Starting phenix.real_space_refine on Thu Feb 5 02:24:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e4i_47511/02_2026/9e4i_47511.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e4i_47511/02_2026/9e4i_47511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e4i_47511/02_2026/9e4i_47511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e4i_47511/02_2026/9e4i_47511.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e4i_47511/02_2026/9e4i_47511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e4i_47511/02_2026/9e4i_47511.map" } resolution = 2.33 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= 0.001 sd= 0.006 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 156 5.16 5 C 9012 2.51 5 N 2403 2.21 5 O 2670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14241 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3305 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 394} Chain: "B" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3305 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 394} Chain: "C" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3305 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 394} Chain: "D" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 499 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 113} Chain: "F" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 499 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 113} Chain: "H" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 499 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 113} Time building chain proxies: 3.10, per 1000 atoms: 0.22 Number of scatterers: 14241 At special positions: 0 Unit cell: (134.31, 140.008, 134.31, 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 156 16.00 O 2670 8.00 N 2403 7.00 C 9012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 314 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 58 " distance=2.03 Simple disulfide: pdb=" SG CYS D 17 " - pdb=" SG CYS D 41 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 54 " distance=2.03 Simple disulfide: pdb=" SG CYS E 11 " - pdb=" SG CYS E 70 " distance=2.03 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 118 " distance=2.03 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 43 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 100 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 86 " distance=2.03 Simple disulfide: pdb=" SG CYS E 79 " - pdb=" SG CYS E 91 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 17 " - pdb=" SG CYS F 41 " distance=2.03 Simple disulfide: pdb=" SG CYS F 33 " - pdb=" SG CYS F 54 " distance=2.03 Simple disulfide: pdb=" SG CYS G 11 " - pdb=" SG CYS G 70 " distance=2.03 Simple disulfide: pdb=" SG CYS G 25 " - pdb=" SG CYS G 118 " distance=2.03 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS G 43 " distance=2.03 Simple disulfide: pdb=" SG CYS G 42 " - pdb=" SG CYS G 100 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 59 " - pdb=" SG CYS G 86 " distance=2.03 Simple disulfide: pdb=" SG CYS G 79 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 7 " - pdb=" SG CYS H 58 " distance=2.03 Simple disulfide: pdb=" SG CYS H 17 " - pdb=" SG CYS H 41 " distance=2.03 Simple disulfide: pdb=" SG CYS H 33 " - pdb=" SG CYS H 54 " distance=2.03 Simple disulfide: pdb=" SG CYS I 11 " - pdb=" SG CYS I 70 " distance=2.03 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 118 " distance=2.03 Simple disulfide: pdb=" SG CYS I 27 " - pdb=" SG CYS I 43 " distance=2.03 Simple disulfide: pdb=" SG CYS I 42 " - pdb=" SG CYS I 100 " distance=2.03 Simple disulfide: pdb=" SG CYS I 49 " - pdb=" SG CYS I 93 " distance=2.03 Simple disulfide: pdb=" SG CYS I 59 " - pdb=" SG CYS I 86 " distance=2.03 Simple disulfide: pdb=" SG CYS I 79 " - pdb=" SG CYS I 91 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 460.0 milliseconds 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3354 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 15 sheets defined 44.8% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 40 through 69 removed outlier: 3.903A pdb=" N ALA A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.664A pdb=" N ALA A 130 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.914A pdb=" N ASP A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 203 " --> pdb=" O GLY A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 203' Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.556A pdb=" N ASN A 216 " --> pdb=" O GLY A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 