Starting phenix.real_space_refine on Sun Jul 5 03:28:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ltv_63382/07_2026/9ltv_63382.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ltv_63382/07_2026/9ltv_63382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ltv_63382/07_2026/9ltv_63382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ltv_63382/07_2026/9ltv_63382.map" model { file = "/net/cci-nas-00/data/ceres_data/9ltv_63382/07_2026/9ltv_63382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ltv_63382/07_2026/9ltv_63382.cif" } resolution = 2.75 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= 0.060 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 Mg 32 5.21 5 S 90 5.16 5 C 17293 2.51 5 N 3555 2.21 5 O 3883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24857 Number of models: 1 Model: "" Number of chains: 64 Chain: "0" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "1" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "2" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "3" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "4" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "5" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "6" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "7" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "8" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "9" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "A" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'TRANS': 75} Chain: "C" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2785 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 27, 'TRANS': 329} Chain: "H" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2015 Classifications: {'peptide': 255} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 236} Chain: "L" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2172 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 16, 'TRANS': 256} Chain: "M" Number of atoms: 2634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2634 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 310} Chain: "a" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "b" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "c" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "d" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "e" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "f" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "g" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "h" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "i" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "j" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "k" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "l" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "m" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "n" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "o" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "p" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "w" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "x" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "0" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'SPN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'SPN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "8" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'HEM': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 273 Unusual residues: {'BCL': 2, 'BPH': 1, 'U10': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'U10:plan-5': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-8': 2, 'U10:plan-9': 2} Unresolved non-hydrogen planarities: 50 Chain: "M" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 368 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'BCL': 2, 'BPH': 2, 'SPN': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 1 Chain: "a" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'SPN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'SPN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "m" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'SPN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "o" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "w" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.90, per 1000 atoms: 0.24 Number of scatterers: 24857 At special positions: 0 Unit cell: (141.62, 141.62, 139.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 90 16.00 Mg 32 11.99 O 3883 8.00 N 3555 7.00 C 17293 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 59 " 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=35, symmetry=0 Number of additional bonds: simple=35, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 987.8 milliseconds 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 8 sheets defined 68.5% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain '0' and resid 12 through 45 Processing helix chain '1' and resid 3 through 10 removed outlier: 3.796A pdb=" N LYS 1 6 " --> pdb=" O LYS 1 3 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP 1 8 " --> pdb=" O TYR 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 12 through 37 Processing helix chain '1' and resid 42 through 50 Processing helix chain '2' and resid 14 through 45 removed outlier: 4.229A pdb=" N GLU 2 18 " --> pdb=" O GLU 2 14 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU 2 19 " --> pdb=" O GLN 2 15 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N HIS 2 20 " --> pdb=" O ALA 2 16 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 10 Processing helix chain '3' and resid 12 through 38 removed outlier: 3.533A pdb=" N VAL 3 18 " --> pdb=" O ARG 3 14 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR 3 38 " --> pdb=" O VAL 3 34 " (cutoff:3.500A) Processing helix chain '3' and resid 42 through 51 Processing helix chain '4' and resid 12 through 45 Processing helix chain '5' and resid 3 through 10 removed outlier: 3.639A pdb=" N LYS 5 6 " --> pdb=" O LYS 5 3 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 37 removed outlier: 3.763A pdb=" N VAL 5 16 " --> pdb=" O ASP 5 12 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE 5 17 " --> pdb=" O PRO 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 50 Processing helix chain '6' and resid 12 through 45 removed outlier: 3.536A pdb=" N LEU 6 29 " --> pdb=" O SER 6 25 " (cutoff:3.500A) Processing helix chain '7' and resid 3 through 10 removed outlier: 3.501A pdb=" N LYS 7 6 " --> pdb=" O LYS 7 3 " (cutoff:3.500A) Processing helix chain '7' and resid 12 through 37 Processing helix chain '7' and resid 42 through 