Starting phenix.real_space_refine on Sun Aug 24 09:51:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmj_41391/08_2025/8tmj_41391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmj_41391/08_2025/8tmj_41391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tmj_41391/08_2025/8tmj_41391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmj_41391/08_2025/8tmj_41391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tmj_41391/08_2025/8tmj_41391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmj_41391/08_2025/8tmj_41391.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1577 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Mg 3 5.21 5 S 65 5.16 5 C 11503 2.51 5 N 2895 2.21 5 O 3292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17758 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "A" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2909 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 15, 'TRANS': 333} Chain: "C" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2804 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "D" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2935 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "E" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.93, per 1000 atoms: 0.28 Number of scatterers: 17758 At special positions: 0 Unit cell: (133.5, 134.568, 161.268, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 Mg 3 11.99 O 3292 8.00 N 2895 7.00 C 11503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 24 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " 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: 1.63 Conformation dependent library (CDL) restraints added in 631.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4132 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 16 sheets defined 48.7% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'A' and resid 46 through 56 removed outlier: 3.576A pdb=" N SER A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 50 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix removed outlier: 3.691A pdb=" N ASP A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 81 removed outlier: 3.906A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 165 through 202 removed outlier: 3.604A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 239 removed outlier: 4.107A pdb=" N VAL A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.830A pdb=" N VAL A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 284 removed outlier: 3.761A pdb=" N ASP A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 312 Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 325 through 345 Processing helix chain 'B' and resid 50 through 56 removed outlier: 3.602A pdb=" N ASP B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 56 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 81 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 165 through 202 removed outlier: 3.676A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 238 Proline residue: B 227 - end of helix removed outlier: 4.253A pdb=" N ASP B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 310 removed outlier: 3.521A pdb=" N PHE B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 325 through 348 removed outlier: 3.788A pdb=" N LYS B 348 " --> pdb=" O TYR B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 50 through 56 removed outlier: 4.175A pdb=" N ARG C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER C 56 " --> pdb=" O PRO C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 50 through 56' Processing helix chain 'C' and resid 69 through 81 Processing helix chain 'C' and resid 83 through 92 removed outlier: 3.599A pdb=" N LEU C 87 " --> pdb=" O HIS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 165 through 202 removed outlier: 3.649A pdb=" N LEU C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 238 Proline residue: C 227 - end of helix removed outlier: 3.616A pdb=" N GLU C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 281 Processing helix chain 'C' and resid 284 through 310 removed outlier: 4.075A pdb=" N ASN C 288 " --> pdb=" O SER C 284 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 318 through 323 removed outlier: 4.226A pdb=" N ARG C 322 " --> pdb=" O MET C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 348 removed outlier: 3.560A pdb=" N LYS C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 removed outlier: 3.502A pdb=" N SER D 49 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU D 51 " --> pdb=" O GLU D 48 " (cutoff:3.500A) Proline residue: D 52 - end of helix removed outlier: 3.506A pdb=" N ASP D 55 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 165 through 202 removed outlier: 3.517A pdb=" N LEU D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 239 removed outlier: 4.462A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.921A pdb=" N VAL D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 removed outlier: 3.565A pdb=" N GLU D 244 " --> pdb=" O PRO D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 312 removed outlier: 4.224A pdb=" N ASP D 253 " --> pdb=" O PRO D 249 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL D 254 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 325 through 349 removed outlier: 3.594A pdb=" N VAL D 329 " --> pdb=" O TRP D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 removed outlier: 3.692A pdb=" N VAL E 50 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU E 51 " --> pdb=" O GLU E 48 " (cutoff:3.500A) Proline residue: E 52 - end of helix Processing helix chain 'E' and resid 69 through 81 removed outlier: 