple disulfide: pdb=" SG CYS B 766 " - pdb=" SG CYS B 772 " distance=2.03 Simple disulfide: pdb=" SG CYS B 863 " - pdb=" SG CYS B 874 " distance=2.03 Simple disulfide: pdb=" SG CYS B1055 " - pdb=" SG CYS B1066 " distance=2.03 Simple disulfide: pdb=" SG CYS B1105 " - pdb=" SG CYS B1149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 389 " distance=2.03 Simple disulfide: pdb=" SG CYS A 407 " - pdb=" SG CYS A 460 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 552 " distance=2.03 Simple disulfide: pdb=" SG CYS A 508 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 617 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 676 " distance=2.03 Simple disulfide: pdb=" SG CYS A 689 " - pdb=" SG CYS A 698 " distance=2.03 Simple disulfide: pdb=" SG CYS A 761 " - pdb=" SG CYS A 783 " distance=2.03 Simple disulfide: pdb=" SG CYS A 766 " - pdb=" SG CYS A 772 " distance=2.03 Simple disulfide: pdb=" SG CYS A 863 " - pdb=" SG CYS A 874 " distance=2.03 Simple disulfide: pdb=" SG CYS A1055 " - pdb=" SG CYS A1066 " distance=2.03 Simple disulfide: pdb=" SG CYS A1105 " - pdb=" SG CYS A1149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS C 200 " distance=2.03 Simple disulfide: pdb=" SG CYS C 319 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 389 " distance=2.03 Simple disulfide: pdb=" SG CYS C 407 " - pdb=" SG CYS C 460 " distance=2.03 Simple disulfide: pdb=" SG CYS C 419 " - pdb=" SG CYS C 552 " distance=2.03 Simple disulfide: pdb=" SG CYS C 508 " - pdb=" SG CYS C 515 " distance=2.03 Simple disulfide: pdb=" SG CYS C 565 " - pdb=" SG CYS C 617 " distance=2.03 Simple disulfide: pdb=" SG CYS C 644 " - pdb=" SG CYS C 676 " distance=2.03 Simple disulfide: pdb=" SG CYS C 689 " - pdb=" SG CYS C 698 " distance=2.03 Simple disulfide: pdb=" SG CYS C 761 " - pdb=" SG CYS C 783 " distance=2.03 Simple disulfide: pdb=" SG CYS C 766 " - pdb=" SG CYS C 772 " distance=2.03 Simple disulfide: pdb=" SG CYS C 863 " - pdb=" SG CYS C 874 " distance=2.03 Simple disulfide: pdb=" SG CYS C1055 " - pdb=" SG CYS C1066 " distance=2.03 Simple disulfide: pdb=" SG CYS C1105 " - pdb=" SG CYS C1149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8262 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 74 sheets defined 17.3% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 184 through 190 removed outlier: 3.511A pdb=" N HIS D 190 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 removed outlier: 3.790A pdb=" N LEU F 126 " --> pdb=" O SER F 122 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 122 through 127' Processing helix chain 'F' and resid 184 through 190 removed outlier: 3.520A pdb=" N HIS F 190 " --> pdb=" O ASP F 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 128 Processing helix chain 'H' and resid 184 through 190 Processing helix chain 'B' and resid 322 through 332 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.509A pdb=" N PHE B 370 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 removed outlier: 4.124A pdb=" N TYR B 397 " --> pdb=" O TYR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 435 No H-bonds generated for 'chain 'B' and resid 433 through 435' Processing helix chain 'B' and resid 529 through 532 Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.610A pdb=" N THR B 649 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 765 Processing helix chain 'B' and resid 769 through 777 removed outlier: 3.721A pdb=" N ALA B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 806 Processing helix chain 'B' and resid 839 through 846 Processing helix chain 'B' and resid 889 through 906 Processing helix chain 'B' and resid 909 through 914 removed outlier: 3.761A pdb=" N GLY B 912 " --> pdb=" O TRP B 909 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY B 914 " --> pdb=" O PHE B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 933 Processing helix chain 'B' and resid 935 through 942 removed outlier: 4.288A pdb=" N LEU B 939 " --> pdb=" O THR B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 963 removed outlier: 3.833A pdb=" N THR B 963 " --> pdb=" O GLU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 990 Processing helix chain 'B' and resid 1003 through 1007 removed outlier: 4.091A pdb=" N ARG B1006 " --> pdb=" O ILE B1003 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B1007 " --> pdb=" O LEU B1004 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1003 through 1007' Processing helix chain 'B' and resid 1008 through 1056 removed outlier: 