Starting phenix.real_space_refine on Mon May 19 19:38:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmj_41391/05_2025/8tmj_41391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmj_41391/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tmj_41391/05_2025/8tmj_41391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmj_41391/05_2025/8tmj_41391.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmj_41391/05_2025/8tmj_41391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmj_41391/05_2025/8tmj_41391.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.19, per 1000 atoms: 0.52 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: 4.86 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.26 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: 5.71 Time building geometry restraints manager: 5.56 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 40.150 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.580 ------------------------------------------------------------------------------- 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 : 9.70 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.022 0.001 TRP C 350 HIS 0.003 0.001 HIS D 83 PHE 0.024 0.001 PHE A 306 TYR 0.020 0.001 TYR E 327 ARG 0.009 0.000 ARG C 269 Details of bonding type rmsd hydrogen bonds : bond 0.16068 ( 1074) hydrogen bonds : angle 6.61877 ( 3147) SS BOND : bond 0.00250 ( 4) SS BOND : angle 0.51901 ( 8) covalent geometry : bond 0.00346 (18162) covalent geometry : angle 0.58569 (24633) *********************** 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 : 2.165 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: 0.2754 time to fit residues: 169.8108 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 : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 192 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 0 HIS D 95 GLN E 74 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.200483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.138842 restraints weight = 20909.187| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.57 r_work: 0.3175 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 18166 Z= 0.232 Angle : 0.643 8.632 24641 Z= 0.340 Chirality : 0.046 0.178 2788 Planarity : 0.005 0.050 3083 Dihedral : 4.453 24.082 2400 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 1.46 % Allowed : 9.53 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 2147 helix: 2.58 (0.16), residues: 954 sheet: 0.57 (0.24), residues: 478 loop : -1.17 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 350 HIS 0.005 0.001 HIS D 94 PHE 0.021 0.002 PHE B 42 TYR 0.020 0.002 TYR D 236 ARG 0.009 0.001 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.06094 ( 1074) hydrogen bonds : angle 5.06736 ( 3147) SS BOND : bond 0.00360 ( 4) SS BOND : angle 1.03899 ( 8) covalent geometry : bond 0.00556 (18162) covalent geometry : angle 0.64323 (24633) *********************** 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 386 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 357 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7790 (tp30) cc_final: 0.7430 (tp30) REVERT: G 25 ARG cc_start: 0.7955 (ttm170) cc_final: 0.7252 (ttm110) REVERT: F 114 ASP cc_start: 0.8817 (p0) cc_final: 0.8527 (p0) REVERT: A 152 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7061 (mt-10) REVERT: A 225 ILE cc_start: 0.8085 (tp) cc_final: 0.7671 (tp) REVERT: A 341 MET cc_start: 0.7660 (mmm) cc_final: 0.7366 (mmm) REVERT: B 148 ASP cc_start: 0.8440 (t0) cc_final: 0.8163 (t0) REVERT: B 263 ASP cc_start: 0.7945 (m-30) cc_final: 0.7620 (m-30) REVERT: B 291 MET cc_start: 0.7869 (mmp) cc_final: 0.7472 (mmp) REVERT: B 297 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7982 (mp) REVERT: C 152 GLU cc_start: 0.7863 (tt0) cc_final: 0.7555 (tt0) REVERT: D 189 ASP cc_start: 0.8304 (t70) cc_final: 0.7995 (t70) REVERT: E 34 TYR cc_start: 0.6142 (p90) cc_final: 0.5889 (p90) REVERT: E 138 MET cc_start: 0.7069 (mmp) cc_final: 0.6418 (mmp) REVERT: E 220 GLU cc_start: 0.8242 (tt0) cc_final: 0.7751 (tt0) REVERT: E 222 ARG cc_start: 0.7495 (ttt180) cc_final: 0.6862 (mtp180) REVERT: E 246 GLU cc_start: 0.8004 (mp0) cc_final: 0.7637 (mp0) REVERT: E 270 ASP cc_start: 0.7945 (m-30) cc_final: 0.7737 (m-30) outliers start: 29 outliers final: 24 residues processed: 371 average time/residue: 0.2775 time to fit residues: 158.9191 Evaluate side-chains 366 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 341 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL 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 G residue 103 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 TYR 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 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 