4.164A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 147 through 157 Processing helix chain 'E' and resid 165 through 202 removed outlier: 3.541A pdb=" N LEU E 169 " --> pdb=" O ARG E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 238 removed outlier: 3.815A pdb=" N TRP E 226 " --> pdb=" O ARG E 222 " (cutoff:3.500A) Proline residue: E 227 - end of helix Processing helix chain 'E' and resid 247 through 311 Proline residue: E 303 - end of helix Processing helix chain 'E' and resid 325 through 348 removed outlier: 4.105A pdb=" N VAL E 329 " --> pdb=" O TRP E 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.577A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TYR H 100 " --> pdb=" O MET H 113 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N MET H 113 " --> pdb=" O TYR H 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.577A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.792A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR L 87 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 5 through 8 removed outlier: 3.563A pdb=" N THR G 23 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.781A pdb=" N VAL G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 3 through 7 removed outlier: 5.698A pdb=" N GLY F 16 " --> pdb=" O SER F 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.576A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS F 96 " --> pdb=" O TRP F 116 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TRP F 116 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG F 98 " --> pdb=" O ASP F 114 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.576A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 39 through 44 removed outlier: 3.562A pdb=" N ILE A 29 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 98 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 39 through 44 removed outlier: 3.543A pdb=" N GLU B 125 " --> pdb=" O MET B 112 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 106 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 39 through 44 removed outlier: 3.668A pdb=" N ILE C 29 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR C 60 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N MET C 138 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE C 62 " --> pdb=" O MET C 138 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLN C 140 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE C 64 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 128 " --> pdb=" O PHE C 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 39 through 44 removed outlier: 4.287A pdb=" N GLU D 121 " --> pdb=" O ASP D 116 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 123 " --> pdb=" O THR D 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 28 through 33 removed outlier: 3.601A pdb=" N ILE E 64 " --> pdb=" O MET E 138 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU E 131 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL E 106 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS E 98 " --> pdb=" O VAL E 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 114 through 115 1098 hydrogen bonds defined for protein. 3147 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5571 1.34 - 1.46: 2867 1.46 - 1.57: 9607 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 18162 Sorted by residual: bond pdb=" CB VAL B 254 " pdb=" CG2 VAL B 254 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CG LYS E 117 " pdb=" CD LYS E 117 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.13e+00 bond pdb=" N PRO D 319 " pdb=" CA PRO D 319 " ideal model delta sigma weight residual 1.469 1.482 -0.013 1.28e-02 6.10e+03 1.09e+00 bond pdb=" CB THR D 20 " pdb=" CG2 THR D 20 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.00e+00 bond pdb=" CB LYS A 22 " pdb=" CG LYS A 22 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.00e+00 ... (remaining 18157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 24189 1.78 - 3.56: 343 3.56 - 5.35: 80 5.35 - 7.13: 17 7.13 - 8.91: 4 Bond angle restraints: 24633 Sorted by residual: angle pdb=" C LEU A 235 " pdb=" N TYR A 236 " pdb=" CA TYR A 236 " ideal model delta sigma weight residual 122.06 113.15 8.91 1.86e+00 2.89e-01 2.30e+01 angle pdb=" C VAL D 333 " pdb=" N MET D 334 " pdb=" CA MET D 334 " ideal model delta sigma weight residual 121.14 114.81 6.33 1.75e+00 3.27e-01 1.31e+01 angle pdb=" C LEU E 235 " pdb=" N TYR E 236 " pdb=" CA TYR E 236 " ideal model delta sigma weight residual 122.54 117.14 5.40 1.65e+00 3.67e-01 1.07e+01 angle pdb=" CB LYS E 117 " pdb=" CG LYS E 117 " pdb=" CD LYS E 117 " ideal model delta sigma weight residual 111.30 118.61 -7.31 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CB LYS C 349 " pdb=" CG LYS C 349 " pdb=" CD LYS C 349 " ideal model delta sigma weight residual 111.30 118.45 -7.15 2.30e+00 1.89e-01 9.68e+00 ... (remaining 24628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9661 17.95 - 35.91: 988 35.91 - 53.86: 174 53.86 - 71.82: 35 71.82 - 89.77: 22 Dihedral angle restraints: 10880 sinusoidal: 4473 harmonic: 6407 Sorted by residual: dihedral pdb=" CA PRO B 240 " pdb=" C PRO B 240 " pdb=" N PRO B 241 " pdb=" CA PRO B 241 " ideal model delta harmonic sigma weight residual -180.00 -155.93 -24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA VAL C 283 " pdb=" C VAL C 283 " pdb=" N SER C 284 " pdb=" CA SER C 284 " ideal model delta harmonic sigma weight residual 180.00 -158.69 -21.31 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA SER C 284 " pdb=" C SER C 284 " pdb=" N ASN C 285 " pdb=" CA ASN C 285 " ideal model delta harmonic sigma weight residual 180.00 -160.59 -19.41 