Starting phenix.real_space_refine on Fri Jun 27 12:05:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pho_17669/06_2025/8pho_17669.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pho_17669/06_2025/8pho_17669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pho_17669/06_2025/8pho_17669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pho_17669/06_2025/8pho_17669.map" model { file = "/net/cci-nas-00/data/ceres_data/8pho_17669/06_2025/8pho_17669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pho_17669/06_2025/8pho_17669.cif" } resolution = 2.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 20400 2.51 5 N 4992 2.21 5 O 6684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32172 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2621 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 311} Chain breaks: 2 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "F" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "J" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "K" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "L" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 9.90, per 1000 atoms: 0.31 Number of scatterers: 32172 At special positions: 0 Unit cell: (170.888, 170.888, 120.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 6684 8.00 N 4992 7.00 C 20400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.72 Conformation dependent library (CDL) restraints added in 3.7 seconds 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7296 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 60 sheets defined 53.9% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL A 32 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU A 93 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 303 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 389 Processing helix chain 'A' and resid 393 through 404 Processing helix chain 'B' and resid 14 through 22 Processing helix chain 'B' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL B 32 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA B 33 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 77 removed outlier: 3.819A pdb=" N ASN B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU B 93 " --> pdb=" O ILE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 303 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 327 through 353 removed outlier: 4.402A pdb=" N LYS B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR B 349 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 389 Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL C 32 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA C 33 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN C 68 " --> pdb=" O ASN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU C 93 " --> pdb=" O ILE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 303 Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 389 Processing helix chain 'C' and resid 393 through 404 Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL D 32 " --> pdb=" O TYR D 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA D 33 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU D 93 " --> pdb=" O ILE D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR D 177 " --> pdb=" O PHE D 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 178 " --> pdb=" O GLU D 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 303 Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS D 347 " --> pdb=" O SER D 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'E' and resid 14 through 22 Processing helix chain 'E' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL E 32 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA E 33 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 77 removed outlier: 3.819A pdb=" N ASN E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU E 93 " --> pdb=" O ILE E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR E 177 " --> pdb=" O PHE E 173 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 178 " --> pdb=" O GLU E 174 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 303 Processing helix chain 'E' and resid 305 through 310 Processing helix chain 'E' and resid 327 through 353 removed outlier: 4.402A pdb=" N LYS E 347 " --> pdb=" O SER E 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR E 349 " --> pdb=" O ASN E 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS E 350 " --> pdb=" O LEU E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 389 Processing helix chain 'E' and resid 393 through 404 Processing helix chain 'F' and resid 14 through 22 Processing helix chain 'F' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL F 32 " --> pdb=" O TYR F 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU F 93 " --> pdb=" O ILE F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR F 177 " --> pdb=" O PHE F 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 178 " --> pdb=" O GLU F 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 303 Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS F 347 " --> pdb=" O SER F 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR F 349 " --> pdb=" O ASN F 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS F 350 " --> pdb=" O LEU F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 389 Processing helix chain 'F' and resid 393 through 404 Processing helix chain 'G' and resid 14 through 22 Processing helix chain 'G' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL G 32 " --> pdb=" O TYR G 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA G 33 " --> pdb=" O ILE G 