427 through 451 removed outlier: 4.148A pdb=" N LEU A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 70 removed outlier: 3.527A pdb=" N LEU B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.789A pdb=" N ASP B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY B 203 " --> pdb=" O GLY B 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 199 through 203' Processing helix chain 'B' and resid 213 through 216 removed outlier: 3.546A pdb=" N ASN B 216 " --> pdb=" O GLY B 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 213 through 216' Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 338 through 345 Processing helix chain 'B' and resid 345 through 356 Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 397 through 404 Processing helix chain 'B' and resid 427 through 447 Processing helix chain 'B' and resid 447 through 452 Processing helix chain 'C' and resid 42 through 70 removed outlier: 4.523A pdb=" N TRP C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.703A pdb=" N ALA C 130 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 199 through 203 removed outlier: 4.074A pdb=" N ASP C 202 " --> pdb=" O SER C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 removed outlier: 3.553A pdb=" N ASN C 216 " --> pdb=" O GLY C 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 213 through 216' Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 338 through 345 Processing helix chain 'C' and resid 345 through 355 Processing helix chain 'C' and resid 386 through 394 Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.508A pdb=" N GLY C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 451 removed outlier: 3.913A pdb=" N LEU C 451 " --> pdb=" O ILE C 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 50 through 59 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 16 through 21 removed outlier: 4.037A pdb=" N PHE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 56 removed outlier: 3.621A pdb=" N CYS E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 Processing helix chain 'E' and resid 84 through 104 Processing helix chain 'E' and resid 107 through 111 Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 50 through 59 Processing helix chain 'G' and resid 2 through 13 Processing helix chain 'G' and resid 16 through 21 removed outlier: 4.130A pdb=" N PHE G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 56 Processing helix chain 'G' and resid 73 through 77 Processing helix chain 'G' and resid 84 through 104 Processing helix chain 'G' and resid 107 through 111 Processing helix chain 'G' and resid 114 through 118 Processing helix chain 'H' and resid 4 through 9 Processing helix chain 'H' and resid 50 through 59 Processing helix chain 'I' and resid 2 through 13 Processing helix chain 'I' and resid 16 through 21 removed outlier: 4.035A pdb=" N PHE I 20 " --> pdb=" O VAL I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 56 Processing helix chain 'I' and resid 73 through 77 Processing helix chain 'I' and resid 84 through 104 removed outlier: 3.646A pdb=" N THR I 103 " --> pdb=" O LEU I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 111 Processing helix chain 'I' and resid 114 through 118 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 80 removed outlier: 3.577A pdb=" N GLU A 418 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE A 269 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP A 223 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU A 169 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 80 removed outlier: 3.577A pdb=" N GLU A 418 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189 removed outlier: 7.050A pdb=" N LYS A 193 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASN A 94 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 80 removed outlier: 4.100A pdb=" N PHE B 269 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP B 223 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU B 169 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 80 Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'B' and resid 184 through 189 removed outlier: 7.066A pdb=" N LYS B 193 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASN B 94 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 80 removed outlier: 3.653A pdb=" N GLU C 418 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE C 269 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP C 223 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU C 169 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 73 through 80 removed outlier: 3.653A pdb=" N GLU C 418 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB3, first strand: chain 'C' and resid 184 through 189 removed outlier: 7.043A pdb=" N LYS C 193 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASN C 94 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 21 through 27 Processing sheet with id=AB5, first strand: chain 'F' and resid 21 through 27 Processing sheet with id=AB6, first strand: chain 'H' and resid 21 through 27 735 hydrogen bonds defined for protein. 