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 10877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1717 0.031 - 0.063: 675 0.063 - 0.094: 249 0.094 - 0.126: 132 0.126 - 0.157: 15 Chirality restraints: 2788 Sorted by residual: chirality pdb=" CA PRO B 241 " pdb=" N PRO B 241 " pdb=" C PRO B 241 " pdb=" CB PRO B 241 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA GLU E 186 " pdb=" N GLU E 186 " pdb=" C GLU E 186 " pdb=" CB GLU E 186 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CB VAL B 239 " pdb=" CA VAL B 239 " pdb=" CG1 VAL B 239 " pdb=" CG2 VAL B 239 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 2785 not shown) Planarity restraints: 3083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 202 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A 203 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 327 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO B 328 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 328 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 328 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 240 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 241 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " -0.022 5.00e-02 4.00e+02 ... (remaining 3080 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 661 2.72 - 3.26: 18006 3.26 - 3.81: 28986 3.81 - 4.35: 35401 4.35 - 4.90: 60718 Nonbonded interactions: 143772 Sorted by model distance: nonbonded pdb=" OG SER G 92 " pdb=" OD1 ASN F 111 " model vdw 2.174 3.040 nonbonded pdb=" OE1 GLU D 196 " pdb=" NH1 ARG E 216 " model vdw 2.182 3.120 nonbonded pdb=" OD2 ASP B 145 " pdb=" NH2 ARG B 151 " model vdw 2.215 3.120 nonbonded pdb=" OH TYR E 19 " pdb=" OE1 GLU E 141 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR C 44 " pdb=" OD1 ASP C 46 " model vdw 2.246 3.040 ... (remaining 143767 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 350) selection = (chain 'B' and resid 17 through 350) selection = (chain 'C' and resid 17 through 350) selection = (chain 'D' and resid 17 through 350) selection = (chain 'E' and resid 17 through 350) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = (chain 'L' and resid 2 through 107) } 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 17.940 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18166 Z= 0.152 Angle : 0.586 8.911 24641 Z= 0.306 Chirality : 0.043 0.157 2788 Planarity : 0.004 0.054 3083 Dihedral : 15.080 89.769 6736 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.19), residues: 2147 helix: 2.70 (0.16), residues: 942 sheet: 0.64 (0.24), residues: 487 loop : -1.08 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 269 TYR 0.020 0.001 TYR E 327 PHE 0.024 0.001 PHE A 306 TRP 0.022 0.001 TRP C 350 HIS 0.003 0.001 HIS D 83 Details of bonding type rmsd covalent geometry : bond 0.00346 (18162) covalent geometry : angle 0.58569 (24633) SS BOND : bond 0.00250 ( 4) SS BOND : angle 0.51901 ( 8) hydrogen bonds : bond 0.16068 ( 1074) hydrogen bonds : angle 6.61877 ( 3147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7176 (tp30) cc_final: 0.6873 (tp30) REVERT: G 25 ARG cc_start: 0.7562 (ttm170) cc_final: 0.6847 (ttm110) REVERT: G 104 LYS cc_start: 0.7880 (ttmt) cc_final: 0.7673 (ttmm) REVERT: A 341 MET cc_start: 0.7406 (mmm) cc_final: 0.7022 (mmm) REVERT: B 259 ILE cc_start: 0.8841 (mt) cc_final: 0.8531 (mt) REVERT: B 263 ASP cc_start: 0.6735 (m-30) cc_final: 0.6502 (m-30) REVERT: C 112 MET cc_start: 0.7687 (mtp) cc_final: 0.7444 (mtm) REVERT: D 116 ASP cc_start: 0.7605 (t0) cc_final: 0.7104 (t0) REVERT: D 189 ASP cc_start: 0.7412 (t70) cc_final: 0.7123 (t70) REVERT: E 133 LYS cc_start: 0.7111 (ttmt) cc_final: 0.6548 (mttp) REVERT: E 138 MET cc_start: 0.7066 (mmp) cc_final: 0.6362 (mmp) REVERT: E 189 ASP cc_start: 0.7454 (t0) cc_final: 0.6746 (t0) REVERT: E 220 GLU cc_start: 0.7428 (tt0) cc_final: 0.7077 (tt0) REVERT: E 246 GLU cc_start: 0.7711 (mp0) cc_final: 0.7461 (mp0) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.1103 time to fit residues: 68.7594 Evaluate side-chains 359 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.4980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.2980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN A 140 GLN B 63 ASN B 140 GLN C 63 ASN C 134 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.203643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.141712 restraints weight = 21027.369| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.53 r_work: 0.3218 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18166 Z= 0.156 Angle : 0.587 7.626 24641 Z= 0.310 Chirality : 0.043 0.173 2788 Planarity : 0.004 0.041 3083 Dihedral : 4.232 23.688 2400 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.69 % Rotamer: Outliers : 1.10 % Allowed : 9.33 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.19), residues: 2147 helix: 2.81 (0.16), residues: 955 sheet: 0.72 (0.24), residues: 474 loop : -1.09 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 269 TYR 0.017 0.001 TYR D 236 PHE 0.017 0.001 PHE B 42 TRP 0.015 0.001 TRP C 350 HIS 0.004 0.001 HIS E 120 Details of bonding type rmsd covalent geometry : bond 0.00349 (18162) covalent geometry : angle 0.58732 (24633) SS BOND : bond 0.00374 ( 4) SS BOND : angle 0.88264 ( 8) hydrogen bonds : bond 0.05626 ( 1074) hydrogen bonds : angle 4.97235 ( 3147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 359 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7735 (tp30) cc_final: 0.7383 (tp30) REVERT: G 25 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7250 (ttm110) REVERT: F 6 GLU cc_start: 0.8026 (mp0) cc_final: 0.7794 (mp0) REVERT: F 114 ASP