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN G 68 " --> pdb=" O ASN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU G 93 " --> pdb=" O ILE G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR G 177 " --> pdb=" O PHE G 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 303 Processing helix chain 'G' and resid 305 through 310 Processing helix chain 'G' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS G 347 " --> pdb=" O SER G 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR G 349 " --> pdb=" O ASN G 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS G 350 " --> pdb=" O LEU G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 389 Processing helix chain 'G' and resid 393 through 404 Processing helix chain 'H' and resid 14 through 22 Processing helix chain 'H' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL H 32 " --> pdb=" O TYR H 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA H 33 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU H 37 " --> pdb=" O ALA H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 77 removed outlier: 3.819A pdb=" N ASN H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU H 93 " --> pdb=" O ILE H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 110 No H-bonds generated for 'chain 'H' and resid 108 through 110' Processing helix chain 'H' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR H 177 " --> pdb=" O PHE H 173 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL H 178 " --> pdb=" O GLU H 174 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 303 Processing helix chain 'H' and resid 305 through 310 Processing helix chain 'H' and resid 327 through 353 removed outlier: 4.402A pdb=" N LYS H 347 " --> pdb=" O SER H 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR H 349 " --> pdb=" O ASN H 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS H 350 " --> pdb=" O LEU H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 389 Processing helix chain 'H' and resid 393 through 404 Processing helix chain 'I' and resid 14 through 22 Processing helix chain 'I' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL I 32 " --> pdb=" O TYR I 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA I 33 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU I 37 " --> pdb=" O ALA I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN I 68 " --> pdb=" O ASN I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU I 93 " --> pdb=" O ILE I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 110 No H-bonds generated for 'chain 'I' and resid 108 through 110' Processing helix chain 'I' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR I 177 " --> pdb=" O PHE I 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL I 178 " --> pdb=" O GLU I 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG I 183 " --> pdb=" O GLU I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 303 Processing helix chain 'I' and resid 305 through 310 Processing helix chain 'I' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS I 347 " --> pdb=" O SER I 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR I 349 " --> pdb=" O ASN I 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS I 350 " --> pdb=" O LEU I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 389 Processing helix chain 'I' and resid 393 through 404 Processing helix chain 'J' and resid 14 through 22 Processing helix chain 'J' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL J 32 " --> pdb=" O TYR J 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA J 33 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU J 93 " --> pdb=" O ILE J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 110 No H-bonds generated for 'chain 'J' and resid 108 through 110' Processing helix chain 'J' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR J 177 " --> pdb=" O PHE J 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL J 178 " --> pdb=" O GLU J 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG J 183 " --> pdb=" O GLU J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 303 Processing helix chain 'J' and resid 305 through 310 Processing helix chain 'J' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS J 347 " --> pdb=" O SER J 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR J 349 " --> pdb=" O ASN J 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS J 350 " --> pdb=" O LEU J 346 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 389 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'K' and resid 14 through 22 Processing helix chain 'K' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL K 32 " --> pdb=" O TYR K 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA K 33 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 77 removed outlier: 3.819A pdb=" N ASN K 68 " --> pdb=" O ASN K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU K 93 " --> pdb=" O ILE K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 110 No H-bonds generated for 'chain 'K' and resid 108 through 110' Processing helix chain 'K' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR K 177 " --> pdb=" O PHE K 173 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL K 178 " --> pdb=" O GLU K 174 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG K 183 " --> pdb=" O GLU K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 303 Processing helix chain 'K' and resid 305 through 310 Processing helix chain 'K' and resid 327 through 353 removed outlier: 4.402A pdb=" N LYS K 347 " --> pdb=" O SER K 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR K 349 " --> pdb=" O