1992 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: 1.83 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4698 1.35 - 1.47: 3544 1.47 - 1.59: 6134 1.59 - 1.70: 0 1.70 - 1.82: 198 Bond restraints: 14574 Sorted by residual: bond pdb=" C HIS A 329 " pdb=" N MET A 330 " ideal model delta sigma weight residual 1.331 1.314 0.017 2.07e-02 2.33e+03 6.98e-01 bond pdb=" CA LEU C 451 " pdb=" C LEU C 451 " ideal model delta sigma weight residual 1.531 1.522 0.009 1.12e-02 7.97e+03 6.01e-01 bond pdb=" CA LEU C 451 " pdb=" CB LEU C 451 " ideal model delta sigma weight residual 1.523 1.530 -0.007 1.21e-02 6.83e+03 3.24e-01 bond pdb=" CB PCA H 1 " pdb=" CG PCA H 1 " ideal model delta sigma weight residual 1.525 1.514 0.011 2.00e-02 2.50e+03 3.20e-01 bond pdb=" CB PCA D 1 " pdb=" CG PCA D 1 " ideal model delta sigma weight residual 1.525 1.514 0.011 2.00e-02 2.50e+03 3.01e-01 ... (remaining 14569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 19537 1.86 - 3.72: 143 3.72 - 5.58: 21 5.58 - 7.43: 0 7.43 - 9.29: 6 Bond angle restraints: 19707 Sorted by residual: angle pdb=" CA PCA F 1 " pdb=" N PCA F 1 " pdb=" CD PCA F 1 " ideal model delta sigma weight residual 114.17 104.88 9.29 3.00e+00 1.11e-01 9.60e+00 angle pdb=" CA PCA H 1 " pdb=" N PCA H 1 " pdb=" CD PCA H 1 " ideal model delta sigma weight residual 114.17 104.97 9.20 3.00e+00 1.11e-01 9.41e+00 angle pdb=" CA PCA D 1 " pdb=" N PCA D 1 " pdb=" CD PCA D 1 " ideal model delta sigma weight residual 114.17 105.07 9.10 3.00e+00 1.11e-01 9.20e+00 angle pdb=" N PCA H 1 " pdb=" CD PCA H 1 " pdb=" CG PCA H 1 " ideal model delta sigma weight residual 107.23 115.63 -8.40 3.00e+00 1.11e-01 7.84e+00 angle pdb=" N PCA F 1 " pdb=" CD PCA F 1 " pdb=" CG PCA F 1 " ideal model delta sigma weight residual 107.23 115.59 -8.36 3.00e+00 1.11e-01 7.77e+00 ... (remaining 19702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8171 17.69 - 35.37: 564 35.37 - 53.06: 111 53.06 - 70.75: 28 70.75 - 88.43: 9 Dihedral angle restraints: 8883 sinusoidal: 3675 harmonic: 5208 Sorted by residual: dihedral pdb=" CA PHE A 257 " pdb=" C PHE A 257 " pdb=" N ILE A 258 " pdb=" CA ILE A 258 " ideal model delta harmonic sigma weight residual -180.00 -155.56 -24.44 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA PHE B 257 " pdb=" C PHE B 257 " pdb=" N ILE B 258 " pdb=" CA ILE B 258 " ideal model delta harmonic sigma weight residual -180.00 -158.18 -21.82 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA PHE C 257 " pdb=" C PHE C 257 " pdb=" N ILE C 258 " pdb=" CA ILE C 258 " ideal model delta harmonic sigma weight residual 180.00 -159.03 -20.97 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 8880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1247 0.027 - 0.053: 549 0.053 - 0.080: 190 0.080 - 0.106: 93 0.106 - 0.133: 18 Chirality restraints: 2097 Sorted by residual: chirality pdb=" CA ILE C 410 " pdb=" N ILE C 410 " pdb=" C ILE C 410 " pdb=" CB ILE C 410 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE B 410 " pdb=" N ILE B 410 " pdb=" C ILE B 410 " pdb=" CB ILE B 410 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE A 410 " pdb=" N ILE A 410 " pdb=" C ILE A 410 " pdb=" CB ILE A 410 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 2094 not shown) Planarity restraints: 2589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 257 " -0.015 2.00e-02 2.50e+03 1.35e-02 3.19e+00 pdb=" CG PHE A 257 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 257 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 257 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 257 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 257 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 257 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 284 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO C 285 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 285 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 