cc_start: 0.8803 (p0) cc_final: 0.8468 (p0) REVERT: A 152 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6991 (mt-10) REVERT: A 162 ARG cc_start: 0.6805 (mtm110) cc_final: 0.6579 (mtp180) REVERT: A 225 ILE cc_start: 0.8012 (tp) cc_final: 0.7594 (tp) REVERT: A 264 THR cc_start: 0.9051 (m) cc_final: 0.8805 (m) REVERT: A 341 MET cc_start: 0.7932 (mmm) cc_final: 0.7703 (mmm) REVERT: B 50 VAL cc_start: 0.9074 (t) cc_final: 0.8860 (m) REVERT: B 263 ASP cc_start: 0.7916 (m-30) cc_final: 0.7596 (m-30) REVERT: B 291 MET cc_start: 0.7836 (mmp) cc_final: 0.7441 (mmp) REVERT: B 297 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7895 (mp) REVERT: C 152 GLU cc_start: 0.7780 (tt0) cc_final: 0.7505 (tt0) REVERT: D 189 ASP cc_start: 0.8113 (t70) cc_final: 0.7810 (t70) REVERT: E 34 TYR cc_start: 0.6267 (p90) cc_final: 0.6023 (p90) REVERT: E 133 LYS cc_start: 0.6870 (ttmt) cc_final: 0.6360 (mmtm) REVERT: E 138 MET cc_start: 0.7037 (mmp) cc_final: 0.6426 (mmp) REVERT: E 191 GLU cc_start: 0.7635 (tt0) cc_final: 0.7393 (tt0) REVERT: E 220 GLU cc_start: 0.8242 (tt0) cc_final: 0.7752 (tt0) REVERT: E 222 ARG cc_start: 0.7373 (ttt180) cc_final: 0.6940 (ttp80) REVERT: E 246 GLU cc_start: 0.8017 (mp0) cc_final: 0.7671 (mp0) REVERT: E 291 MET cc_start: 0.8228 (tpp) cc_final: 0.8025 (tpp) REVERT: E 292 LYS cc_start: 0.7846 (tttp) cc_final: 0.7567 (tptt) outliers start: 22 outliers final: 17 residues processed: 365 average time/residue: 0.1174 time to fit residues: 66.5688 Evaluate side-chains 362 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 344 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 287 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 143 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN D 0 HIS D 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.201158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.133595 restraints weight = 21161.898| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.16 r_work: 0.3179 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18166 Z= 0.185 Angle : 0.589 8.183 24641 Z= 0.310 Chirality : 0.044 0.155 2788 Planarity : 0.004 0.042 3083 Dihedral : 4.316 23.656 2400 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.12 % Favored : 96.79 % Rotamer: Outliers : 2.06 % Allowed : 11.29 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.18), residues: 2147 helix: 2.80 (0.16), residues: 953 sheet: 0.64 (0.24), residues: 477 loop : -1.17 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 67 TYR 0.022 0.001 TYR D 236 PHE 0.018 0.001 PHE B 42 TRP 0.015 0.001 TRP C 350 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00435 (18162) covalent geometry : angle 0.58861 (24633) SS BOND : bond 0.00171 ( 4) SS BOND : angle 0.93428 ( 8) hydrogen bonds : bond 0.05620 ( 1074) hydrogen bonds : angle 4.68103 ( 3147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 363 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7692 (tp30) cc_final: 0.7305 (tp30) REVERT: F 114 ASP cc_start: 0.8813 (p0) cc_final: 0.8494 (p0) REVERT: A 78 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6393 (mp0) REVERT: A 152 GLU cc_start: 0.7331 (mm-30) cc_final: 0.7080 (mt-10) REVERT: A 225 ILE cc_start: 0.8065 (tp) cc_final: 0.7635 (tp) REVERT: A 341 MET cc_start: 0.7846 (mmm) cc_final: 0.7595 (mmm) REVERT: B 148 ASP cc_start: 0.8568 (t0) cc_final: 0.8226 (t0) REVERT: B 263 ASP cc_start: 0.7988 (m-30) cc_final: 0.7656 (m-30) REVERT: B 297 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7933 (mp) REVERT: C 30 GLU cc_start: 0.6646 (pt0) cc_final: 0.6402 (pt0) REVERT: C 98 LYS cc_start: 0.8127 (pttt) cc_final: 0.7858 (pttm) REVERT: C 138 MET cc_start: 0.7950 (ptm) cc_final: 0.7743 (ptm) REVERT: C 152 GLU cc_start: 0.7815 (tt0) cc_final: 0.7440 (tt0) REVERT: E 32 MET cc_start: 0.4775 (OUTLIER) cc_final: 0.4395 (tpt) REVERT: E 95 GLN cc_start: 0.8483 (tt0) cc_final: 0.8238 (tt0) REVERT: E 133 LYS cc_start: 0.6873 (ttmt) cc_final: 0.6358 (mmtm) REVERT: E 138 MET cc_start: 0.6975 (mmp) cc_final: 0.6310 (mmp) REVERT: E 220 GLU cc_start: 0.8227 (tt0) cc_final: 0.7736 (tt0) REVERT: E 222 ARG cc_start: 0.7462 (ttt180) cc_final: 0.7032 (ttp80) REVERT: E 246 GLU cc_start: 0.8047 (mp0) cc_final: 0.7738 (mp0) REVERT: E 270 ASP cc_start: 0.7999 (m-30) cc_final: 0.7774 (m-30) REVERT: E 288 ASN cc_start: 0.7659 (t0) cc_final: 0.7320 (t0) REVERT: E 292 LYS cc_start: 0.7893 (tttp) cc_final: 0.7559 (tptt) outliers start: 41 outliers final: 25 residues processed: 385 average time/residue: 0.1151 time to fit residues: 69.2367 Evaluate side-chains 374 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 346 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 50 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 164 optimal weight: 0.6980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 257 HIS C 134 ASN D 95 GLN E 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.203277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.136869 restraints weight = 20932.329| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.01 r_work: 0.3179 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18166 Z= 0.164 Angle : 0.570 8.243 24641 Z= 0.300 Chirality : 0.043 0.157 2788 Planarity : 0.004 0.040 3083 Dihedral : 4.285 23.763 2400 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.69 % Rotamer: Outliers : 2.56 % Allowed : 13.80 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.19), residues: 2147 helix: 2.87 (0.16), residues: 953 sheet: 0.69 (0.24), residues: 468 loop : -1.13 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 67 TYR 0.020 0.001 TYR D 236 PHE 0.017 0.001 PHE C 301 TRP 0.013 0.001 TRP D 350 HIS 0.005 