ASN K 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS K 350 " --> pdb=" O LEU K 346 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 389 Processing helix chain 'K' and resid 393 through 404 Processing helix chain 'L' and resid 14 through 22 Processing helix chain 'L' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL L 32 " --> pdb=" O TYR L 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA L 33 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU L 37 " --> pdb=" O ALA L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU L 93 " --> pdb=" O ILE L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 110 No H-bonds generated for 'chain 'L' and resid 108 through 110' Processing helix chain 'L' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR L 177 " --> pdb=" O PHE L 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL L 178 " --> pdb=" O GLU L 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG L 183 " --> pdb=" O GLU L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 303 Processing helix chain 'L' and resid 305 through 310 Processing helix chain 'L' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS L 347 " --> pdb=" O SER L 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR L 349 " --> pdb=" O ASN L 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS L 350 " --> pdb=" O LEU L 346 " (cutoff:3.500A) Processing helix chain 'L' and resid 365 through 389 Processing helix chain 'L' and resid 393 through 404 Processing sheet with id=1, first strand: chain 'A' and resid 41 through 45 Processing sheet with id=2, first strand: chain 'A' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR A 80 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=4, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=5, first strand: chain 'A' and resid 188 through 193 Processing sheet with id=6, first strand: chain 'B' and resid 41 through 45 Processing sheet with id=7, first strand: chain 'B' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR B 80 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 112 through 113 Processing sheet with id=9, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=10, first strand: chain 'B' and resid 188 through 193 Processing sheet with id=11, first strand: chain 'C' and resid 41 through 45 Processing sheet with id=12, first strand: chain 'C' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR C 80 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 112 through 113 Processing sheet with id=14, first strand: chain 'C' and resid 151 through 152 Processing sheet with id=15, first strand: chain 'C' and resid 188 through 193 Processing sheet with id=16, first strand: chain 'D' and resid 41 through 45 Processing sheet with id=17, first strand: chain 'D' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR D 80 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=19, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=20, first strand: chain 'D' and resid 188 through 193 Processing sheet with id=21, first strand: chain 'E' and resid 41 through 45 Processing sheet with id=22, first strand: chain 'E' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR E 80 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 112 through 113 Processing sheet with id=24, first strand: chain 'E' and resid 151 through 152 Processing sheet with id=25, first strand: chain 'E' and resid 188 through 193 Processing sheet with id=26, first strand: chain 'F' and resid 41 through 45 Processing sheet with id=27, first strand: chain 'F' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR F 80 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'F' and resid 112 through 113 Processing sheet with id=29, first strand: chain 'F' and resid 151 through 152 Processing sheet with id=30, first strand: chain 'F' and resid 188 through 193 Processing sheet with id=31, first strand: chain 'G' and resid 41 through 45 Processing sheet with id=32, first strand: chain 'G' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR G 80 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'G' and resid 112 through 113 Processing sheet with id=34, first strand: chain 'G' and resid 151 through 152 Processing sheet with id=35, first strand: chain 'G' and resid 188 through 193 Processing sheet with id=36, first strand: chain 'H' and resid 41 through 45 Processing sheet with id=37, first strand: chain 'H' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR H 80 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'H' and resid 112 through 113 Processing sheet with id=39, first strand: chain 'H' and resid 151 through 152 Processing sheet with id=40, first strand: chain 'H' and resid 188 through 193 Processing sheet with id=41, first strand: chain 'I' and resid 41 through 45 Processing sheet with id=42, first strand: chain 'I' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR I 80 " --> pdb=" O LEU I 107 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'I' and resid 112 through 113 Processing sheet with id=44, first strand: chain 'I' and resid 151 through 152 Processing sheet with id=45, first strand: chain 'I' and resid 188 through 193 Processing sheet with id=46, first strand: chain 'J' and resid 41 through 45 Processing sheet with id=47, first strand: chain 'J' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR J 80 " --> pdb=" O LEU J 107 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'J' and resid 112 through 113 Processing sheet with id=49, first strand: chain 'J' and resid 151 through 152 Processing sheet with id=50, first strand: chain 'J' and resid 188 through 193 