285 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 284 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.45e+00 pdb=" N PRO B 285 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 285 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 285 " 0.017 5.00e-02 4.00e+02 ... (remaining 2586 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2526 2.77 - 3.30: 13667 3.30 - 3.83: 24440 3.83 - 4.37: 30452 4.37 - 4.90: 50843 Nonbonded interactions: 121928 Sorted by model distance: nonbonded pdb=" OG1 THR A 236 " pdb=" OG1 THR A 239 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR C 236 " pdb=" OG1 THR C 239 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR B 236 " pdb=" OG1 THR B 239 " model vdw 2.264 3.040 nonbonded pdb=" OD1 ASP E 31 " pdb=" NZ LYS E 47 " model vdw 2.280 3.120 nonbonded pdb=" OE2 GLU A 321 " pdb=" OH TYR A 360 " model vdw 2.283 3.040 ... (remaining 121923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.220 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.770 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 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 : 0.002 0.025 14625 Z= 0.096 Angle : 0.472 9.294 19809 Z= 0.235 Chirality : 0.037 0.133 2097 Planarity : 0.003 0.031 2589 Dihedral : 12.896 88.433 5376 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: 1.30 (0.20), residues: 1752 helix: 1.46 (0.21), residues: 573 sheet: 0.20 (0.27), residues: 318 loop : 0.92 (0.23), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 3 TYR 0.009 0.001 TYR C 342 PHE 0.031 0.001 PHE A 257 TRP 0.020 0.001 TRP A 46 HIS 0.002 0.000 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00218 (14574) covalent geometry : angle 0.46548 (19707) SS BOND : bond 0.00150 ( 51) SS BOND : angle 1.18178 ( 102) hydrogen bonds : bond 0.19988 ( 698) hydrogen bonds : angle 8.04290 ( 1992) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 418 GLU cc_start: 0.7991 (mp0) cc_final: 0.7434 (mp0) REVERT: B 168 MET cc_start: 0.8992 (mtm) cc_final: 0.8596 (mtm) REVERT: C 51 LEU cc_start: 0.9494 (mm) cc_final: 0.9225 (mm) REVERT: C 219 GLU cc_start: 0.8575 (tt0) cc_final: 0.7771 (tm-30) REVERT: C 293 VAL cc_start: 0.7491 (m) cc_final: 0.7063 (t) REVERT: C 321 GLU cc_start: 0.8498 (tt0) cc_final: 0.8214 (tp30) REVERT: C 399 GLN cc_start: 0.8754 (tt0) cc_final: 0.8527 (tt0) REVERT: C 418 GLU cc_start: 0.7920 (pm20) cc_final: 0.7612 (pm20) REVERT: E 48 GLN cc_start: 0.9007 (mt0) cc_final: 0.8689 (mt0) REVERT: E 64 MET cc_start: 0.9157 (ptm) cc_final: 0.8906 (ptp) REVERT: E 88 ASN cc_start: 0.8632 (t0) cc_final: 0.8358 (m-40) REVERT: E 117 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8319 (mmm-85) REVERT: G 103 THR cc_start: 0.9129 (m) cc_final: 0.8909 (p) REVERT: G 107 ASN cc_start: 0.8048 (m110) cc_final: 0.7823 (m-40) REVERT: H 53 GLU cc_start: 0.8659 (tp30) cc_final: 0.8320 (tp30) REVERT: I 52 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7280 (tm-30) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.6536 time to fit residues: 190.7426 Evaluate side-chains 192 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 139 GLN A 329 HIS B 84 GLN B 324 ASN B 358 GLN B 399 GLN B 438 GLN C 66 GLN E 1 ASN E 46 GLN G 107 ASN I 110 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.086315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.057658 restraints weight = 27595.294| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.50 r_work: 0.2734 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14625 Z= 0.140 Angle : 0.583 8.895 19809 Z= 0.297 Chirality : 0.041 0.155 2097 Planarity : 0.004 0.040 2589 Dihedral : 4.563 21.957 1956 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.34 % Allowed : 8.41 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: 1.41 (0.20), residues: 1752 helix: 1.95 (0.21), residues: 594 sheet: -0.03 (0.25), residues: 327 loop : 0.77 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 121 TYR 0.010 0.001 TYR A 417 PHE 0.023 0.001 PHE A 257 TRP 0.012 0.001 TRP A 46 HIS 0.003 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00310 (14574) covalent geometry : angle 0.57760 (19707) SS BOND : bond 0.00270 ( 51) SS BOND : angle 1.22708 ( 102) hydrogen bonds : bond 0.04302 ( 698) hydrogen bonds : angle 5.91885 ( 1992) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8243 (mp0) cc_final: 0.7680 (mp0) REVERT: B 168 MET cc_start: 0.9025 (mtm) cc_final: 0.8719 (mtm) REVERT: C 182 GLU cc_start: 0.8662 (mp0) cc_final: 0.8228 (mp0) REVERT: C 219 GLU cc_start: 0.8856 (tt0) cc_final: 0.7936 (tm-30) REVERT: C 293 VAL cc_start: 0.7659 (m) cc_final: 0.7312 (t) REVERT: C 321 GLU cc_start: 0.8756 (tt0) cc_final: 0.8480 (tp30) REVERT: C 418 GLU cc_start: 0.8049 (pm20) cc_final: 0.7767 (pm20) REVERT: E 41 ARG cc_start: 0.8320 (mtm-85) cc_final: 0.8100 (mtm-85) REVERT: E 55 LYS cc_start: 0.9224 (mptt) cc_final: 0.8964 (mmtm) REVERT: E 64 MET cc_start: 0.9206 (ptm) cc_final: 0.8928 (ptp) REVERT: G 55 LYS cc_start: 0.9435 (ttmm) cc_final: 0.9145 (mppt) REVERT: G 60 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8497 (ptmt) REVERT: I 30 ARG cc_start: 0.8288 (mtp180) cc_final: 0.8028 (mtm180) REVERT: I 52 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7865 (tm-30) outliers start: 21 outliers final: 8 residues processed: 228 average time/residue: 0.6288 time to fit residues: 155.1178 Evaluate side-chains 211 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 202 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 173 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 140 optimal weight: 0.0060 chunk 59 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.085287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.056735 restraints weight = 27830.814| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.53 r_work: 0.2704 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14625 Z= 0.179 Angle : 0.578 10.029 19809 Z= 0.293 Chirality : 0.041 0.162 2097 Planarity : 0.003 0.032 2589 Dihedral : 4.710 22.835 1956 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.17 % Allowed : 9.43 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: 1.47 (0.20), residues: 1752 helix: 1.95 (0.21), residues: 618 sheet: -0.17 (0.26), residues: 303 loop : 0.87 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 121 TYR 0.012 0.001 TYR H 24 PHE 0.015 0.001 PHE A 257 TRP 0.008 0.001 TRP E 17 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00414 (14574) covalent geometry : angle 0.57162 (19707) SS BOND : bond 0.00457 ( 51) SS BOND : angle 1.34666 ( 102) hydrogen bonds : bond 0.04066 ( 698) hydrogen bonds : angle 5.59102 ( 1992) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8297 (mp0) cc_final: 0.7753 (mp0) REVERT: B 46 TRP cc_start: 0.7646 (m100) cc_final: 0.7357 (m100) REVERT: B 168 MET cc_start: 0.9076 (mtm) cc_final: 0.8778 (mtm) REVERT: C 133 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8793 (pttm) REVERT: C 182 GLU cc_start: 0.8662 (mp0) cc_final: 0.8157 (mp0) REVERT: C 219 GLU cc_start: 0.8896 (tt0) cc_final: 0.7976 (tm-30) REVERT: C 293 VAL cc_start: 0.7604 (m) cc_final: 0.7271 (t) REVERT: C 321 GLU cc_start: 0.8775 (tt0) cc_final: 0.8516 (tp30) REVERT: C 418 GLU cc_start: 0.8095 (pm20) cc_final: 0.7784 (pm20) REVERT: E 41 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8105 (mtm-85) REVERT: E 55 LYS cc_start: 0.9198 (mptt) cc_final: 0.8910 (mmtm) REVERT: E 64 MET cc_start: 0.9197 (ptm) cc_final: 0.8979 (ptp) REVERT: G 41 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.7699 (mtm-85) REVERT: H 17 CYS cc_start: 0.7597 (m) cc_final: 0.7184 (m) REVERT: I 30 ARG cc_start: 0.8299 (mtp180) cc_final: 0.7999 (mtm180) REVERT: I 52 GLU cc_start: 0.8461 (tm-30) cc_final: 0.7930 (tm-30) REVERT: I 60 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8406 (ptmt) outliers start: 34 outliers final: 18 residues processed: 223 average time/residue: 0.6565 time to fit residues: 158.1602 Evaluate side-chains 217 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 77 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 22 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 151 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 132 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN B 329 HIS E 1 ASN G 46 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.086123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.057668 restraints weight = 27909.489| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.52 r_work: 0.2739 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14625 Z= 0.110 Angle : 0.537 10.370 19809 Z= 0.269 Chirality : 0.039 0.175 2097 Planarity : 0.003 0.031 2589 Dihedral : 4.472 21.051 1956 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.72 % Allowed : 10.52 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: 1.53 (0.20), residues: 1752 helix: 2.06 (0.21), residues: 618 sheet: -0.18 (0.26), residues: 303 loop : 0.84 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 121 TYR 0.009 0.001 TYR A 417 PHE 