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00380 (18162) covalent geometry : angle 0.56962 (24633) SS BOND : bond 0.00592 ( 4) SS BOND : angle 1.01040 ( 8) hydrogen bonds : bond 0.05359 ( 1074) hydrogen bonds : angle 4.50938 ( 3147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 359 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7606 (tp30) cc_final: 0.7213 (tp30) REVERT: L 49 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8644 (mt) REVERT: F 114 ASP cc_start: 0.8767 (p0) cc_final: 0.8457 (p0) REVERT: A 78 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: A 152 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7245 (mt-10) REVERT: A 225 ILE cc_start: 0.8000 (tp) cc_final: 0.7558 (tp) REVERT: A 341 MET cc_start: 0.7831 (mmm) cc_final: 0.7563 (mmm) REVERT: B 263 ASP cc_start: 0.7969 (m-30) cc_final: 0.7641 (m-30) REVERT: B 297 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7965 (mp) REVERT: C 30 GLU cc_start: 0.6634 (pt0) cc_final: 0.6412 (pt0) REVERT: C 121 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: C 152 GLU cc_start: 0.7806 (tt0) cc_final: 0.7414 (tt0) REVERT: C 186 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7914 (mm-30) REVERT: E 32 MET cc_start: 0.4818 (OUTLIER) cc_final: 0.4469 (tpt) REVERT: E 95 GLN cc_start: 0.8512 (tt0) cc_final: 0.8259 (tt0) REVERT: E 133 LYS cc_start: 0.6866 (ttmt) cc_final: 0.6345 (mmtm) REVERT: E 138 MET cc_start: 0.6982 (mmp) cc_final: 0.6317 (mmp) REVERT: E 186 GLU cc_start: 0.5913 (mp0) cc_final: 0.5511 (mp0) REVERT: E 220 GLU cc_start: 0.8258 (tt0) cc_final: 0.7727 (tt0) REVERT: E 222 ARG cc_start: 0.7503 (ttt180) cc_final: 0.7055 (ttp80) REVERT: E 246 GLU cc_start: 0.8030 (mp0) cc_final: 0.7715 (mp0) REVERT: E 288 ASN cc_start: 0.7713 (t0) cc_final: 0.7360 (t0) REVERT: E 292 LYS cc_start: 0.7892 (tttp) cc_final: 0.7644 (tptt) REVERT: E 331 LEU cc_start: 0.6174 (mp) cc_final: 0.5902 (mp) outliers start: 51 outliers final: 29 residues processed: 388 average time/residue: 0.1177 time to fit residues: 71.4341 Evaluate side-chains 381 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 347 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 33 optimal weight: 0.0370 chunk 42 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 201 optimal weight: 0.0570 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.0670 chunk 152 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 GLN D 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.203136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.139012 restraints weight = 21063.895| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.17 r_work: 0.3190 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18166 Z= 0.131 Angle : 0.545 7.992 24641 Z= 0.287 Chirality : 0.042 0.170 2788 Planarity : 0.004 0.041 3083 Dihedral : 4.162 23.497 2400 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 2.36 % Allowed : 15.40 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.19), residues: 2147 helix: 3.01 (0.16), residues: 954 sheet: 0.76 (0.24), residues: 479 loop : -1.11 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 67 TYR 0.021 0.001 TYR E 327 PHE 0.015 0.001 PHE A 27 TRP 0.012 0.001 TRP C 350 HIS 0.003 0.001 HIS D 83 Details of bonding type rmsd covalent geometry : bond 0.00287 (18162) covalent geometry : angle 0.54498 (24633) SS BOND : bond 0.00428 ( 4) SS BOND : angle 0.95839 ( 8) hydrogen bonds : bond 0.04943 ( 1074) hydrogen bonds : angle 4.33354 ( 3147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 378 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7342 (tp30) cc_final: 0.6986 (tp30) REVERT: L 49 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8473 (mt) REVERT: G 25 ARG cc_start: 0.7861 (ttm170) cc_final: 0.7182 (tpp-160) REVERT: F 11 LEU cc_start: 0.7173 (tp) cc_final: 0.6813 (tp) REVERT: F 114 ASP cc_start: 0.8686 (p0) cc_final: 0.8353 (p0) REVERT: A 78 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6345 (mp0) REVERT: A 341 MET cc_start: 0.7971 (mmm) cc_final: 0.7678 (mmm) REVERT: B 242 LEU cc_start: 0.8354 (mm) cc_final: 0.8041 (mm) REVERT: B 263 ASP cc_start: 0.7564 (m-30) cc_final: 0.7216 (m-30) REVERT: B 291 MET cc_start: 0.7892 (mmp) cc_final: 0.7178 (mmm) REVERT: B 297 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7748 (mp) REVERT: C 30 GLU cc_start: 0.6654 (pt0) cc_final: 0.6432 (pt0) REVERT: C 121 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: C 152 GLU cc_start: 0.7641 (tt0) cc_final: 0.7207 (tt0) REVERT: C 272 VAL cc_start: 0.9041 (m) cc_final: 0.8355 (p) REVERT: E 32 MET cc_start: 0.4765 (OUTLIER) cc_final: 0.4477 (tpt) REVERT: E 42 PHE cc_start: 0.5941 (m-80) cc_final: 0.5505 (m-80) REVERT: E 95 GLN cc_start: 0.8419 (tt0) cc_final: 0.8161 (tt0) REVERT: E 138 MET cc_start: 0.6831 (mmp) cc_final: 0.6277 (mmp) REVERT: E 220 GLU cc_start: 0.7969 (tt0) cc_final: 0.7410 (tt0) REVERT: E 222 ARG cc_start: 0.7176 (ttt180) cc_final: 0.6771 (ttp80) REVERT: E 246 GLU cc_start: 0.8010 (mp0) cc_final: 0.7677 (mp0) REVERT: E 292 LYS cc_start: 0.7621 (tttp) cc_final: 0.7307 (tptt) outliers start: 47 outliers final: 26 residues processed: 400 average time/residue: 0.1289 time to fit residues: 80.7576 Evaluate side-chains 386 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 355 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 79 optimal weight: 0.9990 chunk 13 optimal weight: 0.0570 chunk 105 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 125 optimal weight: 0.0020 chunk 113 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.202811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.135643 restraints weight = 