51 removed outlier: 3.720A pdb=" N ALA 7 51 " --> pdb=" O ALA 7 47 " (cutoff:3.500A) Processing helix chain '8' and resid 12 through 45 Processing helix chain '9' and resid 12 through 38 removed outlier: 3.663A pdb=" N VAL 9 18 " --> pdb=" O ARG 9 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR 9 38 " --> pdb=" O VAL 9 34 " (cutoff:3.500A) Processing helix chain '9' and resid 42 through 50 removed outlier: 3.557A pdb=" N ALA 9 47 " --> pdb=" O TRP 9 43 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA 9 48 " --> pdb=" O PHE 9 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 33 Processing helix chain 'A' and resid 35 through 58 removed outlier: 3.540A pdb=" N MET A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 79 removed outlier: 3.548A pdb=" N GLU A 70 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 75 " --> pdb=" O MET A 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 39 removed outlier: 3.686A pdb=" N VAL C 31 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 108 through 117 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 135 through 155 removed outlier: 3.654A pdb=" N LYS C 139 " --> pdb=" O HIS C 135 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 195 through 199 removed outlier: 4.034A pdb=" N VAL C 199 " --> pdb=" O TRP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 263 Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.924A pdb=" N HIS C 281 " --> pdb=" O PRO C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 302 removed outlier: 4.329A pdb=" N ALA C 286 " --> pdb=" O THR C 282 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR C 287 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 293 " --> pdb=" O MET C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.639A pdb=" N LEU C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 removed outlier: 4.130A pdb=" N CYS C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'H' and resid 10 through 34 removed outlier: 3.544A pdb=" N ASN H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'H' and resid 212 through 216 Processing helix chain 'H' and resid 229 through 247 removed outlier: 3.791A pdb=" N GLY H 243 " --> pdb=" O TYR H 239 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR H 244 " --> pdb=" O TYR H 240 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU H 245 " --> pdb=" O ALA H 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 33 through 58 Processing helix chain 'L' and resid 71 through 75 Processing helix chain 'L' and resid 84 through 113 removed outlier: 3.678A pdb=" N GLN L 88 " --> pdb=" O GLY L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 134 removed outlier: 3.625A pdb=" N PHE L 120 " --> pdb=" O TYR L 116 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL L 124 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 141 Processing helix chain 'L' and resid 142 through 146 removed outlier: 3.619A pdb=" N HIS L 145 " --> pdb=" O ALA L 142 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY L 146 " --> pdb=" O TRP L 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 142 through 146' Processing helix chain 'L' and resid 155 through 164 Processing helix chain 'L' and resid 165 through 166 No H-bonds generated for 'chain 'L' and resid 165 through 166' Processing helix chain 'L' and resid 167 through 170 Processing helix chain 'L' and resid 171 through 200 Processing helix chain 'L' and resid 209 through 222 Processing helix chain 'L' and resid 228 through 253 removed outlier: 3.651A pdb=" N ARG L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER L 252 " --> pdb=" O CYS L 248 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY L 253 " --> pdb=" O ILE L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 263 Processing helix chain 'L' and resid 264 through 269 Processing helix chain 'M' and resid 26 through 31 removed outlier: 3.567A pdb=" N GLU M 29 " --> pdb=" O ASN M 26 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU M 30 " --> pdb=" O LEU M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 44 removed outlier: 3.622A pdb=" N TRP M 43 " --> pdb=" O LEU M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 79 Processing helix chain 'M' and resid 83 through 90 Processing helix chain 'M' and resid 91 through 94 removed outlier: 3.662A pdb=" N LEU M 94 " --> pdb=" O LEU M 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 91 through 94' Processing helix chain 'M' and resid 100 through 104 removed outlier: 3.564A pdb=" N GLY M 104 " --> pdb=" O PRO M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 112 Processing helix chain 'M' and resid 113 through 141 removed outlier: 3.643A pdb=" N ALA M 138 " --> pdb=" O THR M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 163 removed outlier: 3.745A pdb=" N ALA M 154 " --> pdb=" O ALA M 150 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU M 157 " --> pdb=" O ALA M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 170 Processing helix chain 'M' and resid 171 through 175 removed outlier: 3.851A pdb=" N GLU M 174 " --> pdb=" O SER M 171 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA M 175 " --> pdb=" O TRP M 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 171 through 175' Processing helix chain 'M' and resid 179 through 194 removed outlier: 3.506A pdb=" N HIS M 183 " --> pdb=" O GLY M 179 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU M 184 " --> pdb=" O ILE M 180 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR M 194 " --> pdb=" O PHE M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 199 Processing helix chain 'M' and resid 200 through 227 Processing helix chain 'M' and resid 228 through 231 Processing helix chain 'M' and resid 234 through 241 Processing helix chain 'M' and resid 243 through 258 removed outlier: 3.635A pdb=" N GLU M 247 " --> pdb=" O GLY M 243 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP M 253 " --> pdb=" O ALA M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 287 removed outlier: 3.807A pdb=" N ARG M 268 " --> pdb=" O GLU M 264 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR M 277 " --> pdb=" O PHE M 273 " (cutoff:3.500A) Proline residue: M 278 - end of helix removed outlier: 3.515A pdb=" N LEU M 287 " --> pdb=" O ILE M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 302 Processing helix chain 'M' and resid 313 through 317 removed outlier: 3.628A pdb=" N ALA M 316 " --> pdb=" O GLY M 313 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 325 Processing helix chain 'a' and resid 3 through 