3.946A pdb=" N VAL B1014 " --> pdb=" O PRO B1010 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN B1015 " --> pdb=" O GLU B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1172 removed outlier: 3.808A pdb=" N GLU B1167 " --> pdb=" O PRO B1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 removed outlier: 4.118A pdb=" N ASN A 137 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 138 " --> pdb=" O LYS A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 134 through 138' Processing helix chain 'A' and resid 191 through 195 removed outlier: 4.074A pdb=" N PHE A 194 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 195 " --> pdb=" O MET A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 191 through 195' Processing helix chain 'A' and resid 322 through 332 Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 529 through 532 Processing helix chain 'A' and resid 645 through 654 Processing helix chain 'A' and resid 760 through 765 Processing helix chain 'A' and resid 769 through 780 removed outlier: 3.912A pdb=" N ALA A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASN A 774 " --> pdb=" O THR A 770 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 806 removed outlier: 3.886A pdb=" N LEU A 786 " --> pdb=" O PHE A 782 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN A 787 " --> pdb=" O CYS A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 847 Processing helix chain 'A' and resid 889 through 906 Processing helix chain 'A' and resid 907 through 911 removed outlier: 3.706A pdb=" N THR A 910 " --> pdb=" O ALA A 907 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE A 911 " --> pdb=" O GLY A 908 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 907 through 911' Processing helix chain 'A' and resid 920 through 933 removed outlier: 3.675A pdb=" N ILE A 932 " --> pdb=" O ARG A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 942 removed outlier: 4.244A pdb=" N LEU A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 963 Processing helix chain 'A' and resid 969 through 990 Processing helix chain 'A' and resid 1002 through 1006 removed outlier: 3.541A pdb=" N ARG A1006 " --> pdb=" O ILE A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1056 removed outlier: 4.214A pdb=" N VAL A1014 " --> pdb=" O PRO A1010 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1173 removed outlier: 3.728A pdb=" N GLU A1167 " --> pdb=" O PRO A1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 312 removed outlier: 3.574A pdb=" N GLY C 311 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 332 Processing helix chain 'C' and resid 393 through 398 removed outlier: 4.139A pdb=" N TYR C 397 " --> pdb=" O TYR C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 435 No H-bonds generated for 'chain 'C' and resid 433 through 435' Processing helix chain 'C' and resid 529 through 532 Processing helix chain 'C' and resid 645 through 653 Processing helix chain 'C' and resid 760 through 765 Processing helix chain 'C' and resid 769 through 777 Processing helix chain 'C' and resid 781 through 806 Processing helix chain 'C' and resid 839 through 847 Processing helix chain 'C' and resid 889 through 906 Processing helix chain 'C' and resid 909 through 914 removed outlier: 3.725A pdb=" N GLY C 912 " --> pdb=" O TRP C 909 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY C 914 " --> pdb=" O PHE C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 933 Processing helix chain 'C' and resid 935 through 942 removed outlier: 4.170A pdb=" N LEU C 939 " --> pdb=" O THR C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 963 removed outlier: 3.838A pdb=" N THR C 963 " --> pdb=" O GLU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 990 Processing helix chain 'C' and resid 1002 through 1006 removed outlier: 3.515A pdb=" N SER C1005 " --> pdb=" O ASP C1002 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG C1006 " --> pdb=" O ILE C1003 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1002 through 1006' Processing helix chain 'C' and resid 1008 through 1056 removed outlier: 4.150A pdb=" N VAL C1014 " --> pdb=" O PRO C1010 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN C1015 " --> pdb=" O GLU C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1173 removed outlier: 3.531A pdb=" N GLU C1167 " --> pdb=" O PRO C1163 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 6 through 7 removed outlier: 4.084A pdb=" N SER E 7 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER E 77 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR E 68 " --> pdb=" O GLN E 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 35 through 39 removed outlier: 3.627A pdb=" N VAL E 96 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL E 37 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA E 91 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 149 through 150 Processing sheet with id=AA4, first strand: chain 'D' and resid 35 through 37 removed outlier: 7.185A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.832A pdb=" N ARG D 65 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR D 72 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER D 67 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 115 through 119 removed outlier: 6.311A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 155 through 156 removed outlier: 4.205A pdb=" N TRP D 149 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR D 193 " --> pdb=" O PHE D 210 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE D 210 " --> pdb=" O TYR D 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 6 through 7 removed outlier: 4.090A pdb=" N SER G 7 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER G 77 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR G 68 " --> pdb=" O GLN G 81 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 35 through 39 removed outlier: 3.571A pdb=" N VAL G 96 " --> pdb=" O HIS G 35 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL G 37 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 127 through 128 Processing sheet with id=AB2, first strand: chain 'F' and resid 35 through 37 removed outlier: 7.217A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.761A pdb=" N ARG F 65 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR F 72 " --> pdb=" O ARG F 65 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER F 67 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 115 through 119 removed outlier: 3.664A pdb=" N ASN F 138 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR F 174 " --> pdb=" O ASN F 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 155 through 156 removed outlier: 4.174A pdb=" N TRP F 149 " --> pdb=" O GLN F 156 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR F 193 " --> pdb=" O PHE F 210 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE F 210 " --> pdb=" O TYR F 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 6 through 7 removed outlier: 4.055A pdb=" N SER I 7 " --> pdb=" O SER I 21 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU I 18 " --> pdb=" O MET I 82 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER I 77 " --> pdb=" O GLU I 72 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR I 68 " --> pdb=" O GLN I 81 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.625A pdb=" N ALA I 91 " --> pdb=" O VAL I 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AB9, first strand: chain 'H' and resid 35 through 37 removed outlier: 7.239A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.802A pdb=" N ARG H 65 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR H 72 " --> pdb=" O ARG H 65 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER H 67 " --> pdb=" O ASP H 70 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'H' and resid 117 through 119 removed outlier: 3.521A pdb=" N VAL H 134 " --> pdb=" O PHE H 119 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR H 174 " --> pdb=" O ASN H 139 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 155 through 156 removed outlier: 4.138A pdb=" N TRP H 149 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR H 193 " --> pdb=" O PHE H 210 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE H 210 " --> pdb=" O TYR H 193 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.618A pdb=" N PHE B 88 " --> pdb=" O PHE C 592 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 92 through 96 removed outlier: 3.655A pdb=" N THR B 92 " --> pdb=" O TYR B 307 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 144 through 145 removed outlier: 3.514A pdb=" N ASN B 271 " --> pdb=" O GLY B 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.615A pdb=" N ILE B 158 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 165 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 204 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AC9, first strand: chain 'B' and resid 224 through 225 removed outlier: 6.290A pdb=" N LEU B 235 " --> pdb=" O LYS B 262 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS B 262 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL B 237 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 339 through 342 removed outlier: 3.839A pdb=" N THR B 626 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 346 through 347 removed outlier: 3.512A pdb=" N GLY B 620 " --> pdb=" O PHE B 346 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 353 through 354 removed outlier: 7.706A pdb=" N VAL B 354 " --> pdb=" O ASN B 569 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 568 " --> pdb=" O GLY B 575 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 575 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 383 through 386 removed outlier: 3.525A pdb=" N LYS B 384 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 425 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 386 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL B 423 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS B 460 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 480 through 482 removed outlier: 3.579A pdb=" N ASN B 520 " --> pdb=" O TYR B 481 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 592 through 594 removed outlier: 7.154A pdb=" N GLY B 593 " --> pdb=" O ASP B 601 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 691 through 694 removed outlier: 3.959A pdb=" N ILE B 693 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE B 697 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 700 " --> pdb=" O VAL B 716 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 724 through 725 removed outlier: 6.373A pdb=" N ALA B 724 " --> pdb=" O MET A 811 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 741 through 751 Processing sheet with id=AE2, first strand: chain 'B' and resid 757 through 759 Processing sheet with id=AE3, first strand: chain 'B' and resid 810 through 811 Processing sheet with id=AE4, first strand: chain 'B' and resid 819 through 820 removed outlier: 3.570A pdb=" N PHE B 820 " --> pdb=" O PHE B 823 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1111 through 1113 removed outlier: 3.788A pdb=" N PHE B1112 " --> pdb=" O PHE B1144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 92 through 96 removed outlier: 3.698A pdb=" N VAL A 317 " --> pdb=" O MET A 304 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 130 through 132 removed outlier: 3.604A pdb=" N LEU A 223 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 130 through 132 removed outlier: 3.604A pdb=" N LEU A 223 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL A 237 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 158 through 159 removed outlier: 3.828A pdb=" N VAL A 164 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 339 through 347 removed outlier: 6.075A pdb=" N ILE A 340 " --> pdb=" O THR A 626 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR A 626 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLN A 342 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 624 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER A 344 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY A 620 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 353 through 356 Processing sheet with id=AF3, first strand: chain 'A' and resid 383 through 386 removed outlier: 3.833A pdb=" N LYS A 384 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 425 " --> pdb=" O LYS A 384 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 386 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 423 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS A 460 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 480 through 482 Processing sheet with id=AF5, first strand: chain 'A' and resid 600 through 603 removed outlier: 7.466A pdb=" N PHE A 592 " --> pdb=" O PHE C 88 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.583A pdb=" N SER A 700 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 718 " --> pdb=" O CYS A 698 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N CYS A 698 " --> pdb=" O TYR A 718 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA A 699 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 724 through 725 removed outlier: 6.071A pdb=" N ALA A 724 " --> pdb=" O MET C 811 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'A' and resid 735 through 751 removed outlier: 3.604A pdb=" N ARG A1096 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLN A1094 " --> pdb=" O