20891.374| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.12 r_work: 0.3187 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18166 Z= 0.151 Angle : 0.560 8.477 24641 Z= 0.294 Chirality : 0.043 0.170 2788 Planarity : 0.004 0.040 3083 Dihedral : 4.194 23.431 2400 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.26 % Favored : 96.65 % Rotamer: Outliers : 2.66 % Allowed : 16.46 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.19), residues: 2147 helix: 2.98 (0.16), residues: 955 sheet: 0.82 (0.24), residues: 472 loop : -1.13 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 67 TYR 0.017 0.001 TYR A 236 PHE 0.015 0.001 PHE A 27 TRP 0.014 0.001 TRP C 350 HIS 0.003 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00347 (18162) covalent geometry : angle 0.55970 (24633) SS BOND : bond 0.00394 ( 4) SS BOND : angle 1.11681 ( 8) hydrogen bonds : bond 0.05069 ( 1074) hydrogen bonds : angle 4.29747 ( 3147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 365 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7485 (tp30) cc_final: 0.7112 (tp30) REVERT: L 49 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8661 (mt) REVERT: G 25 ARG cc_start: 0.7961 (ttm170) cc_final: 0.7691 (tpp80) REVERT: F 11 LEU cc_start: 0.7291 (tp) cc_final: 0.6943 (tp) REVERT: F 114 ASP cc_start: 0.8794 (p0) cc_final: 0.8445 (p0) REVERT: A 54 ARG cc_start: 0.6532 (ttp80) cc_final: 0.6286 (ttp80) REVERT: A 78 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6360 (mp0) REVERT: A 230 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 306 PHE cc_start: 0.6978 (t80) cc_final: 0.6542 (t80) REVERT: A 341 MET cc_start: 0.8023 (mmm) cc_final: 0.7724 (mmm) REVERT: B 242 LEU cc_start: 0.8603 (mm) cc_final: 0.8271 (mm) REVERT: B 263 ASP cc_start: 0.8021 (m-30) cc_final: 0.7693 (m-30) REVERT: B 297 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7930 (mp) REVERT: C 30 GLU cc_start: 0.6665 (pt0) cc_final: 0.6449 (pt0) REVERT: C 121 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: C 152 GLU cc_start: 0.7612 (tt0) cc_final: 0.7197 (tt0) REVERT: E 32 MET cc_start: 0.4636 (OUTLIER) cc_final: 0.4330 (tpt) REVERT: E 42 PHE cc_start: 0.5989 (m-80) cc_final: 0.5565 (m-80) REVERT: E 95 GLN cc_start: 0.8477 (tt0) cc_final: 0.8219 (tt0) REVERT: E 133 LYS cc_start: 0.6925 (ttmt) cc_final: 0.6345 (mmtm) REVERT: E 138 MET cc_start: 0.7082 (mmp) cc_final: 0.6460 (mmp) REVERT: E 220 GLU cc_start: 0.8219 (tt0) cc_final: 0.7670 (tt0) REVERT: E 222 ARG cc_start: 0.7476 (ttt180) cc_final: 0.7001 (ttp80) REVERT: E 246 GLU cc_start: 0.8080 (mp0) cc_final: 0.7668 (mp0) REVERT: E 292 LYS cc_start: 0.7799 (tttp) cc_final: 0.7466 (tptt) outliers start: 53 outliers final: 40 residues processed: 391 average time/residue: 0.1263 time to fit residues: 77.0410 Evaluate side-chains 398 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 353 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 44 optimal weight: 0.2980 chunk 157 optimal weight: 0.9980 chunk 189 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 177 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.201939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.135048 restraints weight = 21028.118| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.14 r_work: 0.3172 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18166 Z= 0.165 Angle : 0.582 8.847 24641 Z= 0.303 Chirality : 0.043 0.168 2788 Planarity : 0.004 0.041 3083 Dihedral : 4.238 23.441 2400 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 2.46 % Allowed : 17.41 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.19), residues: 2147 helix: 2.93 (0.16), residues: 955 sheet: 0.80 (0.24), residues: 472 loop : -1.14 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 67 TYR 0.017 0.001 TYR B 236 PHE 0.020 0.001 PHE C 301 TRP 0.014 0.001 TRP C 350 HIS 0.003 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00385 (18162) covalent geometry : angle 0.58182 (24633) SS BOND : bond 0.00184 ( 4) SS BOND : angle 1.22813 ( 8) hydrogen bonds : bond 0.05173 ( 1074) hydrogen bonds : angle 4.32005 ( 3147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 360 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7309 (tp30) cc_final: 0.6951 (tp30) REVERT: L 49 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8494 (mt) REVERT: G 25 ARG cc_start: 0.7826 (ttm170) cc_final: 0.7556 (tpp80) REVERT: F 11 LEU cc_start: 0.7247 (tp) cc_final: 0.6918 (tp) REVERT: F 114 ASP cc_start: 0.8685 (p0) cc_final: 0.8394 (p0) REVERT: A 54 ARG cc_start: 0.6585 (ttp80) cc_final: 0.6024 (ttp-170) REVERT: A 78 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6352 (mp0) REVERT: A 341 MET cc_start: 0.7957 (mmm) cc_final: 0.7640 (mmm) REVERT: B 242 LEU cc_start: 0.8551 (mm) cc_final: 0.8237 (mm) REVERT: B 263 ASP cc_start: 0.7642 (m-30) cc_final: 0.7309 (m-30) REVERT: B 297 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7809 (mp) REVERT: C 121 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: C 152 GLU cc_start: 0.7502 (tt0) cc_final: 0.7046 (tt0) REVERT: C 269 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7958 (ttm170) REVERT: C 346 LYS cc_start: 0.8509 (mmmt) cc_final: 0.8192 (mmtm) REVERT: E 32 MET cc_start: 0.4622 (OUTLIER) cc_final: 0.4338 (tpt) REVERT: E 42 PHE cc_start: 0.6008 (m-80) cc_final: 0.5591 (m-80) REVERT: E 95 GLN cc_start: 0.8490 (tt0) cc_final: 0.8244 (tt0) REVERT: E 133 LYS cc_start: 0.6833 (ttmt) cc_final: 0.6322 (mmtm) REVERT: E 138 MET cc_start: 0.7026 (mmp) cc_final: 0.6358 (mmp) REVERT: E 220 GLU cc_start: 0.8012 (tt0) cc_final: 0.7453 (tt0) REVERT: E 222 ARG cc_start: 0.7245 (ttt180) cc_final: 0.6804 (ttp80) REVERT: E 246 GLU cc_start: 0.8038 (mp0) cc_final: 0.7657 (mp0) REVERT: E 292 LYS cc_start: 0.7705 (tttp) cc_final: 0.7335 (tptt) outliers start: 49 outliers final: 39 residues processed: 388 average time/residue: 0.1269 time to fit residues: 76.7992 Evaluate side-chains 397 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 352 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 78 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 178 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.204120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.140429 restraints weight = 21031.200| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.36 r_work: 0.3189 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18166 Z= 0.137 Angle : 0.560 7.492 24641 Z= 0.292 Chirality : 0.043 0.204 2788 Planarity : 0.004 0.040 3083 Dihedral : 4.169 23.113 2400 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 2.51 % Allowed : 18.01 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.19), residues: 2147 helix: 3.01 (0.16), residues: 955 sheet: 0.87 (0.24), residues: 466 loop : -1.10 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 202 TYR 0.017 0.001 TYR A 236 PHE 0.014 0.001 PHE A 27 TRP 0.012 0.001 TRP D 350 HIS 0.003 0.001 HIS D 83 Details of bonding type rmsd covalent geometry : bond 0.00304 (18162) covalent geometry : angle 0.55985 (24633) SS BOND : bond 0.00186 ( 4) SS BOND : angle 1.25210 ( 8) hydrogen bonds : bond 0.04906 ( 1074) hydrogen bonds : angle 4.23432 ( 3147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 366 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7299 (tp30) cc_final: 0.6609 (tt0) REVERT: L 49 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8480 (mt) REVERT: G 25 ARG cc_start: 0.7809 (ttm170) cc_final: 0.7552 (tpp80) REVERT: F 11 LEU cc_start: 0.7180 (tp) cc_final: 0.6860 (tp) REVERT: F 114 ASP cc_start: 0.8687 (p0) cc_final: 0.8433 (p0) REVERT: A 54 ARG cc_start: 0.6543 (ttp80) cc_final: 0.5980 (ttp-170) REVERT: A 78 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6288 (mp0) REVERT: A 341 MET cc_start: 0.7975 (mmm) cc_final: 0.7661 (mmm) REVERT: B 242 LEU cc_start: 0.8527 (mm) cc_final: 0.8221 (mm) REVERT: B 263 ASP cc_start: 0.7585 (m-30) cc_final: 0.7232 (m-30) REVERT: B 297 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7765 (mp) REVERT: C 152 GLU cc_start: 0.7467 (tt0) cc_final: 0.6996 (tt0) REVERT: C 272 VAL cc_start: 0.9043 (m) cc_final: 0.8359 (p) REVERT: D 313 MET cc_start: 0.2902 (tmm) cc_final: 0.2460 (tmm) REVERT: E 32 MET cc_start: 0.4606 (OUTLIER) cc_final: 0.4317 (tpt) REVERT: E 42 PHE cc_start: 0.5990 (m-80) cc_final: 0.5577 (m-80) REVERT: E 95 GLN cc_start: 0.8466 (tt0) cc_final: 0.8224 (tt0) REVERT: E 133 LYS cc_start: 0.6816 (ttmt) cc_final: 0.6274 (mmtm) REVERT: E 138 MET cc_start: 0.6969 (mmp) cc_final: 0.6301 (mmp) REVERT: E 198 GLU cc_start: 0.6972 (tt0) cc_final: 0.6047 (mm-30) REVERT: E 220 GLU cc_start: 0.8000 (tt0) cc_final: 0.7435 (tt0) REVERT: E 222 ARG cc_start: 0.7211 (ttt180) cc_final: 0.6776 (ttp80) REVERT: E 246 GLU cc_start: 0.8071 (mp0) cc_final: 0.7665 (mp0) REVERT: E 292 LYS cc_start: 0.7640 (tttp) cc_final: 0.7262 (tptt) outliers start: 50 outliers final: 42 residues processed: 391 average time/residue: 0.1192 time to fit residues: 73.5631 Evaluate side-chains 400 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 354 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 41 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 164 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.201484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.136187 restraints weight = 20863.865| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.32 r_work: 0.3118 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18166 Z= 0.175 Angle : 0.592 8.046 24641 Z= 0.309 Chirality : 0.044 0.247 2788 Planarity : 0.004 0.041 3083 Dihedral : 4.295 23.269 2400 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 2.61 % Allowed : 18.16 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.19), residues: 2147 helix: 2.88 (0.16), residues: 955 sheet: 0.79 (0.24), residues: 472 loop : -1.18 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 67 TYR 0.017 0.001 TYR B 236 PHE 0.015 0.001 PHE B 42 TRP 0.014 0.001 TRP C 350 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00413 (18162) covalent geometry : angle 0.59147 (24633) SS BOND : bond 0.00161 ( 4) SS BOND : angle 1.50331 ( 8) hydrogen bonds : bond 0.05265 ( 1074) hydrogen bonds : angle 4.32060 ( 3147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 358 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7431 (tp30) cc_final: 0.7061 (tp30) REVERT: L 49 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8543 (mt) REVERT: G 25 ARG cc_start: 0.7881 (ttm170) cc_final: 0.7619 (tpp80) REVERT: F 11 LEU cc_start: 0.7278 (tp) cc_final: 0.6955 (tp) REVERT: A 54 ARG cc_start: 0.6654 (ttp80) cc_final: 0.6096 (ttp-170) REVERT: A 78 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6310 (mp0) REVERT: A 306 PHE cc_start: 0.6907 (t80) cc_final: 0.6532 (t80) REVERT: A 341 MET cc_start: 0.7970 (mmm) cc_final: 0.7658 (mmm) REVERT: B 242 LEU cc_start: 0.8590 (mm) cc_final: 0.8276 (mm) REVERT: B 263 ASP cc_start: 0.7775 (m-30) cc_final: 0.7435 (m-30) REVERT: B 297 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7844 (mp) REVERT: C 152 GLU cc_start: 0.7544 (tt0) cc_final: 0.7086 (tt0) REVERT: D 313 MET cc_start: 0.2961 (tmm) cc_final: 0.2541 (tmm) REVERT: E 32 MET cc_start: 0.4688 (OUTLIER) cc_final: 0.4270 (tpt) REVERT: E 42 PHE cc_start: 0.6009 (m-80) cc_final: 0.5612 (m-80) REVERT: E 95 GLN cc_start: 0.8483 (tt0) cc_final: 0.8226 (tt0) REVERT: E 133 LYS