0.011 0.001 PHE F 6 TRP 0.006 0.001 TRP G 17 HIS 0.005 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00245 (14574) covalent geometry : angle 0.53313 (19707) SS BOND : bond 0.00254 ( 51) SS BOND : angle 1.01794 ( 102) hydrogen bonds : bond 0.03442 ( 698) hydrogen bonds : angle 5.29548 ( 1992) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8022 (mmm) cc_final: 0.7690 (mmm) REVERT: A 418 GLU cc_start: 0.8270 (mp0) cc_final: 0.7752 (mp0) REVERT: B 46 TRP cc_start: 0.7593 (m100) cc_final: 0.7302 (m100) REVERT: B 168 MET cc_start: 0.9081 (mtm) cc_final: 0.8694 (mtm) REVERT: C 70 HIS cc_start: 0.8464 (m-70) cc_final: 0.7379 (t-90) REVERT: C 133 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8855 (pttm) REVERT: C 182 GLU cc_start: 0.8672 (mp0) cc_final: 0.8320 (mp0) REVERT: C 219 GLU cc_start: 0.8856 (tt0) cc_final: 0.7941 (tm-30) REVERT: C 293 VAL cc_start: 0.7502 (m) cc_final: 0.7158 (t) REVERT: C 321 GLU cc_start: 0.8746 (tt0) cc_final: 0.8469 (tp30) REVERT: C 418 GLU cc_start: 0.8071 (pm20) cc_final: 0.7756 (pm20) REVERT: E 41 ARG cc_start: 0.8440 (mtm-85) cc_final: 0.8169 (mtm-85) REVERT: E 52 GLU cc_start: 0.8781 (tt0) cc_final: 0.8418 (tm-30) REVERT: E 55 LYS cc_start: 0.9160 (mptt) cc_final: 0.8879 (mmtm) REVERT: E 108 ARG cc_start: 0.7985 (tpp80) cc_final: 0.7452 (tpp-160) REVERT: F 51 MET cc_start: 0.8270 (ttp) cc_final: 0.8069 (tpp) REVERT: G 41 ARG cc_start: 0.8280 (mtm-85) cc_final: 0.8075 (mtm-85) REVERT: I 30 ARG cc_start: 0.8261 (mtp180) cc_final: 0.7929 (mtm180) REVERT: I 52 GLU cc_start: 0.8497 (tm-30) cc_final: 0.7880 (tm-30) REVERT: I 60 LYS cc_start: 0.8659 (ptpp) cc_final: 0.8446 (ptmt) outliers start: 27 outliers final: 13 residues processed: 229 average time/residue: 0.6416 time to fit residues: 159.2356 Evaluate side-chains 211 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 49 CYS Chi-restraints excluded: chain I residue 77 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 24 optimal weight: 0.0040 chunk 153 optimal weight: 0.0980 chunk 9 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 45 GLN E 33 ASN G 46 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.086443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.058033 restraints weight = 27821.365| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.53 r_work: 0.2752 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14625 Z= 0.109 Angle : 0.541 10.949 19809 Z= 0.269 Chirality : 0.039 0.166 2097 Planarity : 0.003 0.031 2589 Dihedral : 4.419 20.808 1956 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.78 % Allowed : 11.66 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: 1.58 (0.20), residues: 1752 helix: 2.18 (0.21), residues: 618 sheet: -0.11 (0.26), residues: 309 loop : 0.80 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 56 TYR 0.008 0.001 TYR H 24 PHE 0.011 0.001 PHE F 6 TRP 0.006 0.001 TRP E 17 HIS 0.002 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00246 (14574) covalent geometry : angle 0.53638 (19707) SS BOND : bond 0.00212 ( 51) SS BOND : angle 1.16599 ( 102) hydrogen bonds : bond 0.03294 ( 698) hydrogen bonds : angle 5.13429 ( 1992) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8258 (mp0) cc_final: 0.7750 (mp0) REVERT: A 439 MET cc_start: 0.8831 (ttt) cc_final: 0.8600 (ptm) REVERT: B 46 TRP cc_start: 0.7565 (m100) cc_final: 0.7256 (m100) REVERT: B 399 GLN cc_start: 0.8396 (tt0) cc_final: 0.8155 (tt0) REVERT: C 70 HIS cc_start: 0.8450 (m-70) cc_final: 0.7356 (t-90) REVERT: C 133 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8862 (ptmm) REVERT: C 219 GLU cc_start: 0.8877 (tt0) cc_final: 0.7961 (tm-30) REVERT: C 321 GLU cc_start: 0.8773 (tt0) cc_final: 0.8490 (tp30) REVERT: C 418 GLU cc_start: 0.8047 (pm20) cc_final: 0.7720 (pm20) REVERT: E 41 ARG cc_start: 0.8454 (mtm-85) cc_final: 0.8194 (mtm-85) REVERT: E 55 LYS cc_start: 0.9175 (mptt) cc_final: 0.8888 (mmtm) REVERT: E 64 MET cc_start: 0.9168 (ptp) cc_final: 0.8888 (ptp) REVERT: E 108 ARG cc_start: 0.8089 (tpp80) cc_final: 0.7645 (tpp-160) REVERT: G 41 ARG cc_start: 0.8299 (mtm-85) cc_final: 0.8088 (mtm-85) REVERT: G 60 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8415 (ptmt) REVERT: I 30 ARG cc_start: 0.8279 (mtp180) cc_final: 0.8002 (mtm110) REVERT: I 52 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7844 (tm-30) outliers start: 28 outliers final: 17 residues processed: 229 average time/residue: 0.7060 time to fit residues: 174.9467 Evaluate side-chains 215 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 49 CYS Chi-restraints excluded: chain I residue 77 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 54 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 160 optimal weight: 0.3980 chunk 167 optimal weight: 9.9990 chunk 75 optimal weight: 0.0370 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 overall best weight: 0.