278 VAL Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 106 VAL 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 219 VAL Chi-restraints excluded: chain E residue 284 SER 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 133 optimal weight: 0.0670 chunk 157 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.202627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.137125 restraints weight = 20883.594| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.18 r_work: 0.3174 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1208 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 : 0.569 7.982 24641 Z= 0.300 Chirality : 0.043 0.158 2788 Planarity : 0.004 0.040 3083 Dihedral : 4.283 23.733 2400 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.83 % Rotamer: Outliers : 1.91 % Allowed : 11.99 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.18), residues: 2147 helix: 2.82 (0.16), residues: 953 sheet: 0.68 (0.24), residues: 470 loop : -1.13 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 350 HIS 0.003 0.001 HIS D 83 PHE 0.016 0.001 PHE A 27 TYR 0.020 0.001 TYR D 236 ARG 0.005 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.05439 ( 1074) hydrogen bonds : angle 4.70169 ( 3147) SS BOND : bond 0.00484 ( 4) SS BOND : angle 0.92842 ( 8) covalent geometry : bond 0.00343 (18162) covalent geometry : angle 0.56853 (24633) *********************** 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 407 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 369 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7524 (tp30) cc_final: 0.7154 (tp30) REVERT: H 37 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8824 (t) REVERT: A 78 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6366 (mp0) REVERT: A 152 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6900 (mt-10) REVERT: A 225 ILE cc_start: 0.7946 (tp) cc_final: 0.7519 (tp) REVERT: A 341 MET cc_start: 0.7787 (mmm) cc_final: 0.7531 (mmm) REVERT: B 148 ASP cc_start: 0.8352 (t0) cc_final: 0.7969 (t0) REVERT: B 263 ASP cc_start: 0.7555 (m-30) cc_final: 0.7220 (m-30) REVERT: B 297 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7817 (mp) REVERT: C 30 GLU cc_start: 0.6612 (pt0) cc_final: 0.6390 (pt0) REVERT: C 98 LYS cc_start: 0.8054 (pttt) cc_final: 0.7846 (pttm) REVERT: C 152 GLU cc_start: 0.7655 (tt0) cc_final: 0.7287 (tt0) REVERT: D 189 ASP cc_start: 0.7816 (t70) cc_final: 0.7493 (t70) REVERT: E 32 MET cc_start: 0.4657 (ttt) cc_final: 0.4400 (tpt) REVERT: E 133 LYS cc_start: 0.6919 (ttmt) cc_final: 0.6355 (mmtm) REVERT: E 138 MET cc_start: 0.6840 (mmp) cc_final: 0.6181 (mmp) REVERT: E 220 GLU cc_start: 0.7951 (tt0) cc_final: 0.7427 (tt0) REVERT: E 222 ARG cc_start: 0.7183 (ttt180) cc_final: 0.6799 (ttp80) REVERT: E 246 GLU cc_start: 0.8037 (mp0) cc_final: 0.7714 (mp0) REVERT: E 292 LYS cc_start: 0.7761 (tttp) cc_final: 0.7393 (tptt) outliers start: 38 outliers final: 22 residues processed: 389 average time/residue: 0.2722 time to fit residues: 163.5245 Evaluate side-chains 370 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 345 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 54 SER 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 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 C residue 196 GLU 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 86 VAL 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 287 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 34 optimal weight: 0.5980 chunk 189 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 0.0570 chunk 150 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.205634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.141294 restraints weight = 20605.691| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.16 r_work: 0.3147 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18166 Z= 0.193 Angle : 0.594 8.030 24641 Z= 0.313 Chirality : 0.044 0.159 2788 Planarity : 0.004 0.045 3083 Dihedral : 4.380 23.770 2400 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 2.96 % Allowed : 13.85 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 2147 helix: 2.76 (0.16), residues: 953 sheet: 0.51 (0.24), residues: 479 loop : -1.21 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 350 HIS 0.005 0.001 HIS B 257 PHE 0.019 0.001 PHE C 301 TYR 0.021 0.001 TYR D 236 ARG 0.008 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.05631 ( 1074) hydrogen bonds : angle 4.59005 ( 3147) SS BOND : bond 0.00219 ( 4) SS BOND : angle 1.15538 ( 8) covalent geometry : bond 0.00458 (18162) covalent geometry : angle 0.59386 (24633) *********************** 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 417 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 358 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7473 (tp30) cc_final: 0.7097 (tp30) REVERT: L 49 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8472 (mt) REVERT: F 114 ASP cc_start: 0.8669 (p0) cc_final: 0.8363 (p0) REVERT: A 78 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6387 (mp0) REVERT: A 152 GLU cc_start: 0.7214 (mm-30) cc_final: 0.7013 (mt-10) REVERT: A 162 ARG cc_start: 0.7206 (mtm110) cc_final: 0.6742 (mtp180) REVERT: A 225 ILE cc_start: 0.7976 (tp) cc_final: 0.7546 (tp) REVERT: A 341 MET cc_start: 0.7813 (mmm) cc_final: 0.7549 (mmm) REVERT: B 148 ASP cc_start: 0.8427 (t0) cc_final: 0.7990 (t0) REVERT: B 242 LEU cc_start: 0.8507 (mm) cc_final: 0.8193 (mm) REVERT: B 263 ASP cc_start: 0.7620 (m-30) cc_final: 0.7270 (m-30) REVERT: B 297 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7780 (mp) REVERT: C 30 GLU cc_start: 0.6592 (pt0) cc_final: 0.6371 (pt0) REVERT: C 98 LYS cc_start: 0.8028 (pttt) cc_final: 0.7809 (pttm) REVERT: C 121 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: C 152 GLU cc_start: 0.7670 (tt0) cc_final: 0.7251 (tt0) REVERT: D 189 ASP cc_start: 0.8031 (t70) cc_final: 0.7688 (t70) REVERT: E 32 MET cc_start: 0.4695 (OUTLIER) cc_final: 0.4354 (tpt) REVERT: E 138 MET cc_start: 0.6843 (mmp) cc_final: 0.6139 (mmp) REVERT: E 186 GLU cc_start: 0.5604 (mp0) cc_final: 0.5254 (mp0) REVERT: E 220 GLU cc_start: 0.8018 (tt0) cc_final: 0.7457 (tt0) REVERT: E 222 ARG cc_start: 0.7277 (ttt180) cc_final: 0.6884 (ttp80) REVERT: E 246 GLU cc_start: 0.8010 (mp0) cc_final: 0.7680 (mp0) REVERT: E 256 ASP cc_start: 0.7511 (t0) cc_final: 0.7244 (t0) REVERT: E 331 LEU cc_start: 0.6147 (mp) cc_final: 0.5912 (mp) outliers start: 59 outliers final: 34 residues processed: 392 average time/residue: 0.2718 time to fit residues: 165.0754 Evaluate side-chains 393 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 354 time to evaluate : 2.144 ------------------------------------------------------------------------------- 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 49 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain F residue 83 MET 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 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 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 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 86 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 200 LEU 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 170 optimal weight: 0.3980 chunk 137 optimal weight: 0.0870 chunk 42 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN A 314 ASN E 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.203004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.137069 restraints weight = 21123.250| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.39 r_work: 0.3153 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18166 Z= 0.141 Angle : 0.556 7.580 24641 Z= 0.292 Chirality : 0.043 0.178 2788 Planarity : 0.004 0.041 3083 Dihedral : 4.241 23.832 2400 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.88 % Rotamer: Outliers : 2.96 % Allowed : 15.70 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.19), residues: 2147 helix: 2.92 (0.16), residues: 954 sheet: 0.65 (0.24), residues: 465 loop : -1.15 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 350 HIS 0.004 0.001 HIS E 83 PHE 0.015 0.001 PHE A 27 TYR 0.017 0.001 TYR B 236 ARG 0.004 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.05140 ( 1074) hydrogen bonds : angle 4.39671 ( 3147) SS BOND : bond 0.00437 ( 4) SS BOND : angle 1.04209 ( 8) covalent geometry : bond 0.00316 (18162) covalent geometry : angle 0.55626 (24633) *********************** 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 433 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 374 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7446 (tp30) cc_final: 0.7087 (tp30) REVERT: L 49 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8496 (mt) REVERT: G 25 ARG cc_start: 0.7882 (ttm170) cc_final: 0.7213 (tpp-160) REVERT: F 11 LEU cc_start: 0.7233 (tp) cc_final: 0.6874 (tp) REVERT: F 114 ASP cc_start: 0.8712 (p0) cc_final: 0.8366 (p0) REVERT: A 78 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6322 (mp0) REVERT: A 225 ILE cc_start: 0.8014 (tp) cc_final: 0.7550 (tp) REVERT: A 341 MET cc_start: 0.7959 (mmm) cc_final: 0.7656 (mmm) REVERT: B 242 LEU cc_start: 0.8535 (mm) cc_final: 0.8207 (mm) REVERT: B 263 ASP cc_start: 0.7669 (m-30) cc_final: 0.7330 (m-30) REVERT: B 297 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7813 (mp) REVERT: C 30 GLU cc_start: 0.6621 (pt0) cc_final: 0.6417 (pt0) REVERT: C 98 LYS cc_start: 0.8019 (pttt) cc_final: 0.7811 (pttm) REVERT: C 121 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: C 152 GLU cc_start: 0.7569 (tt0) cc_final: 0.7149 (tt0) REVERT: C 186 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7684 (mm-30) REVERT: D 189 ASP cc_start: 0.7978 (t70) cc_final: 0.7638 (t70) REVERT: E 42 PHE cc_start: 0.5898 (m-80) cc_final: 0.5452 (m-80) REVERT: E 95 GLN cc_start: 0.8443 (tt0) cc_final: 0.8153 (tt0) REVERT: E 133 LYS cc_start: 0.6899 (ttmt) cc_final: 0.6332 (mmtm) REVERT: E 138 MET cc_start: 0.6869 (mmp) cc_final: 0.6290 (mmp) REVERT: E 186 GLU cc_start: 0.5649 (mp0) cc_final: 0.5277 (mp0) REVERT: E 220 GLU cc_start: 0.8068 (tt0) cc_final: 0.7493 (tt0) REVERT: E 222 ARG cc_start: 0.7298 (ttt180) cc_final: 0.6868 (ttp80) REVERT: E 246 GLU cc_start: 0.8035 (mp0) cc_final: 0.7695 (mp0) REVERT: E 291 MET cc_start: 0.7869 (tpp) cc_final: 0.7605 (tpp) REVERT: E 292 LYS cc_start: 0.7692 (tttp) cc_final: 0.7476 (tptt) REVERT: E 331 LEU cc_start: 0.6183 (mp) cc_final: 0.5954 (mp) outliers start: 59 outliers final: 34 residues processed: 405 average time/residue: 0.2708 time to fit residues: 169.3074 Evaluate side-chains 395 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 357 time to evaluate : 2.231 ------------------------------------------------------------------------------- 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 49 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 30 VAL 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 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 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 281 SER Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 334 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 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 167 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 175 optimal weight: 0.0670 chunk 151 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.200434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.135172 restraints weight = 21068.592| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.23 r_work: 0.3141 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18166 Z= 0.203 Angle : 0.607 9.037 24641 Z= 0.317 Chirality : 0.045 0.242 2788 Planarity : 0.004 0.047 3083 Dihedral : 4.398 23.371 2400 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.55 % Rotamer: Outliers : 2.81 % Allowed : 17.61 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.18), residues: 2147 helix: 2.76 (0.16), residues: 955 sheet: 0.51 (0.23), residues: 478 loop : -1.20 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 350 HIS 0.004 0.001 HIS D 94 PHE 0.018 0.001 PHE B 42 TYR 0.019 0.002 TYR D 236 ARG 0.010 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.05635 ( 1074) hydrogen bonds : angle 4.49260 ( 3147) SS BOND : bond 0.00263 ( 4) SS BOND : angle 1.23201 ( 8) covalent geometry : bond 0.00483 (18162) covalent geometry : angle 0.60624 (24633) *********************** 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 422 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 366 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7436 (tp30) cc_final: 0.7065 (tp30) REVERT: L 49 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8478 (mt) REVERT: G 25 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7581 (tpp80) REVERT: F 114 ASP cc_start: 0.8681 (p0) cc_final: 0.8435 (p0) REVERT: A 78 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6331 (mp0) REVERT: A 225 ILE cc_start: 0.7981 (tp) cc_final: 0.7547 (tp) REVERT: A 341 MET cc_start: 0.7877 (mmm) cc_final: 0.7596 (mmm) REVERT: B 242 LEU cc_start: 0.8543 (mm) cc_final: 0.8217 (mm) REVERT: B 263 ASP cc_start: 0.7684 (m-30) cc_final: 0.7338 (m-30) REVERT: B 297 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7818 (mp) REVERT: C 121 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: C 152 GLU cc_start: 0.7499 (tt0) cc_final: 0.7056 (tt0) REVERT: C 173 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7852 (mm) REVERT: D 189 ASP cc_start: 0.8041 (t70) cc_final: 0.7701 (t70) REVERT: E 95 GLN cc_start: 0.8487 (tt0) cc_final: 0.8194 (tt0) REVERT: E 133 LYS cc_start: 0.6873 (ttmt) cc_final: 0.6305 (mmtm) REVERT: E 138 MET cc_start: 0.7001 (mmp) cc_final: 0.6311 (mmp) REVERT: E 220 GLU cc_start: 0.8031 (tt0) cc_final: 0.7459 (tt0) REVERT: E 222 ARG cc_start: 0.7309 (ttt180) cc_final: 0.6881 (ttp80) REVERT: E 246 GLU cc_start: 0.8032 (mp0) cc_final: 0.7666 (mp0) REVERT: E 270 ASP cc_start: 0.7884 (m-30) cc_final: 0.7619 (m-30) REVERT: E 288 ASN cc_start: 0.7660 (t0) cc_final: 0.7274 (t0) REVERT: E 292 LYS cc_start: 0.7704 (tttp) cc_final: 0.7455 (tptt) REVERT: E 331 LEU cc_start: 0.6272 (mp) cc_final: 0.5969 (mp) outliers start: 56 outliers final: 45 residues processed: 400 average time/residue: 0.2683 time to fit residues: 166.1679 Evaluate side-chains 406 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 