10 removed outlier: 3.537A pdb=" N TRP a 8 " --> pdb=" O TYR a 5 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 38 removed outlier: 3.650A pdb=" N VAL a 18 " --> pdb=" O ARG a 14 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR a 38 " --> pdb=" O VAL a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 50 removed outlier: 3.586A pdb=" N ALA a 47 " --> pdb=" O TRP a 43 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA a 48 " --> pdb=" O PHE a 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 45 removed outlier: 3.763A pdb=" N SER b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY b 26 " --> pdb=" O VAL b 22 " (cutoff:3.500A) Processing helix chain 'c' and resid 1 through 10 removed outlier: 4.291A pdb=" N TYR c 5 " --> pdb=" O SER c 2 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE c 7 " --> pdb=" O PHE c 4 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP c 8 " --> pdb=" O TYR c 5 " (cutoff:3.500A) Processing helix chain 'c' and resid 12 through 37 removed outlier: 3.606A pdb=" N VAL c 18 " --> pdb=" O ARG c 14 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 50 Processing helix chain 'd' and resid 12 through 45 Processing helix chain 'e' and resid 3 through 10 removed outlier: 3.847A pdb=" N LYS e 6 " --> pdb=" O LYS e 3 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE e 7 " --> pdb=" O PHE e 4 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP e 8 " --> pdb=" O TYR e 5 " (cutoff:3.500A) Processing helix chain 'e' and resid 12 through 37 removed outlier: 3.538A pdb=" N PHE e 25 " --> pdb=" O GLY e 21 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 51 Processing helix chain 'f' and resid 12 through 45 Processing helix chain 'g' and resid 3 through 10 removed outlier: 3.585A pdb=" N TRP g 8 " --> pdb=" O TYR g 5 " (cutoff:3.500A) Processing helix chain 'g' and resid 12 through 37 removed outlier: 3.585A pdb=" N VAL g 18 " --> pdb=" O ARG g 14 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU g 36 " --> pdb=" O HIS g 32 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 50 Processing helix chain 'h' and resid 12 through 45 removed outlier: 3.663A pdb=" N VAL h 22 " --> pdb=" O GLU h 18 " (cutoff:3.500A) Processing helix chain 'i' and resid 3 through 10 Processing helix chain 'i' and resid 12 through 37 removed outlier: 3.554A pdb=" N VAL i 16 " --> pdb=" O ASP i 12 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL i 18 " --> pdb=" O ARG i 14 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE i 25 " --> pdb=" O GLY i 21 " (cutoff:3.500A) Processing helix chain 'i' and resid 42 through 51 removed outlier: 3.707A pdb=" N ALA i 47 " --> pdb=" O TRP i 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 12 through 45 Processing helix chain 'k' and resid 3 through 10 removed outlier: 3.617A pdb=" N LYS k 6 " --> pdb=" O LYS k 3 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 37 removed outlier: 4.008A pdb=" N VAL k 18 " --> pdb=" O ARG k 14 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA k 19 " --> pdb=" O ARG k 15 " (cutoff:3.500A) Processing helix chain 'k' and resid 42 through 51 removed outlier: 3.668A pdb=" N ALA k 47 " --> pdb=" O TRP k 43 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA k 48 " --> pdb=" O PHE k 44 " (cutoff:3.500A) Processing helix chain 'l' and resid 12 through 45 removed outlier: 3.574A pdb=" N VAL l 22 " --> pdb=" O GLU l 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 3 through 10 removed outlier: 3.801A pdb=" N LYS m 6 " --> pdb=" O LYS m 3 " (cutoff:3.500A) Processing helix chain 'm' and resid 12 through 37 Processing helix chain 'm' and resid 42 through 50 removed outlier: 3.533A pdb=" N LEU m 46 " --> pdb=" O ASN m 42 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA m 47 " --> pdb=" O TRP m 43 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA m 48 " --> pdb=" O PHE m 44 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 45 removed outlier: 3.618A pdb=" N ALA n 16 " --> pdb=" O THR n 12 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU n 29 " --> pdb=" O SER n 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 10 removed outlier: 3.904A pdb=" N LYS o 6 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE o 7 " --> pdb=" O PHE o 4 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP o 8 " --> pdb=" O TYR o 5 " (cutoff:3.500A) Processing helix chain 'o' and resid 12 through 35 Processing helix chain 'o' and resid 46 through 51 removed outlier: 3.742A pdb=" N ASN o 50 " --> pdb=" O LEU o 46 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA o 51 " --> pdb=" O ALA o 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 46 through 51' Processing helix chain 'p' and resid 12 through 45 removed outlier: 3.857A pdb=" N SER p 21 " --> pdb=" O GLN p 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL p 22 " --> pdb=" O GLU p 18 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR p 23 " --> pdb=" O LEU p 19 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA p 32 " --> pdb=" O TRP p 28 " (cutoff:3.500A) Processing helix chain 'w' and resid 3 through 10 Processing helix chain 'w' and resid 12 through 37 removed outlier: 3.614A pdb=" N PHE w 25 " --> pdb=" O GLY w 21 " (cutoff:3.500A) Processing helix chain 'w' and resid 42 through 50 removed outlier: 3.595A pdb=" N ALA w 48 " --> pdb=" O PHE w 44 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 45 Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 50 Processing sheet with id=AA2, first strand: chain 'H' and resid 61 through 64 Processing sheet with id=AA3, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.457A pdb=" N GLY H 162 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU H 183 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL H 164 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU H 181 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP H 166 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU H 179 " --> pdb=" O ASP H 166 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP H 168 " --> pdb=" O ARG H 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 131 through 133 removed outlier: 4.138A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 141 through 145 removed outlier: 6.543A pdb=" N GLN M 12 " --> pdb=" O SER H 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 25 through 27 removed outlier: 4.087A pdb=" N PHE L 25 " --> pdb=" O VAL L 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 36 through 37 1282 hydrogen bonds defined for protein. 