Processing sheet with id=51, first strand: chain 'K' and resid 41 through 45 Processing sheet with id=52, first strand: chain 'K' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR K 80 " --> pdb=" O LEU K 107 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'K' and resid 112 through 113 Processing sheet with id=54, first strand: chain 'K' and resid 151 through 152 Processing sheet with id=55, first strand: chain 'K' and resid 188 through 193 Processing sheet with id=56, first strand: chain 'L' and resid 41 through 45 Processing sheet with id=57, first strand: chain 'L' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR L 80 " --> pdb=" O LEU L 107 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'L' and resid 112 through 113 Processing sheet with id=59, first strand: chain 'L' and resid 151 through 152 Processing sheet with id=60, first strand: chain 'L' and resid 188 through 193 1740 hydrogen bonds defined for protein. 5040 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: 13.68 Time building geometry restraints manager: 9.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9912 1.34 - 1.46: 7388 1.46 - 1.58: 14596 1.58 - 1.70: 0 1.70 - 1.81: 144 Bond restraints: 32040 Sorted by residual: bond pdb=" CB ASN E 394 " pdb=" CG ASN E 394 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.83e+00 bond pdb=" CB ASN B 394 " pdb=" CG ASN B 394 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.83e+00 bond pdb=" CB ASN H 394 " pdb=" CG ASN H 394 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.83e+00 bond pdb=" CB ASN K 394 " pdb=" CG ASN K 394 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.83e+00 bond pdb=" CB ASN J 394 " pdb=" CG ASN J 394 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.77e+00 ... (remaining 32035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 39038 1.20 - 2.40: 3300 2.40 - 3.59: 574 3.59 - 4.79: 180 4.79 - 5.99: 36 Bond angle restraints: 43128 Sorted by residual: angle pdb=" CB ARG J 326 " pdb=" CG ARG J 326 " pdb=" CD ARG J 326 " ideal model delta sigma weight residual 111.30 116.66 -5.36 2.30e+00 1.89e-01 5.43e+00 angle pdb=" CB ARG A 326 " pdb=" CG ARG A 326 " pdb=" CD ARG A 326 " ideal model delta sigma weight residual 111.30 116.66 -5.36 2.30e+00 1.89e-01 5.43e+00 angle pdb=" CB ARG D 326 " pdb=" CG ARG D 326 " pdb=" CD ARG D 326 " ideal model delta sigma weight residual 111.30 116.66 -5.36 2.30e+00 1.89e-01 5.43e+00 angle pdb=" CB ARG G 326 " pdb=" CG ARG G 326 " pdb=" CD ARG G 326 " ideal model delta sigma weight residual 111.30 116.66 -5.36 2.30e+00 1.89e-01 5.43e+00 angle pdb=" CB ARG F 326 " pdb=" CG ARG F 326 " pdb=" CD ARG F 326 " ideal model delta sigma weight residual 111.30 116.66 -5.36 2.30e+00 1.89e-01 5.43e+00 ... (remaining 43123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 17616 16.52 - 33.03: 1296 33.03 - 49.55: 288 49.55 - 66.07: 96 66.07 - 82.58: 60 Dihedral angle restraints: 19356 sinusoidal: 8004 harmonic: 11352 Sorted by residual: dihedral pdb=" CB GLU F 266 " pdb=" CG GLU F 266 " pdb=" CD GLU F 266 " pdb=" OE1 GLU F 266 " ideal model delta sinusoidal sigma weight residual 0.00 82.58 -82.58 1 3.00e+01 1.11e-03 9.29e+00 dihedral pdb=" CB GLU L 266 " pdb=" CG GLU L 266 " pdb=" CD GLU L 266 " pdb=" OE1 GLU L 266 " ideal model delta sinusoidal sigma weight residual 0.00 82.58 -82.58 1 3.00e+01 1.11e-03 9.29e+00 dihedral pdb=" CB GLU I 266 " pdb=" CG GLU I 266 " pdb=" CD GLU I 266 " pdb=" OE1 GLU I 266 " ideal model delta sinusoidal sigma weight residual 0.00 82.58 -82.58 1 3.00e+01 1.11e-03 9.29e+00 ... (remaining 19353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4210 0.085 - 0.171: 482 0.171 - 0.256: 12 0.256 - 0.341: 48 0.341 - 0.427: 12 Chirality restraints: 4764 Sorted by residual: chirality pdb=" CG LEU I 115 " pdb=" CB LEU I 115 " pdb=" CD1 LEU I 115 " pdb=" CD2 LEU I 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CG LEU L 115 " pdb=" CB LEU L 115 " pdb=" CD1 LEU L 115 " pdb=" CD2 LEU L 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CG LEU F 115 " pdb=" CB LEU F 115 " pdb=" CD1 LEU F 115 " pdb=" CD2 LEU F 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 4761 not shown) Planarity restraints: 5448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN L 150 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" CG ASN L 150 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN L 150 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN L 150 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 150 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" CG ASN I 150 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN I 150 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN I 150 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 150 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" CG ASN C 150 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN C 150 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN C 150 " -0.016 2.00e-02 2.50e+03 ... (remaining 5445 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 396 2.68 - 3.24: 30172 3.24 - 3.79: 50584 3.79 - 4.35: 72748 4.35 - 4.90: 113646 Nonbonded interactions: 267546 Sorted by model distance: nonbonded pdb=" O HOH G 502 " pdb=" O HOH G 533 " model vdw 2.128 3.040 nonbonded pdb=" O HOH D 502 " pdb=" O HOH D 533 " model vdw 2.128 3.040 nonbonded pdb=" O HOH J 502 " pdb=" O HOH J 533 " model vdw 2.128 3.040 nonbonded pdb=" O HOH A 502 " pdb=" O HOH A 533 " model vdw 2.128 3.040 nonbonded pdb=" O HOH I 502 " pdb=" O HOH I 533 " model vdw 2.128 3.040 ... (remaining 267541 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: 