356 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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 49 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 30 VAL 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 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 121 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 199 VAL 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 72 VAL 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 184 LEU Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 200 LEU 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 58 optimal weight: 0.5980 chunk 52 optimal weight: 0.2980 chunk 54 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4160 r_free = 0.4160 target = 0.207945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.146235 restraints weight = 20649.257| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.13 r_work: 0.3188 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 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 = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1721 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= 0.138 Angle : 0.559 8.419 24641 Z= 0.292 Chirality : 0.043 0.238 2788 Planarity : 0.004 0.041 3083 Dihedral : 4.247 23.766 2400 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 2.31 % Allowed : 18.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.19), residues: 2147 helix: 2.95 (0.16), residues: 955 sheet: 0.64 (0.24), residues: 478 loop : -1.14 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 350 HIS 0.003 0.001 HIS D 83 PHE 0.015 0.001 PHE A 27 TYR 0.017 0.001 TYR A 236 ARG 0.005 0.000 ARG F 87 Details of bonding type rmsd hydrogen bonds : bond 0.05066 ( 1074) hydrogen bonds : angle 4.29764 ( 3147) SS BOND : bond 0.00223 ( 4) SS BOND : angle 1.22985 ( 8) covalent geometry : bond 0.00306 (18162) covalent geometry : angle 0.55909 (24633) *********************** 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 416 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 370 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7489 (tp30) cc_final: 0.7122 (tp30) REVERT: L 49 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8650 (mt) REVERT: G 25 ARG cc_start: 0.7971 (ttm170) cc_final: 0.7701 (tpp80) REVERT: F 11 LEU cc_start: 0.7322 (tp) cc_final: 0.6972 (tp) REVERT: F 114 ASP cc_start: 0.8805 (p0) cc_final: 0.8542 (p0) REVERT: A 78 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6378 (mp0) REVERT: A 162 ARG cc_start: 0.6999 (mtm110) cc_final: 0.6798 (mtp180) REVERT: A 341 MET cc_start: 0.8020 (mmm) cc_final: 0.7716 (mmm) REVERT: B 202 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.5871 (ptt-90) REVERT: B 242 LEU cc_start: 0.8580 (mm) cc_final: 0.8187 (mm) REVERT: B 263 ASP cc_start: 0.7916 (m-30) cc_final: 0.7558 (m-30) REVERT: B 297 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7918 (mp) REVERT: C 152 GLU cc_start: 0.7565 (tt0) cc_final: 0.7141 (tt0) REVERT: C 173 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7832 (mm) REVERT: C 272 VAL cc_start: 0.9126 (m) cc_final: 0.8426 (p) REVERT: C 291 MET cc_start: 0.6983 (tpp) cc_final: 0.6666 (tpp) REVERT: D 189 ASP cc_start: 0.8227 (t70) cc_final: 0.7912 (t70) REVERT: E 42 PHE cc_start: 0.5917 (m-80) cc_final: 0.5483 (m-80) REVERT: E 95 GLN cc_start: 0.8547 (tt0) cc_final: 0.8285 (tt0) REVERT: E 133 LYS cc_start: 0.6854 (ttmt) cc_final: 0.6320 (mmtm) REVERT: E 138 MET cc_start: 0.7103 (mmp) cc_final: 0.6442 (mmp) REVERT: E 220 GLU cc_start: 0.8164 (tt0) cc_final: 0.7603 (tt0) REVERT: E 222 ARG cc_start: 0.7459 (ttt180) cc_final: 0.6961 (ttp80) REVERT: E 246 GLU cc_start: 0.8071 (mp0) cc_final: 0.7687 (mp0) REVERT: E 291 MET cc_start: 0.7946 (tpp) cc_final: 0.7689 (tpp) REVERT: E 292 LYS cc_start: 0.7798 (tttp) cc_final: 0.7527 (tptt) REVERT: E 331 LEU cc_start: 0.6211 (mp) cc_final: 0.5981 (mp) outliers start: 46 outliers final: 36 residues processed: 398 average time/residue: 0.2626 time to fit residues: 161.9096 Evaluate side-chains 400 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 359 time to evaluate : 1.895 ------------------------------------------------------------------------------- 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 49 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 30 VAL 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 192 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 202 ARG 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 127 VAL Chi-restraints excluded: chain C residue 173 LEU 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 281 SER Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 334 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 236 TYR Chi-restraints