3591 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: 3.62 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 7664 1.37 - 1.55: 17804 1.55 - 1.74: 46 1.74 - 1.92: 168 1.92 - 2.11: 140 Bond restraints: 25822 Sorted by residual: bond pdb=" N PRO c 13 " pdb=" CD PRO c 13 " ideal model delta sigma weight residual 1.473 1.701 -0.228 1.40e-02 5.10e+03 2.65e+02 bond pdb=" N PRO H 54 " pdb=" CD PRO H 54 " ideal model delta sigma weight residual 1.473 1.664 -0.191 1.40e-02 5.10e+03 1.85e+02 bond pdb=" N PRO d 46 " pdb=" CD PRO d 46 " ideal model delta sigma weight residual 1.473 1.658 -0.185 1.40e-02 5.10e+03 1.75e+02 bond pdb=" N PRO C 283 " pdb=" CD PRO C 283 " ideal model delta sigma weight residual 1.473 1.650 -0.177 1.40e-02 5.10e+03 1.60e+02 bond pdb=" C21 SPN d 102 " pdb=" C22 SPN d 102 " ideal model delta sigma weight residual 1.531 1.340 0.191 2.00e-02 2.50e+03 9.11e+01 ... (remaining 25817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 34001 3.70 - 7.39: 1032 7.39 - 11.09: 284 11.09 - 14.78: 190 14.78 - 18.48: 60 Bond angle restraints: 35567 Sorted by residual: angle pdb=" N ILE 9 7 " pdb=" CA ILE 9 7 " pdb=" C ILE 9 7 " ideal model delta sigma weight residual 113.47 100.56 12.91 1.01e+00 9.80e-01 1.64e+02 angle pdb=" N THR C 124 " pdb=" CA THR C 124 " pdb=" C THR C 124 " ideal model delta sigma weight residual 109.07 94.61 14.46 1.61e+00 3.86e-01 8.07e+01 angle pdb=" N LEU 9 9 " pdb=" CA LEU 9 9 " pdb=" C LEU 9 9 " ideal model delta sigma weight residual 113.17 103.39 9.78 1.26e+00 6.30e-01 6.03e+01 angle pdb=" N PHE o 44 " pdb=" CA PHE o 44 " pdb=" C PHE o 44 " ideal model delta sigma weight residual 111.07 103.79 7.28 1.07e+00 8.73e-01 4.63e+01 angle pdb=" N MET M 140 " pdb=" CA MET M 140 " pdb=" C MET M 140 " ideal model delta sigma weight residual 113.18 121.39 -8.21 1.21e+00 6.83e-01 4.60e+01 ... (remaining 35562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 12985 35.68 - 71.35: 919 71.35 - 107.03: 45 107.03 - 142.71: 7 142.71 - 178.38: 3 Dihedral angle restraints: 13959 sinusoidal: 6402 harmonic: 7557 Sorted by residual: dihedral pdb=" C1 BCL d 101 " pdb=" CGA BCL d 101 " pdb=" O2A BCL d 101 " pdb=" CBA BCL d 101 " ideal model delta sinusoidal sigma weight residual -180.00 -1.62 -178.38 1 6.00e+00 2.78e-02 5.33e+02 dihedral pdb=" C1 BCL h 101 " pdb=" CGA BCL h 101 " pdb=" O2A BCL h 101 " pdb=" CBA BCL h 101 " ideal model delta sinusoidal sigma weight residual 180.00 26.15 153.85 1 6.00e+00 2.78e-02 5.06e+02 dihedral pdb=" C1 BCL p 101 " pdb=" CGA BCL p 101 " pdb=" O2A BCL p 101 " pdb=" CBA BCL p 101 " ideal model delta sinusoidal sigma weight residual -180.00 -39.40 -140.60 1 6.00e+00 2.78e-02 4.73e+02 ... (remaining 13956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.520: 3511 0.520 - 1.039: 1 1.039 - 1.559: 0 1.559 - 2.078: 0 2.078 - 2.598: 27 Chirality restraints: 3539 Sorted by residual: chirality pdb=" C22 SPN l 102 " pdb=" C21 SPN l 102 " pdb=" C23 SPN l 102 " pdb=" CM7 SPN l 102 " both_signs ideal model delta sigma weight residual False -2.58 0.02 -2.60 2.00e-01 2.50e+01 1.69e+02 chirality pdb=" C22 SPN 1 103 " pdb=" C21 SPN 1 103 " pdb=" C23 SPN 1 103 " pdb=" CM7 SPN 1 103 " both_signs ideal model delta sigma weight residual False -2.58 0.02 -2.60 2.00e-01 2.50e+01 1.68e+02 chirality pdb=" C22 SPN g 103 " pdb=" C21 SPN g 103 " pdb=" C23 SPN g 103 " pdb=" CM7 SPN g 103 " both_signs ideal model delta sigma weight residual False -2.58 0.02 -2.59 2.00e-01 2.50e+01 1.68e+02 ... (remaining 3536 not shown) Planarity restraints: 4315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL L 301 " 0.364 1.50e-02 4.44e+03 3.07e-01 2.09e+03 pdb=" C2 BCL L 301 " -0.533 1.50e-02 4.44e+03 pdb=" C3 BCL L 301 " -0.113 1.50e-02 4.44e+03 pdb=" C4 BCL L 301 " 0.162 1.50e-02 4.44e+03 pdb=" C5 BCL L 301 " 0.120 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL l 101 " -0.359 1.50e-02 4.44e+03 3.02e-01 2.02e+03 pdb=" C2 BCL l 101 " 0.522 1.50e-02 4.44e+03 pdb=" C3 BCL l 101 " 0.111 1.50e-02 4.44e+03 pdb=" C4 BCL l 101 " -0.181 1.50e-02 4.44e+03 pdb=" C5 BCL l 101 " -0.093 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL m 101 " -0.357 1.50e-02 4.44e+03 3.01e-01 2.01e+03 pdb=" C2 BCL m 101 " 0.520 1.50e-02 4.44e+03 pdb=" C3 BCL m 101 " 0.112 1.50e-02 4.44e+03 pdb=" C4 BCL m 101 " -0.094 1.50e-02 4.44e+03 pdb=" C5 BCL m 101 " -0.181 1.50e-02 4.44e+03 ... (remaining 4312 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 100 2.63 - 3.20: 19462 3.20 - 3.76: 37059 3.76 - 4.33: 53210 4.33 - 4.90: 88161 Nonbonded interactions: 197992 Sorted by model distance: nonbonded pdb=" CE MET w 1 " pdb=" CE2 PHE w 4 " model vdw 2.062 3.760 nonbonded pdb=" OE2 GLU M 235 " pdb="FE FE M 401 " model vdw 2.063 3.000 nonbonded pdb=" NE1 TRP 2 47 " pdb=" CZ PHE 2 48 " model vdw 2.187 3.420 nonbonded pdb=" OE1 GLN 3 20 " pdb=" OH TYR 4 23 " model vdw 2.196 3.040 nonbonded pdb=" CD1 TRP 2 47 " pdb=" CE1 PHE 2 48 " model vdw 2.210 3.560 ... (remaining 197987 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 '0' and resid 5 through 101) selection = chain '2' selection = (chain '4' and resid 5 through 101) selection = chain '6' selection = (chain '8' and resid 5 through 101) selection = (chain 'b' and resid 5 through 101) selection = (chain 'd' and resid 5 through 101) selection = (chain 'f' and resid 5 through 101) selection = (chain 'h' and resid 5 through 101) selection = chain 'j' selection = (chain 'l' and resid 5 through 101) selection = (chain 'n' and resid 5 through 101) selection = (chain 'p' and resid 5 through 101) selection = chain 'x' } ncs_group { reference = (chain '1' and resid 1 through 51) selection = (chain '3' and resid 1 through 51) selection = (chain '5' and resid 1 through 51) selection = (chain '7' and resid 1 through 51) selection = (chain '9' and resid 1 through 51) selection = (chain 'a' and resid 1 through 51) selection = (chain 'c' and resid 1 through 51) selection = (chain 'e' and resid 1 through 51) selection = (chain 'g' and resid 1 through 51) selection = (chain 'i' and resid 1 through 51) selection = (chain 'k' and resid 1 through 51) selection = (chain 'm' and resid 1 through 51) selection = (chain 'o' and resid 1 through 51) selection = (chain 'w' and resid 1 through 51) } 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: 3.020 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.960 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 : 0.026 0.406 25858 Z= 1.791 Angle : 1.812 18.478 35569 Z= 0.735 Chirality : 0.239 2.598 3539 Planarity : 0.032 0.331 4315 Dihedral : 20.911 178.382 9060 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.18 % Allowed : 9.29 % Favored : 90.53 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 2.91 % 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: 1.46 (0.17), residues: 2550 helix: 2.22 (0.13), residues: 1579 sheet: 0.20 (1.11), residues: 17 loop : -1.27 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 174 TYR 0.016 0.001 TYR L 170 PHE 0.022 0.001 PHE p 30 TRP 0.024 0.001 TRP h 47 HIS 0.014 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.02237 / 1.11 (25822) covalent geometry : angle 1.81183 / 0.74 (35567) SS BOND : bond 0.00072 / 0.04 ( 1) SS BOND : angle 0.26003 / 0.15 ( 2) hydrogen bonds : bond 0.16115 / 10.47 ( 1280) hydrogen bonds : angle 4.45067 / 3.29 ( 3591) Misc. bond : bond 0.38338 / 22.67 ( 35) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 246 time to evaluate : 0.746 Fit side-chains REVERT: L 203 LYS cc_start: 0.7813 (mttt) cc_final: 0.7244 (mppt) outliers start: 4 outliers final: 0 residues processed: 250 average time/residue: 0.6689 time to fit residues: 192.2679 Evaluate side-chains 202 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 40 HIS ** L 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 ASN m 20 GLN o 32 HIS p 17 GLN p 38 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.171373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123207 restraints weight = 29886.957| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.88 r_work: 0.3149 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.317 25858 Z= 0.235 Angle : 0.763 23.653 35569 Z= 0.282 Chirality : 0.037 0.173 3539 Planarity : 0.004 0.103 4315 Dihedral : 19.460 179.850 4506 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.56 % Allowed : 11.95 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 1.72 (0.17), residues: 2550 helix: 2.48 (0.13), residues: 1586 sheet: -0.03 (1.05), residues: 17 loop : -1.27 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 115 TYR 0.013 0.001 TYR L 165 PHE 0.023 0.001 PHE M 158 TRP 0.013 0.001 TRP 5 43 HIS 0.010 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (25822) covalent geometry : angle 0.76304 / 0.28 (35567) SS BOND : bond 0.00036 / 0.02 ( 1) SS BOND : angle 0.24682 / 0.14 ( 2) hydrogen bonds : bond 0.05898 / 3.98 ( 1280) hydrogen bonds : angle 3.43228 / 2.54 ( 3591) Misc. bond : bond 0.05714 / 2.15 ( 35) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.816 Fit side-chains REVERT: 1 30 MET cc_start: 0.2948 (OUTLIER) cc_final: 0.2123 (tpp) REVERT: C 237 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7230 (tm-30) REVERT: C 294 MET cc_start: 0.9526 (ttp) cc_final: 0.9317 (ttp) REVERT: C 297 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8046 (tp30) REVERT: L 83 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: L 203 LYS cc_start: 0.7958 (mttt) cc_final: 0.7112 (mppt) REVERT: M 264 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8472 (tt0) REVERT: a 2 SER cc_start: 0.7542 (t) cc_final: 0.7135 (m) REVERT: a 15 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7029 (mtm-85) REVERT: e 6 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7997 (mmtp) REVERT: j 24 MET cc_start: 0.8783 (mmp) cc_final: 0.8273 (mmt) outliers start: 34 outliers final: 14 residues processed: 227 average time/residue: 0.6121 time to fit residues: 160.8160 Evaluate side-chains 224 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 9 residue 7 ILE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 264 GLU Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 39 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 180 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 184 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 40 HIS ** 6 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 ASN i 20 GLN k 20 GLN o 20 GLN p 17 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.169511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.121178 restraints weight = 30033.539| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.88 r_work: 0.3116 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 25858 Z= 0.139 Angle : 0.696 15.708 35569 Z= 0.272 Chirality : 0.038 0.277 3539 Planarity : 0.004 0.054 4315 Dihedral : 17.834 179.955 4506 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.98 % Allowed : 11.72 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 2.11 (0.16), residues: 2550 helix: 2.99 (0.12), residues: 1495 sheet: -0.11 (1.07), residues: 17 loop : -1.09 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 11 TYR 0.016 0.001 TYR L 165 PHE 0.018 0.001 PHE C 268 TRP 0.013 0.001 TRP 9 8 HIS 0.013 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (25822) covalent geometry : angle 0.69552 / 0.27 (35567) SS BOND : bond 0.00076 / 0.04 ( 1) SS BOND : angle 0.22836 / 0.12 ( 2) hydrogen bonds : bond 0.06200 / 4.20 ( 1280) hydrogen bonds : angle 3.35541 / 2.48 ( 3591) Misc. bond : bond 0.02502 / 1.50 ( 35) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 0.904 Fit side-chains REVERT: 6 38 HIS cc_start: 0.6059 (OUTLIER) cc_final: 0.5273 (m90) REVERT: C 164 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: C 237 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7176 (tm-30) REVERT: C 297 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8047 (tp30) REVERT: H 81 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.6913 (ttm170) REVERT: L 13 ARG cc_start: 0.8512 (ptm160) cc_final: 0.8173 (ptm-80) REVERT: L 83 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: L 203 LYS cc_start: 0.7998 (mttt) cc_final: 0.7171 (mppt) REVERT: M 264 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: a 2 SER cc_start: 0.7533 (t) cc_final: 0.7096 (m) REVERT: a 15 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7000 (mtm-85) REVERT: e 6 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8039 (mmtp) outliers start: 43 outliers final: 19 residues processed: 228 average time/residue: 0.6716 time to fit residues: 176.7549 Evaluate side-chains 226 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 34 VAL Chi-restraints excluded: chain 6 residue 38 HIS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 75 ASN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 264 GLU Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain h residue 19 LEU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain i residue 39 GLU Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 36 VAL Chi-restraints excluded: chain n residue 39 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 