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN E 33 ASN G 46 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.086226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.057861 restraints weight = 27857.210| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.52 r_work: 0.2748 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14625 Z= 0.113 Angle : 0.556 11.125 19809 Z= 0.274 Chirality : 0.039 0.194 2097 Planarity : 0.003 0.031 2589 Dihedral : 4.409 21.596 1956 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.72 % Allowed : 12.81 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: 1.59 (0.20), residues: 1752 helix: 2.23 (0.21), residues: 618 sheet: -0.11 (0.26), residues: 309 loop : 0.78 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 56 TYR 0.008 0.001 TYR A 305 PHE 0.012 0.001 PHE F 6 TRP 0.006 0.001 TRP E 17 HIS 0.003 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00262 (14574) covalent geometry : angle 0.54951 (19707) SS BOND : bond 0.00253 ( 51) SS BOND : angle 1.29965 ( 102) hydrogen bonds : bond 0.03245 ( 698) hydrogen bonds : angle 5.07785 ( 1992) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8288 (mp0) cc_final: 0.7813 (mp0) REVERT: A 439 MET cc_start: 0.8802 (ttt) cc_final: 0.8574 (ptm) REVERT: B 46 TRP cc_start: 0.7571 (m100) cc_final: 0.7281 (m100) REVERT: B 148 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8866 (mmtm) REVERT: B 399 GLN cc_start: 0.8376 (tt0) cc_final: 0.8140 (tt0) REVERT: C 70 HIS cc_start: 0.8477 (m-70) cc_final: 0.7407 (t-90) REVERT: C 133 LYS cc_start: 0.9161 (mtmm) cc_final: 0.8880 (ptmm) REVERT: C 219 GLU cc_start: 0.8866 (tt0) cc_final: 0.7942 (tm-30) REVERT: C 321 GLU cc_start: 0.8761 (tt0) cc_final: 0.8500 (tp30) REVERT: C 418 GLU cc_start: 0.8064 (pm20) cc_final: 0.7716 (pm20) REVERT: E 41 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8226 (mtm-85) REVERT: E 52 GLU cc_start: 0.8820 (tt0) cc_final: 0.8507 (tp30) REVERT: E 55 LYS cc_start: 0.9175 (mptt) cc_final: 0.8898 (mmtm) REVERT: E 64 MET cc_start: 0.9152 (ptp) cc_final: 0.8895 (ptp) REVERT: G 41 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.7528 (mtm-85) REVERT: G 49 CYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7424 (t) REVERT: G 60 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8351 (ptmt) REVERT: H 17 CYS cc_start: 0.7382 (m) cc_final: 0.7023 (m) REVERT: H 40 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8360 (mm-40) REVERT: H 53 GLU cc_start: 0.8917 (tp30) cc_final: 0.8596 (tm-30) REVERT: I 30 ARG cc_start: 0.8308 (mtp180) cc_final: 0.8018 (mtm110) REVERT: I 52 GLU cc_start: 0.8515 (tm-30) cc_final: 0.7827 (tm-30) outliers start: 27 outliers final: 17 residues processed: 222 average time/residue: 0.6763 time to fit residues: 162.1639 Evaluate side-chains 217 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 49 CYS Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 49 CYS Chi-restraints excluded: chain I residue 77 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 99 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 41 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 1 ASN E 33 ASN E 46 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.086099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.057760 restraints weight = 27793.526| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.52 r_work: 0.2743 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14625 Z= 0.120 Angle : 0.559 11.703 19809 Z= 0.274 Chirality : 0.039 0.174 2097 Planarity : 0.003 0.031 2589 Dihedral : 4.394 20.283 1956 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.66 % Allowed : 13.26 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: 1.62 (0.20), residues: 1752 helix: 2.30 (0.21), residues: 615 sheet: -0.10 (0.26), residues: 309 loop : 0.76 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 41 TYR 0.011 0.001 TYR H 24 PHE 0.012 0.001 PHE F 6 TRP 0.006 0.001 TRP E 17 HIS 0.002 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00280 (14574) covalent geometry : angle 0.55311 (19707) SS BOND : bond 0.00233 ( 51) SS BOND : angle 1.24307 ( 102) hydrogen bonds : bond 0.03243 ( 698) hydrogen