excluded: chain E residue 284 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 114 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 121 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 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 = 0.4086 r_free = 0.4086 target = 0.201162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.134488 restraints weight = 20903.291| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.14 r_work: 0.3168 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18166 Z= 0.175 Angle : 0.587 8.090 24641 Z= 0.307 Chirality : 0.044 0.274 2788 Planarity : 0.004 0.040 3083 Dihedral : 4.322 23.118 2400 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.55 % Rotamer: Outliers : 2.86 % Allowed : 18.62 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.19), residues: 2147 helix: 2.85 (0.16), residues: 955 sheet: 0.59 (0.24), residues: 478 loop : -1.18 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 350 HIS 0.003 0.001 HIS D 94 PHE 0.016 0.001 PHE A 27 TYR 0.018 0.001 TYR B 236 ARG 0.008 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.05323 ( 1074) hydrogen bonds : angle 4.35049 ( 3147) SS BOND : bond 0.00161 ( 4) SS BOND : angle 1.54579 ( 8) covalent geometry : bond 0.00413 (18162) covalent geometry : angle 0.58597 (24633) *********************** 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: 57 poor density : 359 time to evaluate : 2.465 Fit side-chains revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7576 (tp30) cc_final: 0.7197 (tp30) REVERT: L 49 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8645 (mt) REVERT: G 25 ARG cc_start: 0.7991 (ttm170) cc_final: 0.7721 (tpp80) REVERT: F 11 LEU cc_start: 0.7455 (tp) cc_final: 0.7096 (tp) REVERT: F 114 ASP cc_start: 0.8811 (p0) cc_final: 0.8573 (p0) REVERT: A 54 ARG cc_start: 0.6475 (ttp80) cc_final: 0.6079 (ttp80) REVERT: A 78 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: A 162 ARG cc_start: 0.7163 (mtm110) cc_final: 0.6891 (mtp180) REVERT: A 341 MET cc_start: 0.8035 (mmm) cc_final: 0.7734 (mmm) REVERT: B 202 ARG cc_start: 0.6563 (ttp-110) cc_final: 0.5944 (ptt-90) REVERT: B 242 LEU cc_start: 0.8609 (mm) cc_final: 0.8221 (mm) REVERT: B 263 ASP cc_start: 0.8026 (m-30) cc_final: 0.7676 (m-30) REVERT: B 297 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7931 (mp) REVERT: C 152 GLU cc_start: 0.7584 (tt0) cc_final: 0.7144 (tt0) REVERT: C 173 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7868 (mm) REVERT: C 269 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8107 (ttm170) REVERT: C 291 MET cc_start: 0.6975 (tpp) cc_final: 0.6677 (tpp) REVERT: D 189 ASP cc_start: 0.8279 (t70) cc_final: 0.7956 (t70) REVERT: D 231 VAL cc_start: 0.9466 (t) cc_final: 0.9257 (t) REVERT: D 313 MET cc_start: 0.3180 (tmm) cc_final: 0.2715 (tmm) REVERT: E 42 PHE cc_start: 0.5870 (m-80) cc_final: 0.5437 (m-80) REVERT: E 95 GLN cc_start: 0.8527 (tt0) cc_final: 0.8248 (tt0) REVERT: E 116 ASP cc_start: 0.6668 (p0) cc_final: 0.6344 (p0) REVERT: E 133 LYS cc_start: 0.6841 (ttmt) cc_final: 0.6278 (mmtm) REVERT: E 138 MET cc_start: 0.7099 (mmp) cc_final: 0.6409 (mmp) REVERT: E 220 GLU cc_start: 0.8188 (tt0) cc_final: 0.7634 (tt0) REVERT: E 222 ARG cc_start: 0.7472 (ttt180) cc_final: 0.6979 (ttp80) REVERT: E 246 GLU cc_start: 0.8096 (mp0) cc_final: 0.7715 (mp0) REVERT: E 288 ASN cc_start: 0.7798 (t0) cc_final: 0.7462 (t0) REVERT: E 292 LYS cc_start: 0.7839 (tttp) cc_final: 0.7565 (tptt) REVERT: E 331 LEU cc_start: 0.6284 (mp) cc_final: 0.6064 (mp) outliers start: 57 outliers final: 46 residues processed: 396 average time/residue: 0.2622 time to fit residues: 160.8023 Evaluate side-chains 404 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 353 time to evaluate : 1.882 ------------------------------------------------------------------------------- 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 49 ILE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain A residue 30 GLU 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 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 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 173 LEU 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 218 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 234 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 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 183 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 173 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 193 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.201969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.135418 restraints weight = 21022.247| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.06 r_work: 0.3161 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 