52 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 40 HIS ** 6 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 32 HIS g 50 ASN p 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.166197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117638 restraints weight = 29900.056| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.88 r_work: 0.3062 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.380 25858 Z= 0.303 Angle : 0.767 16.858 35569 Z= 0.309 Chirality : 0.041 0.246 3539 Planarity : 0.005 0.058 4315 Dihedral : 17.342 179.938 4506 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.71 % Allowed : 11.82 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 1.40 (0.17), residues: 2550 helix: 2.25 (0.13), residues: 1586 sheet: -0.35 (1.10), residues: 17 loop : -1.46 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 248 TYR 0.022 0.002 TYR L 165 PHE 0.022 0.002 PHE M 158 TRP 0.015 0.002 TRP e 43 HIS 0.015 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (25822) covalent geometry : angle 0.76687 / 0.31 (35567) SS BOND : bond 0.00087 / 0.05 ( 1) SS BOND : angle 0.22760 / 0.12 ( 2) hydrogen bonds : bond 0.07644 / 5.17 ( 1280) hydrogen bonds : angle 3.51491 / 2.60 ( 3591) Misc. bond : bond 0.07126 / 4.11 ( 35) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 203 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: 5 40 HIS cc_start: 0.5202 (t70) cc_final: 0.4992 (t-90) REVERT: 6 38 HIS cc_start: 0.6094 (OUTLIER) cc_final: 0.5757 (m90) REVERT: C 8 GLU cc_start: 0.3377 (OUTLIER) cc_final: 0.3172 (pp20) REVERT: C 237 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: C 297 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7946 (tp30) REVERT: H 81 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.6916 (ttm170) REVERT: L 83 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8372 (mm-30) REVERT: L 203 LYS cc_start: 0.7981 (mttt) cc_final: 0.7209 (mppt) REVERT: M 39 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: M 264 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: a 15 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.5816 (mmp-170) REVERT: e 6 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8057 (mmtp) REVERT: k 45 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7360 (mt-10) outliers start: 59 outliers final: 25 residues processed: 241 average time/residue: 0.6860 time to fit residues: 190.5498 Evaluate side-chains 235 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 34 VAL Chi-restraints excluded: chain 6 residue 38 HIS Chi-restraints excluded: chain 9 residue 7 ILE Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 75 ASN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 264 GLU Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain h residue 19 LEU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 38 HIS Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain m residue 35 LEU Chi-restraints excluded: chain n residue 39 LEU Chi-restraints excluded: chain o residue 2 SER Chi-restraints excluded: chain x residue 24 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 198 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 234 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 217 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 15 GLN ** L 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 70 ASN g 32 HIS g 50 ASN p 17 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.166629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.118168 restraints weight = 29962.667| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.90 r_work: 0.3069 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 25858 Z= 0.179 Angle : 0.730 16.915 35569 Z= 0.295 Chirality : 0.040 0.210 3539 Planarity : 0.004 0.057 4315 Dihedral : 16.859 179.923 4506 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.39 % Allowed : 12.83 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 1.42 (0.17), residues: 2550 helix: 2.28 (0.13), residues: 1586 sheet: -0.40 (1.09), residues: 17 loop : -1.48 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 11 TYR 0.020 0.002 TYR L 165 PHE 0.025 0.002 PHE M 158 TRP 0.014 0.001 TRP e 43 HIS 0.014 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.17 (25822) covalent geometry : angle 0.72973 / 0.30 (35567) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 0.19074 / 0.11 ( 2) hydrogen bonds : bond 0.07111 / 4.82 ( 1280) hydrogen bonds : angle 3.43655 / 2.54 ( 3591) Misc. bond : bond 0.03152 / 1.87 ( 35) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 0.854 Fit side-chains REVERT: 1 30 MET cc_start: 0.2692 (OUTLIER) cc_final: 0.2346 (tpp) REVERT: 6 38 HIS cc_start: 0.6011 (OUTLIER) cc_final: 0.5674 (m90) REVERT: C 16 ASP cc_start: 0.6535 (t70) cc_final: 0.6202 (t70) REVERT: C 237 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7236 (tm-30) REVERT: C 297 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7969 (tp30) REVERT: H 81 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.6817 (ttm170) REVERT: H 116 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8443 (ttpp) REVERT: L 83 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8164 (mm-30) REVERT: L 203 LYS cc_start: 0.7975 (mttt) cc_final: 0.7183 (mppt) REVERT: M 49 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8540 (mt) REVERT: M 264 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: a 15 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.5772 (mmp-170) REVERT: b 8 PHE cc_start: 0.6365 (m-80) cc_final: 0.6077 (m-80) REVERT: c 1 MET cc_start: 0.6326 (ttm) cc_final: 0.6064 (ttm) REVERT: e 6 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8013 (mmtp) REVERT: k 45 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7432 (mt-10) REVERT: n 24 MET cc_start: 0.8993 (mmp) cc_final: 0.8765 (mmm) outliers start: 52 outliers final: 24 residues processed: 236 average time/residue: 0.6510 time to fit residues: 177.5861 Evaluate side-chains 235 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 5 residue 34 VAL Chi-restraints excluded: chain 6 residue 38 HIS Chi-restraints excluded: chain 9 residue 7 ILE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 75 ASN Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 264 GLU Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain e residue 10 ILE Chi-restraints excluded: chain h residue 19 LEU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 38 HIS Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain m residue 35 LEU Chi-restraints excluded: chain n residue 39 LEU Chi-restraints excluded: chain o residue 2 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 245 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 26 optimal weight: 0.0570 chunk 154 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 159 optimal weight: 0.7980 overall best weight: 0.