0.26 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 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: 0.030 Extract box with map and model: 1.380 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 62.090 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 : 0.005 0.044 32040 Z= 0.212 Angle : 0.766 5.989 43128 Z= 0.406 Chirality : 0.062 0.427 4764 Planarity : 0.010 0.072 5448 Dihedral : 13.642 82.583 12060 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.13), residues: 3732 helix: 0.55 (0.11), residues: 2004 sheet: -0.38 (0.21), residues: 624 loop : -0.58 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.024 0.007 HIS E 48 PHE 0.034 0.008 PHE I 358 TYR 0.036 0.008 TYR D 192 ARG 0.023 0.005 ARG I 157 Details of bonding type rmsd hydrogen bonds : bond 0.15495 ( 1740) hydrogen bonds : angle 7.01158 ( 5040) covalent geometry : bond 0.00457 (32040) covalent geometry : angle 0.76648 (43128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 696 time to evaluate : 3.637 Fit side-chains REVERT: A 181 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7871 (tm-30) REVERT: A 326 ARG cc_start: 0.7114 (mmt90) cc_final: 0.6818 (mmt180) REVERT: A 382 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7647 (mmmt) REVERT: A 403 LYS cc_start: 0.6967 (ptmt) cc_final: 0.6558 (ptmt) REVERT: B 382 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7689 (mptt) REVERT: C 121 HIS cc_start: 0.7593 (p-80) cc_final: 0.7383 (p-80) REVERT: C 185 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7307 (mp0) REVERT: C 363 MET cc_start: 0.7463 (mtp) cc_final: 0.7080 (mmt) REVERT: C 382 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7606 (mmmt) REVERT: D 181 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7869 (tm-30) REVERT: D 326 ARG cc_start: 0.7114 (mmt90) cc_final: 0.6818 (mmt180) REVERT: D 382 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7646 (mmmt) REVERT: D 403 LYS cc_start: 0.6963 (ptmt) cc_final: 0.6555 (ptmt) REVERT: E 382 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7690 (mptt) REVERT: F 121 HIS cc_start: 0.7593 (p-80) cc_final: 0.7384 (p-80) REVERT: F 185 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7308 (mp0) REVERT: F 363 MET cc_start: 0.7467 (mtp) cc_final: 0.7082 (mmt) REVERT: F 382 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7608 (mmmt) REVERT: G 181 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7868 (tm-30) REVERT: G 326 ARG cc_start: 0.7114 (mmt90) cc_final: 0.6819 (mmt180) REVERT: G 382 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7646 (mmmt) REVERT: G 403 LYS cc_start: 0.6964 (ptmt) cc_final: 0.6556 (ptmt) REVERT: H 382 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7689 (mptt) REVERT: I 121 HIS cc_start: 0.7592 (p-80) cc_final: 0.7382 (p-80) REVERT: I 185 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7308 (mp0) REVERT: I 363 MET cc_start: 0.7466 (mtp) cc_final: 0.7082 (mmt) REVERT: I 382 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7609 (mmmt) REVERT: J 181 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7868 (tm-30) REVERT: J 326 ARG cc_start: 0.7115 (mmt90) cc_final: 0.6820 (mmt180) REVERT: J 382 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7644 (mmmt) REVERT: J 403 LYS cc_start: 0.6964 (ptmt) cc_final: 0.6556 (ptmt) REVERT: K 382 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7689 (mptt) REVERT: L 121 HIS cc_start: 0.7591 (p-80) cc_final: 0.7382 (p-80) REVERT: L 185 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7306 (mp0) REVERT: L 363 MET cc_start: 0.7465 (mtp) cc_final: 0.7081 (mmt) REVERT: L 382 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7610 (mmmt) outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 1.9709 time to fit residues: 1550.8462 Evaluate side-chains 492 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 4.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.9639 > 50: distance: 30 - 53: 26.425 distance: 48 - 53: 23.682 distance: 53 - 54: 12.496 distance: 54 - 55: 31.931 distance: 54 - 57: 29.132 distance: 55 - 56: 41.939 distance: 55 - 59: 23.057 distance: 57 - 58: 20.568 distance: 59 - 60: 43.843 distance: 60 - 61: 14.533 distance: 60 - 63: 24.645 distance: 61 - 62: 42.717 distance: 61 - 70: 44.872 distance: 63 - 64: 24.836 distance: 64 - 65: 28.449 distance: 64 - 66: 39.242 distance: 65 - 67: 18.853 distance: 66 - 68: 59.964 distance: 67 - 69: 9.978 distance: 68 - 69: 36.023 distance: 70 - 71: 23.433 distance: 71 - 72: 17.840 distance: 71 - 74: 12.291 distance: 72 - 73: 13.284 distance: 72 - 78: 4.800 distance: 74 - 75: 38.262 distance: 75 - 76: 44.048 distance: 75 - 77: 44.142 distance: 78 - 79: 5.955 distance: 79 - 80: 4.465 distance: 79 - 82: 8.405 distance: 80 - 81: 16.918 distance: 80 - 87: 12.754 distance: 87 - 88: 13.001 distance: 88 - 89: 27.990 distance: 88 - 91: 19.719 distance: 89 - 90: 17.403 distance: 89 - 96: 21.154 distance: 91 - 92: 21.159 distance: 92 - 93: 7.542 distance: 93 - 94: 8.201 distance: 93 - 95: 6.013 distance: 96 - 97: 13.234 distance: 97 - 98: 17.389 distance: 97 - 100: 19.996 distance: 98 - 99: 29.005 distance: 98 - 101: 27.959 distance: 101 - 102: 10.615 distance: 102 - 103: 21.569 distance: 102 - 105: 13.682 distance: 103 - 104: 20.333 distance: 103 - 110: 22.621 distance: 105 - 106: 5.687 distance: 110 - 111: 7.280 distance: 111 - 112: 19.078 distance: 112 - 113: 23.981 distance: 112 - 114: 22.015 distance: 114 - 115: 6.433 distance: 115 - 116: 3.211 distance: 115 - 118: 4.788 distance: 116 - 117: 3.111 distance: 118 - 119: 17.334 distance: 119 - 120: 12.119 distance: 119 - 121: 18.370