THR A 739 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE A 741 " --> pdb=" O PRO A1092 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE A 743 " --> pdb=" O TYR A1090 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N TYR A1090 " --> pdb=" O ILE A 743 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE A 745 " --> pdb=" O VAL A1088 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A1088 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR A 747 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU A1086 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A 749 " --> pdb=" O VAL A1084 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A1084 " --> pdb=" O VAL A 749 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLY A1082 " --> pdb=" O PRO A 751 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 756 through 759 removed outlier: 4.341A pdb=" N LYS A 756 " --> pdb=" O LEU A 884 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AG2, first strand: chain 'A' and resid 863 through 864 Processing sheet with id=AG3, first strand: chain 'A' and resid 1104 through 1105 removed outlier: 3.658A pdb=" N CYS A1105 " --> pdb=" O ILE A1156 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'A' and resid 1111 through 1113 removed outlier: 3.717A pdb=" N PHE A1112 " --> pdb=" O PHE A1144 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 92 through 96 Processing sheet with id=AG6, first strand: chain 'C' and resid 204 through 207 removed outlier: 4.118A pdb=" N TYR C 204 " --> pdb=" O ILE C 166 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AG8, first strand: chain 'C' and resid 224 through 225 removed outlier: 7.156A pdb=" N VAL C 237 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 339 through 347 removed outlier: 3.666A pdb=" N THR C 626 " --> pdb=" O GLY C 339 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR C 343 " --> pdb=" O VAL C 622 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL C 622 " --> pdb=" O THR C 343 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASN C 345 " --> pdb=" O GLY C 620 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLY C 620 " --> pdb=" O ASN C 345 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 353 through 355 Processing sheet with id=AH2, first strand: chain 'C' and resid 383 through 386 removed outlier: 3.760A pdb=" N LYS C 384 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 425 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 423 " --> pdb=" O ILE C 386 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN C 422 " --> pdb=" O GLU C 543 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS C 460 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 480 through 482 removed outlier: 3.508A pdb=" N ASN C 520 " --> pdb=" O TYR C 481 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 691 through 694 removed outlier: 3.888A pdb=" N ILE C 693 " --> pdb=" O ILE C 697 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE C 697 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER C 700 " --> pdb=" O VAL C 716 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AH6, first strand: chain 'C' and resid 741 through 751 Processing sheet with id=AH7, first strand: chain 'C' and resid 757 through 759 Processing sheet with id=AH8, first strand: chain 'C' and resid 819 through 820 Processing sheet with id=AH9, first strand: chain 'C' and resid 863 through 864 Processing sheet with id=AI1, first strand: chain 'C' and resid 1104 through 1105 removed outlier: 4.011A pdb=" N CYS C1105 " --> pdb=" O ILE C1156 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'C' and resid 1111 through 1113 removed outlier: 3.791A pdb=" N PHE C1112 " --> pdb=" O PHE C1144 " (cutoff:3.500A) 890 hydrogen bonds defined for protein. 2436 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: 9.20 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10377 1.34 - 1.46: 6091 1.46 - 1.58: 18467 1.58 - 1.70: 0 1.70 - 1.82: 222 Bond restraints: 35157 Sorted by residual: bond pdb=" N ILE C 360 " pdb=" CA ILE C 360 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.08e-02 8.57e+03 1.28e+01 bond pdb=" N ILE B 360 " pdb=" CA ILE B 360 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N VAL F 116 " pdb=" CA VAL F 116 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.75e+00 bond pdb=" N VAL E 118 " pdb=" CA VAL E 118 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.08e-02 8.57e+03 9.00e+00 bond pdb=" N ILE A 360 " pdb=" CA ILE A 360 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.74e+00 ... (remaining 35152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 47061 1.89 - 3.78: 711 3.78 - 5.67: 45 5.67 - 7.56: 14 7.56 - 9.45: 1 Bond angle restraints: 47832 Sorted by residual: angle pdb=" C THR B 558 " pdb=" CA THR B 558 " pdb=" CB THR B 558 " ideal model delta sigma weight residual 114.10 104.65 9.45 2.11e+00 2.25e-01 2.01e+01 angle pdb=" C SER G 121 " pdb=" CA SER G 121 " pdb=" CB SER G 121 " ideal model delta sigma weight residual 116.54 111.41 5.13 1.15e+00 7.56e-01 1.99e+01 angle pdb=" C SER I 121 " pdb=" CA SER I 121 " pdb=" CB SER I 121 " ideal model delta sigma weight residual 116.54 111.65 4.89 1.15e+00 7.56e-01 1.81e+01 angle pdb=" CA GLY B 553 " pdb=" C GLY B 553 " pdb=" O GLY B 553 " ideal model delta sigma weight residual 122.46 118.41 4.05 9.70e-01 1.06e+00 1.75e+01 angle pdb=" CA THR C 361 " pdb=" C THR C 361 " pdb=" O THR C 361 " ideal model delta sigma weight residual 121.84 117.34 4.50 1.16e+00 7.43e-01 1.51e+01 ... (remaining 47827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 20051 17.73 - 35.46: 748 35.46 - 53.19: 127 53.19 - 70.92: 31 70.92 - 88.65: 10 Dihedral angle restraints: 20967 sinusoidal: 8082 harmonic: 12885 Sorted by residual: dihedral pdb=" CA LYS B 555 " pdb=" C LYS B 555 " pdb=" N LEU B 556 " pdb=" CA LEU B 556 " ideal model delta harmonic sigma weight residual -180.00 -155.62 -24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA SER E 121 " pdb=" C SER E 121 " pdb=" N SER E 122 " pdb=" CA SER E 122 " ideal model delta harmonic sigma weight residual -180.00 -159.79 -20.21 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ALA A 512 " pdb=" C ALA A 512 " pdb=" N LEU A 513 " pdb=" CA LEU A 513 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 20964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4440 0.053 - 0.105: 785 0.105 - 0.158: 162 0.158 - 0.211: 18 0.211 - 0.264: 1 Chirality restraints: 5406 Sorted by residual: chirality pdb=" CA ILE B 561 " pdb=" N ILE B 561 " pdb=" C ILE B 561 " pdb=" CB ILE B 561 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA VAL F 111 " pdb=" N VAL F 111 " pdb=" C VAL F 111 " pdb=" CB VAL F 111 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA VAL D 111 " pdb=" N VAL D 111 " pdb=" C VAL D 111 " pdb=" CB VAL D 111 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 5403 not shown) Planarity restraints: 6174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 356 " 0.252 9.50e-02 1.11e+02 1.13e-01 7.80e+00 pdb=" NE ARG B 356 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 356 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 356 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 356 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 604 " 0.229 9.50e-02 1.11e+02 1.03e-01 6.45e+00 pdb=" NE ARG C 604 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 604 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 604 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 604 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B1008 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO B1009 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B1009 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B1009 " 0.028 5.00e-02 4.00e+02 ... (remaining 6171 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3246 2.75 - 3.29: 33521 3.29 - 3.83: 55621 3.83 - 4.36: 62354 4.36 - 4.90: 109245 Nonbonded interactions: 263987 Sorted by model distance: nonbonded pdb=" O PHE A 144 " pdb=" OG SER A 154 " model vdw 2.215 3.040 nonbonded pdb=" OD2 ASP B 318 " pdb=" OG SER B 320 " model vdw 2.261 3.040 nonbonded pdb=" OG SER C 700 " pdb=" OH TYR C 718 " model vdw 2.270 3.040 nonbonded pdb=" O SER B 960 " pdb=" OG1 THR B 964 " model vdw 2.274 3.040 nonbonded pdb=" O SER C 960 " pdb=" OG1 THR C 964 " model vdw 2.276 3.040 ... (remaining 263982 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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: 2.010 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.100 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35211 Z= 0.192 Angle : 0.511 9.449 47940 Z= 0.305 Chirality : 0.043 0.264 5406 Planarity : 0.004 0.113 6174 Dihedral : 9.376 88.648 12543 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.04 % Favored : 92.69 % Rotamer: Outliers : 5.28 % Allowed : 6.75 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.93 (0.11), residues: 4392 helix: 0.97 (0.19), residues: 661 sheet: -2.64 (0.14), residues: 1054 loop : -3.78 (0.09), residues: 2677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 109 TYR 0.004 0.000 TYR D 141 PHE 0.008 0.001 PHE B 357 TRP 0.006 0.000 TRP A 464 HIS 0.003 0.000 HIS C1071 Details of bonding type rmsd covalent geometry : bond 0.00286 (35157) covalent geometry : angle 0.51078 (47832) SS BOND : bond 0.00131 ( 54) SS BOND : angle 0.53052 ( 108) hydrogen bonds : bond 0.21314 ( 879) hydrogen bonds : angle 8.20286 ( 2436) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 377 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 85 LEU cc_start: -0.0546 (OUTLIER) cc_final: -0.1193 (tp) REVERT: E 90 THR cc_start: 0.7582 (OUTLIER) cc_final: 0.7282 (m) REVERT: D 135 CYS cc_start: 0.7726 (t) cc_final: 0.7420 (p) REVERT: G 63 VAL cc_start: 0.5223 (OUTLIER) cc_final: 0.4246 (p) REVERT: F 35 TRP cc_start: 0.6931 (OUTLIER) cc_final: 0.6438 (t-100) REVERT: F 115 SER cc_start: 0.5718 (OUTLIER) cc_final: 0.5460 (p) REVERT: I 28 THR cc_start: 0.8935 (m) cc_final: 0.8639 (t) REVERT: I 90 THR cc_start: 0.7289 (OUTLIER) cc_final: 0.6686 (m) REVERT: I 117 ARG cc_start: 0.6468 (OUTLIER) cc_final: 0.6188 (mtt-85) REVERT: H 35 TRP cc_start: 0.3810 (OUTLIER) cc_final: 0.1927 (m100) REVERT: B 192 MET cc_start: 0.5783 (mmt) cc_final: 0.4896 (mmt) REVERT: B 293 TYR cc_start: 0.7027 (m-10) cc_final: 0.6667 (m-10) REVERT: B 298 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6421 (pp) REVERT: B 508 CYS cc_start: 0.1484 (OUTLIER) cc_final: 0.1159 (t) REVERT: B 782 PHE cc_start: 0.7343 (m-80) cc_final: 0.6188 (m-80) REVERT: B 1109 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8834 (pttm) REVERT: A 192 MET cc_start: 0.4609 (mmt) cc_final: 0.4313 (mmt) REVERT: A 400 THR cc_start: 0.5477 (OUTLIER) cc_final: 0.5129 (m) REVERT: A 952 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8848 (tppt) REVERT: C 192 MET cc_start: 0.4950 (mmt) cc_final: 0.4647 (mmt) REVERT: C 235 LEU cc_start: 0.9182 (tp) cc_final: 0.8940 (tt) REVERT: C 400 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7771 (m) REVERT: C 508 CYS cc_start: 0.3806 (OUTLIER) cc_final: 0.3403 (t) REVERT: C 641 ASP cc_start: 0.8161 (m-30) cc_final: 0.7862 (m-30) REVERT: C 824 ASN cc_start: 0.6658 (OUTLIER) cc_final: 0.6430 (t0) outliers start: 202 outliers final: 41 residues processed: 561 average time/residue: 0.2492 time to fit residues: 220.7903 Evaluate side-chains 244 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 187 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain F residue 35 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 117 ARG Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 142 TRP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 712 GLN Chi-restraints excluded: chain B residue 761 CYS Chi-restraints excluded: chain B residue 1109 LYS Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 142 TRP Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 508 CYS Chi-restraints excluded: chain C residue 607 LYS Chi-restraints excluded: chain C residue 676 CYS Chi-restraints excluded: chain C residue 761 CYS Chi-restraints excluded: chain C residue 824 ASN Chi-restraints excluded: chain C residue 1109 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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: 71.0116 > 50: distance: 15 - 97: 35.104 distance: 67 - 72: 35.890 distance: 72 - 73: 40.230 distance: 73 - 74: 56.939 distance: 73 - 76: 56.963 distance: 74 - 75: 57.275 distance: 74 - 84: 39.341 distance: 76 - 77: 40.202 distance: 77 - 78: 40.717 distance: 79 - 81: 39.935 distance: 80 - 82: 56.390 distance: 82 - 83: 41.379 distance: 86 - 87: 21.521 distance: 89 - 91: 38.984 distance: 93 - 94: 56.703 distance: 94 - 98: 39.538 distance: 96 - 97: 55.700 distance: 98 - 99: 39.959 distance: 99 - 102: 40.142 distance: 102 - 103: 40.452 distance: 103 - 105: 40.656 distance: 106 - 107: 69.695 distance: 108 - 113: 40.163 distance: 113 - 114: 39.308 distance: 114 - 115: 38.684 distance: 114 - 117: 41.439 distance: 115 - 121: 40.751 distance: 121 - 122: 38.739 distance: 122 - 123: 56.768 distance: 123 - 124: 40.384 distance: 125 - 126: 40.802 distance: 126 - 127: 56.592 distance: 129 - 130: 56.945 distance: 135 - 136: 55.924 distance: 138 - 139: 39.175 distance: 141 - 144: 39.020 distance: 142 - 147: 23.221 distance: 145 - 146: 40.121 distance: 147 - 148: 21.801 distance: 148 - 151: 57.573 distance: 149 - 153: 34.916 distance: 151 - 152: 56.481