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 40 HIS L 169 HIS g 50 ASN p 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.172539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125100 restraints weight = 29866.630| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.85 r_work: 0.3187 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 25858 Z= 0.103 Angle : 0.587 14.215 35569 Z= 0.235 Chirality : 0.034 0.138 3539 Planarity : 0.004 0.055 4315 Dihedral : 15.684 179.993 4506 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.38 % Allowed : 14.21 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 2.03 (0.17), residues: 2550 helix: 2.78 (0.13), residues: 1586 sheet: -0.19 (1.08), residues: 17 loop : -1.27 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 115 TYR 0.010 0.001 TYR C 257 PHE 0.020 0.001 PHE L 217 TRP 0.014 0.001 TRP e 43 HIS 0.007 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (25822) covalent geometry : angle 0.58677 / 0.24 (35567) SS BOND : bond 0.00099 / 0.05 ( 1) SS BOND : angle 0.17816 / 0.09 ( 2) hydrogen bonds : bond 0.04815 / 3.27 ( 1280) hydrogen bonds : angle 3.12886 / 2.32 ( 3591) Misc. bond : bond 0.01942 / 1.14 ( 35) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.862 Fit side-chains REVERT: 6 38 HIS cc_start: 0.6133 (OUTLIER) cc_final: 0.5417 (m90) REVERT: C 237 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: L 203 LYS cc_start: 0.8073 (mttt) cc_final: 0.7272 (mppt) REVERT: L 217 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7668 (t80) REVERT: a 2 SER cc_start: 0.7567 (t) cc_final: 0.7192 (m) REVERT: a 15 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.5501 (mmp-170) REVERT: i 39 GLU cc_start: 0.8112 (pp20) cc_final: 0.7911 (tt0) outliers start: 30 outliers final: 11 residues processed: 218 average time/residue: 0.6299 time to fit residues: 158.8912 Evaluate side-chains 211 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 38 HIS Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 9 residue 7 ILE Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain h residue 19 LEU Chi-restraints excluded: chain h residue 38 HIS Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 39 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 16 optimal weight: 20.0000 chunk 189 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 184 optimal weight: 0.1980 chunk 77 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 237 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 40 HIS g 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.171286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.123510 restraints weight = 30029.445| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.88 r_work: 0.3151 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 25858 Z= 0.109 Angle : 0.599 15.923 35569 Z= 0.239 Chirality : 0.035 0.146 3539 Planarity : 0.004 0.054 4315 Dihedral : 15.411 179.987 4506 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.06 % Allowed : 15.13 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 2.07 (0.17), residues: 2550 helix: 2.82 (0.13), residues: 1586 sheet: -0.30 (1.01), residues: 17 loop : -1.25 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 115 TYR 0.013 0.001 TYR L 165 PHE 0.019 0.001 PHE M 158 TRP 0.011 0.001 TRP g 43 HIS 0.010 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (25822) covalent geometry : angle 0.59887 / 0.24 (35567) SS BOND : bond 0.00116 / 0.06 ( 1) SS BOND : angle 0.25423 / 0.13 ( 2) hydrogen bonds : bond 0.05087 / 3.45 ( 1280) hydrogen bonds : angle 3.11478 / 2.31 ( 3591) Misc. bond : bond 0.02333 / 1.44 ( 35) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.627 Fit side-chains REVERT: 4 24 MET cc_start: 0.4038 (OUTLIER) cc_final: 0.3778 (mpm) REVERT: 6 38 HIS cc_start: 0.6023 (OUTLIER) cc_final: 0.5742 (m90) REVERT: C 237 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7217 (tt0) REVERT: L 203 LYS cc_start: 0.7965 (mttt) cc_final: 0.7159 (mppt) REVERT: L 217 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7527 (t80) REVERT: a 2 SER cc_start: 0.7504 (t) cc_final: 0.7077 (m) REVERT: a 15 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.5481 (mmp-170) outliers start: 23 outliers final: 12 residues processed: 208 average time/residue: 0.6412 time to fit residues: 153.9704 Evaluate side-chains 212 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 6 residue 38 HIS Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 9 residue 7 ILE Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain h residue 19 LEU Chi-restraints excluded: chain h residue 38 HIS Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain k residue 46 LEU Chi-restraints excluded: chain n residue 39 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 236 optimal weight: 0.9990 chunk 238 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 40 HIS g 32 HIS g 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.169980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121993 restraints weight = 29959.089| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.83 r_work: 0.3135 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.310 25858 Z= 0.228 Angle : 0.624 16.502 35569 Z= 0.251 Chirality : 0.036 0.161 3539 Planarity : 0.004 0.053 4315 Dihedral : 15.418 179.997 4506 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.20 % Allowed : 15.17 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 1.99 (0.17), residues: 2550 helix: 2.75 (0.13), residues: 1586 sheet: -0.47 (1.01), residues: 17 loop : -1.28 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 115 TYR 0.015 0.001 TYR L 165 PHE 0.020 0.001 PHE M 158 TRP 0.011 0.001 TRP e 43 HIS 0.011 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (25822) covalent geometry : angle 0.62361 / 0.25 (35567) SS BOND : bond 0.00117 / 0.06 ( 1) SS BOND : angle 0.21005 / 0.11 ( 2) hydrogen bonds : bond 0.05610 / 3.81 ( 1280) hydrogen bonds : angle 3.18016 / 2.36 ( 3591) Misc. bond : bond 0.05657 / 3.26 ( 35) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.718 Fit side-chains REVERT: 1 30 MET cc_start: 0.2813 (OUTLIER) cc_final: 0.2083 (tpt) REVERT: 4 24 MET cc_start: 0.4076 (OUTLIER) cc_final: 0.3702 (mpm) REVERT: 6 38 HIS cc_start: 