cc_start: 0.6828 (ttmt) cc_final: 0.6300 (mmtm) REVERT: E 138 MET cc_start: 0.7020 (mmp) cc_final: 0.6342 (mmp) REVERT: E 198 GLU cc_start: 0.6984 (tt0) cc_final: 0.6019 (mm-30) REVERT: E 220 GLU cc_start: 0.8053 (tt0) cc_final: 0.7505 (tt0) REVERT: E 222 ARG cc_start: 0.7372 (ttt180) cc_final: 0.6908 (ttp80) REVERT: E 246 GLU cc_start: 0.8111 (mp0) cc_final: 0.7737 (mp0) REVERT: E 288 ASN cc_start: 0.7678 (t0) cc_final: 0.7375 (t0) outliers start: 52 outliers final: 45 residues processed: 387 average time/residue: 0.1345 time to fit residues: 80.9616 Evaluate side-chains 400 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 351 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 94 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 133 optimal weight: 0.0670 chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 ASN E 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.202049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.135164 restraints weight = 20840.327| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.08 r_work: 0.3195 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18166 Z= 0.151 Angle : 0.578 7.630 24641 Z= 0.302 Chirality : 0.043 0.206 2788 Planarity : 0.004 0.041 3083 Dihedral : 4.250 23.142 2400 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.55 % Rotamer: Outliers : 2.56 % Allowed : 18.56 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.19), residues: 2147 helix: 2.94 (0.16), residues: 954 sheet: 0.82 (0.24), residues: 472 loop : -1.17 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 67 TYR 0.020 0.001 TYR E 327 PHE 0.014 0.001 PHE B 42 TRP 0.013 0.001 TRP C 350 HIS 0.003 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00348 (18162) covalent geometry : angle 0.57754 (24633) SS BOND : bond 0.00185 ( 4) SS BOND : angle 1.50850 ( 8) hydrogen bonds : bond 0.05043 ( 1074) hydrogen bonds : angle 4.26888 ( 3147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 357 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7460 (tp30) cc_final: 0.6724 (tt0) REVERT: L 49 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8649 (mt) REVERT: G 25 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7717 (tpp80) REVERT: F 11 LEU cc_start: 0.7329 (tp) cc_final: 0.6998 (tp) REVERT: A 54 ARG cc_start: 0.6665 (ttp80) cc_final: 0.6105 (ttp-170) REVERT: A 78 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6294 (mp0) REVERT: A 162 ARG cc_start: 0.6775 (mtm110) cc_final: 0.6563 (mtp180) REVERT: A 306 PHE cc_start: 0.7033 (t80) cc_final: 0.6616 (t80) REVERT: A 341 MET cc_start: 0.7941 (mmm) cc_final: 0.7620 (mmm) REVERT: B 242 LEU cc_start: 0.8625 (mm) cc_final: 0.8259 (mm) REVERT: B 263 ASP cc_start: 0.7953 (m-30) cc_final: 0.7612 (m-30) REVERT: B 297 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7933 (mp) REVERT: C 152 GLU cc_start: 0.7573 (tt0) cc_final: 0.7113 (tt0) REVERT: C 162 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7237 (mtt180) REVERT: C 269 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8111 (ttm170) REVERT: D 313 MET cc_start: 0.3009 (tmm) cc_final: 0.2267 (tmm) REVERT: E 32 MET cc_start: 0.4638 (OUTLIER) cc_final: 0.4228 (tpt) REVERT: E 42 PHE cc_start: 0.6079 (m-80) cc_final: 0.5681 (m-80) REVERT: E 95 GLN cc_start: 0.8484 (tt0) cc_final: 0.8228 (tt0) REVERT: E 133 LYS cc_start: 0.6830 (ttmt) cc_final: 0.6305 (mmtm) REVERT: E 138 MET cc_start: 0.7090 (mmp) cc_final: 0.6433 (mmp) REVERT: E 198 GLU cc_start: 0.6941 (tt0) cc_final: 0.5926 (mm-30) REVERT: E 220 GLU cc_start: 0.8182 (tt0) cc_final: 0.7647 (tt0) REVERT: E 222 ARG cc_start: 0.7496 (ttt180) cc_final: 0.6984 (ttp80) REVERT: E 246 GLU cc_start: 0.8119 (mp0) cc_final: 0.7715 (mp0) outliers start: 51 outliers final: 44 residues processed: 385 average time/residue: 0.1365 time to fit residues: 81.1142 Evaluate side-chains 401 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 352 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.8491 > 50: distance: 4 - 5: 7.462 distance: 5 - 8: 4.358 distance: 6 - 7: 9.580 distance: 6 - 12: 6.047 distance: 8 - 9: 7.127 distance: 9 - 10: 4.022 distance: 9 - 11: 7.187 distance: 13 - 14: 4.468 distance: 13 - 16: 6.966 distance: 14 - 15: 4.221 distance: 14 - 20: 3.547 distance: 16 - 17: 3.925 distance: 16 - 18: 7.017 distance: 17 - 19: 9.204 distance: 20 - 21: 5.881 distance: 21 - 22: 7.486 distance: 21 - 24: 13.145 distance: 22 - 23: 18.451 distance: 22 - 29: 8.695 distance: 24 - 25: 12.530 distance: 25 - 26: 14.259 distance: 26 - 28: 12.307 distance: 29 - 30: 4.694 distance: 30 - 31: 10.275 distance: 30 - 33: 5.639 distance: 31 - 32: 4.051 distance: 31 - 37: 8.730 distance: 33 - 34: 14.806 distance: 34 - 35: 10.834 distance: 35 - 36: 19.024 distance: 37 - 38: 9.343 distance: 37 - 106: 13.399 distance: 38 - 39: 7.232 distance: 39 - 40: 10.263 distance: 39 - 44: 5.438 distance: 40 - 103: 5.816 distance: 41 - 42: 9.171 distance: 41 - 43: 11.947 distance: 44 - 45: 12.182 distance: 45 - 48: 6.193 distance: 46 - 53: 9.009 distance: 48 - 49: 10.637 distance: 49 - 50: 5.617 distance: 50 - 51: 11.163 distance: 50 - 52: 8.620 distance: 53 - 54: 3.461 distance: 53 - 93: 5.050 distance: 54 - 55: 11.310 distance: 54 - 57: 7.901 distance: 55 - 56: 11.974 distance: 55 - 59: 7.310 distance: 56 - 90: 11.271 distance: 57 - 58: 3.720 distance: 59 - 60: 4.763 distance: 59 - 65: 3.260 distance: 60 - 61: 3.066 distance: 60 - 63: 4.423 distance: 61 - 62: 10.000 distance: 61 - 66: 10.842 distance: 63 - 64: 7.322 distance: 64 - 65: 3.464 distance: 66 - 67: 8.789 distance: 67 - 68: 14.851 distance: 67 - 70: 13.725 distance: 68 - 69: 25.470 distance: 68 - 72: 4.794 distance: 70 - 71: 14.494