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 = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1834 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= 0.172 Angle : 0.587 8.030 24641 Z= 0.307 Chirality : 0.044 0.239 2788 Planarity : 0.004 0.040 3083 Dihedral : 4.341 23.958 2400 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % Rotamer: Outliers : 2.76 % Allowed : 19.12 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.19), residues: 2147 helix: 2.85 (0.16), residues: 955 sheet: 0.59 (0.23), residues: 485 loop : -1.20 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 350 HIS 0.003 0.001 HIS D 94 PHE 0.032 0.001 PHE E 27 TYR 0.017 0.001 TYR B 236 ARG 0.006 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.05295 ( 1074) hydrogen bonds : angle 4.34682 ( 3147) SS BOND : bond 0.00181 ( 4) SS BOND : angle 1.60193 ( 8) covalent geometry : bond 0.00404 (18162) covalent geometry : angle 0.58609 (24633) *********************** 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 414 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 359 time to evaluate : 2.092 Fit side-chains revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7579 (tp30) cc_final: 0.7192 (tp30) REVERT: L 49 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8654 (mt) REVERT: G 25 ARG cc_start: 0.8033 (ttm170) cc_final: 0.7775 (tpp80) REVERT: F 11 LEU cc_start: 0.7395 (tp) cc_final: 0.7042 (tp) REVERT: F 114 ASP cc_start: 0.8801 (p0) cc_final: 0.8563 (p0) REVERT: A 54 ARG cc_start: 0.6582 (ttp80) cc_final: 0.6200 (ttp80) REVERT: A 78 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6388 (mp0) REVERT: A 162 ARG cc_start: 0.7147 (mtm110) cc_final: 0.6919 (mtp180) REVERT: A 341 MET cc_start: 0.8010 (mmm) cc_final: 0.7716 (mmm) REVERT: B 202 ARG cc_start: 0.6604 (ttp-110) cc_final: 0.6015 (ptt-90) REVERT: B 242 LEU cc_start: 0.8618 (mm) cc_final: 0.8240 (mm) REVERT: B 263 ASP cc_start: 0.8010 (m-30) cc_final: 0.7662 (m-30) REVERT: B 297 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7916 (mp) REVERT: C 152 GLU cc_start: 0.7603 (tt0) cc_final: 0.7168 (tt0) REVERT: C 173 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7930 (mm) REVERT: D 189 ASP cc_start: 0.8277 (t70) cc_final: 0.7950 (t70) REVERT: E 42 PHE cc_start: 0.5901 (m-80) cc_final: 0.5480 (m-80) REVERT: E 95 GLN cc_start: 0.8497 (tt0) cc_final: 0.8207 (tt0) REVERT: E 133 LYS cc_start: 0.6801 (ttmt) cc_final: 0.6274 (mmtm) REVERT: E 138 MET cc_start: 0.7030 (mmp) cc_final: 0.6296 (mmp) REVERT: E 220 GLU cc_start: 0.8222 (tt0) cc_final: 0.7678 (tt0) REVERT: E 222 ARG cc_start: 0.7538 (ttt180) cc_final: 0.7036 (ttp80) REVERT: E 246 GLU cc_start: 0.8083 (mp0) cc_final: 0.7719 (mp0) REVERT: E 288 ASN cc_start: 0.7796 (t0) cc_final: 0.7453 (t0) REVERT: E 292 LYS cc_start: 0.7808 (tttp) cc_final: 0.7525 (tptt) REVERT: E 331 LEU cc_start: 0.6321 (mp) cc_final: 0.6103 (mp) outliers start: 55 outliers final: 47 residues processed: 394 average time/residue: 0.2681 time to fit residues: 163.5100 Evaluate side-chains 405 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 354 time to evaluate : 2.093 ------------------------------------------------------------------------------- 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 49 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 73 THR 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 171 TYR Chi-restraints excluded: chain A residue 236 TYR 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 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 173 LEU 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 199 VAL 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 234 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 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 Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 172 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 201 optimal weight: 0.0270 chunk 27 optimal weight: 0.0470 chunk 52 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 117 optimal weight: 0.0040 chunk 184 optimal weight: 0.0470 chunk 181 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 overall best weight: 0.1646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 28 ASN ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.206163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.141555 restraints weight = 21055.963| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.31 r_work: 0.3176 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 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 = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18166 Z= 0.120 Angle : 0.558 7.808 24641 Z= 0.290 Chirality : 0.042 0.169 2788 Planarity : 0.004 0.040 3083 Dihedral : 4.148 22.594 2400 