0.6081 (OUTLIER) cc_final: 0.5801 (m90) REVERT: C 237 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: L 203 LYS cc_start: 0.8013 (mttt) cc_final: 0.7234 (mppt) REVERT: L 217 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7645 (t80) REVERT: M 49 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8482 (mt) REVERT: a 15 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.5546 (mmp-170) REVERT: h 21 SER cc_start: 0.7733 (OUTLIER) cc_final: 0.7333 (m) REVERT: n 24 MET cc_start: 0.8967 (mmp) cc_final: 0.8648 (mmm) outliers start: 26 outliers final: 12 residues processed: 210 average time/residue: 0.6420 time to fit residues: 155.2679 Evaluate side-chains 214 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 6 residue 38 HIS Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 9 residue 7 ILE Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain h residue 19 LEU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 38 HIS Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain k residue 46 LEU Chi-restraints excluded: chain n residue 39 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 155 optimal weight: 0.0370 chunk 179 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 165 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 overall best weight: 1.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 40 HIS M 70 ASN ** g 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.168706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120525 restraints weight = 29899.477| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.88 r_work: 0.3105 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 25858 Z= 0.136 Angle : 0.653 17.001 35569 Z= 0.264 Chirality : 0.037 0.175 3539 Planarity : 0.004 0.053 4315 Dihedral : 15.546 179.946 4506 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.29 % Allowed : 15.08 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % 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: 1.89 (0.17), residues: 2550 helix: 2.68 (0.13), residues: 1586 sheet: -0.61 (1.00), residues: 17 loop : -1.32 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 115 TYR 0.017 0.001 TYR L 165 PHE 0.021 0.001 PHE M 158 TRP 0.012 0.001 TRP g 43 HIS 0.012 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (25822) covalent geometry : angle 0.65286 / 0.26 (35567) SS BOND : bond 0.00130 / 0.07 ( 1) SS BOND : angle 0.20035 / 0.11 ( 2) hydrogen bonds : bond 0.06097 / 4.13 ( 1280) hydrogen bonds : angle 3.23437 / 2.40 ( 3591) Misc. bond : bond 0.02427 / 1.41 ( 35) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5100 Ramachandran restraints generated. 2550 Oldfield, 0 Emsley, 2550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.714 Fit side-chains REVERT: 1 30 MET cc_start: 0.2713 (OUTLIER) cc_final: 0.2014 (tpt) REVERT: 4 24 MET cc_start: 0.4026 (OUTLIER) cc_final: 0.3702 (mpm) REVERT: 6 38 HIS cc_start: 0.6033 (OUTLIER) cc_final: 0.5711 (m90) REVERT: C 237 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: C 297 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8198 (tp30) REVERT: L 203 LYS cc_start: 0.8003 (mttt) cc_final: 0.7200 (mppt) REVERT: L 217 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7757 (t80) REVERT: M 49 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8443 (mt) REVERT: a 15 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.5550 (mmp-170) REVERT: h 21 SER cc_start: 0.7723 (OUTLIER) cc_final: 0.7317 (m) REVERT: n 24 MET cc_start: 0.8977 (mmp) cc_final: 0.8664 (mmm) outliers start: 28 outliers final: 12 residues processed: 208 average time/residue: 0.6547 time to fit residues: 159.4584 Evaluate side-chains 214 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 6 residue 38 HIS Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 9 residue 7 ILE Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain h residue 19 LEU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 38 HIS Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 39 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.9481 > 50: distance: 79 - 81: 12.584 distance: 81 - 82: 40.422 distance: 81 - 87: 17.286 distance: 82 - 83: 10.034 distance: 82 - 85: 37.273 distance: 83 - 84: 39.135 distance: 83 - 88: 3.614 distance: 85 - 86: 18.635 distance: 86 - 87: 30.338 distance: 88 - 89: 18.731 distance: 89 - 90: 10.633 distance: 89 - 92: 31.804 distance: 90 - 91: 24.213 distance: 90 - 96: 17.023 distance: 92 - 93: 10.948 distance: 92 - 94: 21.530 distance: 93 - 95: 20.065 distance: 96 - 97: 21.838 distance: 97 - 98: 38.414 distance: 97 - 100: 25.429 distance: 98 - 99: 20.734 distance: 98 - 108: 19.783 distance: 100 - 101: 27.518 distance: 101 - 102: 8.911 distance: 101 - 103: 30.784 distance: 102 - 104: 11.650 distance: 103 - 105: 21.619 distance: 104 - 106: 22.873 distance: 105 - 106: 14.011 distance: 106 - 107: 16.216 distance: 108 - 109: 13.164 distance: 109 - 110: 28.267 distance: 109 - 112: 50.346 distance: 110 - 111: 16.411 distance: 112 - 113: 17.039 distance: 113 - 115: 44.454 distance: 116 - 117: 11.427 distance: 117 - 118: 6.130 distance: 118 - 119: 20.409 distance: 118 - 120: 28.059 distance: 120 - 121: 16.905 distance: 121 - 122: 5.421 distance: 121 - 124: 10.967 distance: 122 - 123: 24.480 distance: 122 - 134: 16.415 distance: 123 - 157: 14.100 distance: 124 - 125: 19.204 distance: 125 - 126: 8.654 distance: 125 - 127: 18.515 distance: 126 - 128: 4.514 distance: 127 - 129: 12.119 distance: 127 - 130: 17.568 distance: 128 - 129: 14.035 distance: 129 - 131: 9.214 distance: 130 - 132: 6.850 distance: 131 - 133: 18.488 distance: 132 - 133: 10.837 distance: 134 - 135: 18.937 distance: 135 - 136: 11.010 distance: 135 - 138: 10.099 distance: 136 - 137: 23.018 distance: 136 - 145: 7.207 distance: 137 - 165: 22.217 distance: 138 - 139: 10.891 distance: 139 - 140: 7.615 distance: 139 - 141: 13.980 distance: 140 - 142: 10.022 distance: 141 - 143: 13.954 distance: 142 - 144: 19.492 distance: 143 - 144: 3.055 distance: 145 - 146: 21.145 distance: 146 - 147: 6.497 distance: 147 - 148: 8.685 distance: 147 - 149: 15.421 distance: 148 - 171: 9.480 distance: 149 - 150: 10.786 distance: 150 - 151: 6.112 distance: 150 - 153: 12.787 distance: 151 - 152: 9.081 distance: 151 - 157: 14.621 distance: 152 - 178: 9.462 distance: 153 - 154: 9.655 distance: 153 - 155: 26.997 distance: 154 - 156: 11.110 distance: 157 - 158: 20.004 distance: 158 - 159: 25.745 distance: 158 - 161: 8.211 distance: 159 - 160: 25.237 distance: 160 - 184: 22.382 distance: 161 - 162: 13.135 distance: 161 - 163: 10.239