bonds : angle 5.05233 ( 1992) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8273 (mp0) cc_final: 0.7810 (mp0) REVERT: A 439 MET cc_start: 0.8769 (ttt) cc_final: 0.8546 (ptm) REVERT: B 46 TRP cc_start: 0.7576 (m100) cc_final: 0.7276 (m100) REVERT: B 148 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8902 (mmtm) REVERT: B 399 GLN cc_start: 0.8381 (tt0) cc_final: 0.8154 (tt0) REVERT: C 70 HIS cc_start: 0.8450 (m-70) cc_final: 0.7383 (t-90) REVERT: C 133 LYS cc_start: 0.9174 (mtmm) cc_final: 0.8896 (ptmm) REVERT: C 219 GLU cc_start: 0.8842 (tt0) cc_final: 0.7969 (tm-30) REVERT: C 321 GLU cc_start: 0.8743 (tt0) cc_final: 0.8478 (tp30) REVERT: C 418 GLU cc_start: 0.8063 (pm20) cc_final: 0.7719 (pm20) REVERT: E 41 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.8232 (mtm-85) REVERT: E 52 GLU cc_start: 0.8880 (tt0) cc_final: 0.8445 (tm-30) REVERT: E 55 LYS cc_start: 0.9184 (mptt) cc_final: 0.8907 (mmtm) REVERT: E 64 MET cc_start: 0.9129 (ptp) cc_final: 0.8890 (ptp) REVERT: G 41 ARG cc_start: 0.8312 (mtm-85) cc_final: 0.7514 (mtm-85) REVERT: G 60 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8343 (ptmt) REVERT: H 17 CYS cc_start: 0.7577 (m) cc_final: 0.7232 (m) REVERT: H 40 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8499 (mm-40) REVERT: H 53 GLU cc_start: 0.8932 (tp30) cc_final: 0.8614 (tm-30) REVERT: I 30 ARG cc_start: 0.8314 (mtp180) cc_final: 0.8016 (mtm110) REVERT: I 52 GLU cc_start: 0.8515 (tm-30) cc_final: 0.7830 (tm-30) REVERT: I 69 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8700 (mt-10) outliers start: 26 outliers final: 17 residues processed: 215 average time/residue: 0.6566 time to fit residues: 152.5052 Evaluate side-chains 220 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 49 CYS Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 77 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.7261 > 50: distance: 29 - 35: 15.864 distance: 35 - 36: 7.187 distance: 35 - 180: 14.471 distance: 36 - 37: 13.339 distance: 36 - 39: 26.509 distance: 37 - 38: 7.491 distance: 37 - 46: 18.519 distance: 38 - 188: 21.921 distance: 39 - 40: 28.817 distance: 40 - 41: 20.982 distance: 41 - 42: 13.184 distance: 42 - 43: 17.780 distance: 43 - 44: 14.502 distance: 43 - 45: 18.472 distance: 46 - 47: 9.499 distance: 46 - 156: 14.792 distance: 47 - 48: 24.780 distance: 47 - 50: 32.071 distance: 48 - 49: 12.315 distance: 48 - 54: 20.059 distance: 49 - 153: 23.896 distance: 50 - 51: 19.170 distance: 51 - 52: 13.487 distance: 51 - 53: 21.555 distance: 54 - 55: 9.856 distance: 54 - 191: 22.896 distance: 55 - 56: 13.900 distance: 55 - 58: 21.736 distance: 56 - 57: 9.544 distance: 56 - 62: 18.806 distance: 57 - 205: 27.785 distance: 58 - 59: 24.012 distance: 58 - 60: 16.331 distance: 59 - 61: 11.225 distance: 62 - 63: 25.092 distance: 63 - 64: 39.310 distance: 63 - 66: 37.457 distance: 64 - 65: 16.476 distance: 64 - 74: 26.106 distance: 66 - 67: 6.838 distance: 67 - 68: 35.753 distance: 67 - 69: 15.552 distance: 68 - 70: 20.328 distance: 69 - 71: 5.379 distance: 70 - 72: 17.611 distance: 71 - 72: 19.819 distance: 72 - 73: 34.743 distance: 74 - 75: 8.789 distance: 75 - 76: 7.451 distance: 75 - 78: 43.367 distance: 76 - 77: 29.833 distance: 76 - 82: 14.269 distance: 78 - 79: 24.043 distance: 79 - 80: 42.387 distance: 79 - 81: 57.651 distance: 82 - 83: 25.339 distance: 82 - 88: 25.969 distance: 83 - 84: 15.162 distance: 83 - 86: 31.368 distance: 84 - 85: 15.720 distance: 84 - 89: 36.494 distance: 86 - 87: 20.287 distance: 87 - 88: 17.641 distance: 89 - 90: 20.314 distance: 89 - 95: 30.380 distance: 90 - 91: 36.716 distance: 90 - 93: 12.409 distance: 91 - 92: 10.965 distance: 91 - 96: 18.025 distance: 93 - 94: 15.590 distance: 94 - 95: 14.219 distance: 96 - 97: 9.991 distance: 96 - 102: 23.349 distance: 97 - 98: 15.446 distance: 97 - 100: 29.779 distance: 98 - 99: 9.602 distance: 98 - 103: 14.152 distance: 100 - 101: 6.393 distance: 101 - 102: 24.070 distance: 103 - 104: 3.759 distance: 104 - 105: 10.560 distance: 104 - 107: 16.843 distance: 105 - 106: 21.775 distance: 105 - 117: 23.468 distance: 107 - 108: 8.104 distance: 108 - 109: 18.506 distance: 108 - 110: 6.841 distance: 109 - 111: 19.992 distance: 110 - 112: 21.733 distance: 110 - 113: 11.624 distance: 111 - 112: 8.773 distance: 112 - 114: 12.242 distance: 113 - 115: 11.279 distance: 114 - 116: 17.759 distance: 115 - 116: 22.219 distance: 117 - 118: 15.644 distance: 118 - 119: 51.177 distance: 119 - 120: 41.284 distance: 119 - 121: 34.308