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.83 % Rotamer: Outliers : 2.11 % Allowed : 20.17 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.19), residues: 2147 helix: 3.09 (0.16), residues: 955 sheet: 0.82 (0.24), residues: 470 loop : -1.12 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 350 HIS 0.003 0.000 HIS D 83 PHE 0.026 0.001 PHE E 27 TYR 0.018 0.001 TYR A 236 ARG 0.005 0.000 ARG F 87 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 1074) hydrogen bonds : angle 4.16204 ( 3147) SS BOND : bond 0.00321 ( 4) SS BOND : angle 1.54831 ( 8) covalent geometry : bond 0.00250 (18162) covalent geometry : angle 0.55718 (24633) ********************** 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 438 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 396 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 49 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8490 (mp) REVERT: G 25 ARG cc_start: 0.7884 (ttm170) cc_final: 0.7665 (tpp80) REVERT: G 87 TYR cc_start: 0.8846 (m-80) cc_final: 0.8607 (m-80) REVERT: A 54 ARG cc_start: 0.6488 (ttp80) cc_final: 0.6097 (ttp80) REVERT: A 78 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6295 (mp0) REVERT: A 341 MET cc_start: 0.7969 (mmm) cc_final: 0.7675 (mmm) REVERT: B 34 TYR cc_start: 0.8535 (p90) cc_final: 0.8187 (p90) REVERT: B 242 LEU cc_start: 0.8410 (mm) cc_final: 0.8031 (mm) REVERT: B 263 ASP cc_start: 0.7736 (m-30) cc_final: 0.7361 (m-30) REVERT: B 297 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7799 (mp) REVERT: C 152 GLU cc_start: 0.7509 (tt0) cc_final: 0.7037 (tt0) REVERT: C 173 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7562 (mm) REVERT: C 272 VAL cc_start: 0.9050 (m) cc_final: 0.8335 (p) REVERT: C 313 MET cc_start: 0.1043 (mmm) cc_final: 0.0025 (ppp) REVERT: D 48 GLU cc_start: 0.8109 (mp0) cc_final: 0.7877 (mp0) REVERT: D 189 ASP cc_start: 0.7910 (t70) cc_final: 0.7606 (t70) REVERT: D 313 MET cc_start: 0.4118 (OUTLIER) cc_final: 0.3718 (mpp) REVERT: E 42 PHE cc_start: 0.5943 (m-80) cc_final: 0.5562 (m-80) REVERT: E 95 GLN cc_start: 0.8440 (tt0) cc_final: 0.8190 (tt0) REVERT: E 111 LYS cc_start: 0.6650 (mmtp) cc_final: 0.6296 (mmtp) REVERT: E 133 LYS cc_start: 0.6831 (ttmt) cc_final: 0.6326 (mmtm) REVERT: E 138 MET cc_start: 0.6922 (mmp) cc_final: 0.6197 (mmp) REVERT: E 220 GLU cc_start: 0.8037 (tt0) cc_final: 0.7440 (tt0) REVERT: E 246 GLU cc_start: 0.8056 (mp0) cc_final: 0.7691 (mp0) REVERT: E 291 MET cc_start: 0.7816 (tpp) cc_final: 0.7542 (tpp) REVERT: E 292 LYS cc_start: 0.7633 (tttp) cc_final: 0.7314 (tptt) REVERT: E 331 LEU cc_start: 0.6310 (mp) cc_final: 0.6082 (mp) outliers start: 42 outliers final: 31 residues processed: 420 average time/residue: 0.2692 time to fit residues: 175.9170 Evaluate side-chains 418 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 382 time to evaluate : 1.955 ------------------------------------------------------------------------------- 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 49 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 171 TYR 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 297 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 196 GLU 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 313 MET Chi-restraints excluded: chain D residue 334 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 287 THR Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 186 optimal weight: 0.3980 chunk 142 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 87 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 189 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.202874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.135936 restraints weight = 20957.531| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.12 r_work: 0.3185 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18166 Z= 0.155 Angle : 0.579 8.194 24641 Z= 0.302 Chirality : 0.043 0.196 2788 Planarity : 0.004 0.041 3083 Dihedral : 4.216 23.494 2400 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % Rotamer: Outliers : 1.91 % Allowed : 20.52 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.19), residues: 2147 helix: 2.97 (0.16), residues: 956 sheet: 0.79 (0.24), residues: 482 loop : -1.20 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 350 HIS 0.003 0.001 HIS B 68 PHE 0.029 0.001 PHE E 27 TYR 0.017 0.001 TYR A 236 ARG 0.006 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.04960 ( 1074) hydrogen bonds : angle 4.22354 ( 3147) SS BOND : bond 0.00217 ( 4) SS BOND : angle 1.60800 ( 8) covalent geometry : bond 0.00359 (18162) covalent geometry : angle 0.57819 (24633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11420.33 seconds wall clock time: 198 minutes 9.08 seconds (11889.08 seconds total)