Starting phenix.real_space_refine on Fri Sep 11 02:44:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21lt_67804/09_2026/21lt_67804.cif Found real_map, /net/cci-nas-00/data/ceres_data/21lt_67804/09_2026/21lt_67804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21lt_67804/09_2026/21lt_67804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21lt_67804/09_2026/21lt_67804.map" model { file = "/net/cci-nas-00/data/ceres_data/21lt_67804/09_2026/21lt_67804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21lt_67804/09_2026/21lt_67804.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 54 5.16 5 C 4312 2.51 5 N 1152 2.21 5 O 1229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6748 Number of models: 1 Model: "" Number of chains: 8 Chain: "P" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "P" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Classifications: {'peptide': 2} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 1} Chain: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 3} Chain: "R" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2007 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1887 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2452 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 8, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 94 Chain: "G" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 327 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.27, per 1000 atoms: 0.19 Number of scatterers: 6748 At special positions: 0 Unit cell: (73.13, 100.94, 127.72, 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) Ca 1 19.99 S 54 16.00 O 1229 8.00 N 1152 7.00 C 4312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 8 " distance=2.03 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 279 " distance=2.03 Simple disulfide: pdb=" SG CYS R 271 " - pdb=" SG CYS R 277 " distance=2.04 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 Links applied TRANS " DAL P 3 " - " CYS P 2 " " DPN P 5 " - " HIS P 4 " Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 343.3 milliseconds 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL P 3 " pdb=" CB DPN P 5 " Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 46.9% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 47 through 71 removed outlier: 3.834A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER R 58 " --> pdb=" O LEU R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 106 removed outlier: 3.824A pdb=" N PHE R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA R 89 " --> pdb=" O SER R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 153 removed outlier: 3.957A pdb=" N ASP R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASN R 123 " --> pdb=" O VAL R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 161 Processing helix chain 'R' and resid 162 through 187 Processing helix chain 'R' and resid 190 through 227 removed outlier: 4.117A pdb=" N ILE R 194 " --> pdb=" O SER R 190 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE R 201 " --> pdb=" O LEU R 197 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET R 204 " --> pdb=" O MET R 200 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG R 225 " --> pdb=" O LEU R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 270 removed outlier: 4.049A pdb=" N PHE R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 280 through 282 No H-bonds generated for 'chain 'R' and resid 280 through 282' Processing helix chain 'R' and resid 283 through 303 removed outlier: 3.580A pdb=" N TYR R 287 " --> pdb=" O HIS R 283 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 315 removed outlier: 3.629A pdb=" N LYS R 314 " --> pdb=" O ARG R 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 removed outlier: 4.068A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 removed outlier: 4.051A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.612A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 removed outlier: 3.938A pdb=" N ASN A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.825A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.581A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 318 Processing helix chain 'A' and resid 337 through 359 Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.583A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 13 through 24 removed outlier: 3.764A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.065A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.515A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.965A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.312A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.590A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.752A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.473A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.848A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1391 1.33 - 1.45: 1665 1.45 - 1.58: 3747 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 6878 Sorted by residual: bond pdb=" CA LEU R 75 " pdb=" C LEU R 75 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.14e-02 7.69e+03 1.21e+01 bond pdb=" CA LEU R 75 " pdb=" CB LEU R 75 " ideal model delta sigma weight residual 1.524 1.483 0.041 1.30e-02 5.92e+03 1.00e+01 bond pdb=" CA LYS R 73 " pdb=" C LYS R 73 " ideal model delta sigma weight residual 1.522 1.483 0.039 1.39e-02 5.18e+03 7.87e+00 bond pdb=" CA HIS R 76 " pdb=" C HIS R 76 " ideal model delta sigma weight residual 1.524 1.495 0.029 1.29e-02 6.01e+03 5.06e+00 bond pdb=" CA HIS R 76 " pdb=" CB HIS R 76 " ideal model delta sigma weight residual 1.530 1.500 0.030 1.39e-02 5.18e+03 4.71e+00 ... (remaining 6873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 9203 2.50 - 5.00: 136 5.00 - 7.49: 14 7.49 - 9.99: 0 9.99 - 12.49: 1 Bond angle restraints: 9354 Sorted by residual: angle pdb=" C HIS R 76 " pdb=" N SER R 77 " pdb=" CA SER R 77 " ideal model delta sigma weight residual 120.68 126.67 -5.99 1.52e+00 4.33e-01 1.55e+01 angle pdb=" C LEU R 221 " pdb=" N HIS R 222 " pdb=" CA HIS R 222 " ideal model delta sigma weight residual 122.26 116.13 6.13 1.59e+00 3.96e-01 1.49e+01 angle pdb=" N LEU R 75 " pdb=" CA LEU R 75 " pdb=" CB LEU R 75 " ideal model delta sigma weight residual 110.45 105.71 4.74 1.26e+00 6.30e-01 1.42e+01 angle pdb=" CA LEU A 360 " pdb=" CB LEU A 360 " pdb=" CG LEU A 360 " ideal model delta sigma weight residual 116.30 128.79 -12.49 3.50e+00 8.16e-02 1.27e+01 angle pdb=" N ALA R 68 " pdb=" CA ALA R 68 " pdb=" C ALA R 68 " ideal model delta sigma weight residual 111.82 107.84 3.98 1.16e+00 7.43e-01 1.18e+01 ... (remaining 9349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 3715 17.45 - 34.90: 297 34.90 - 52.36: 47 52.36 - 69.81: 7 69.81 - 87.26: 3 Dihedral angle restraints: 4069 sinusoidal: 1469 harmonic: 2600 Sorted by residual: dihedral pdb=" CB CYS R 271 " pdb=" SG CYS R 271 " pdb=" SG CYS R 277 " pdb=" CB CYS R 277 " ideal model delta sinusoidal sigma weight residual 93.00 -179.74 -87.26 1 1.00e+01 1.00e-02 9.14e+01 dihedral pdb=" CA ASP B 246 " pdb=" C ASP B 246 " pdb=" N ASP B 247 " pdb=" CA ASP B 247 " ideal model delta harmonic sigma weight residual 180.00 -153.39 -26.61 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual -180.00 -157.64 -22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 4066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 556 0.031 - 0.063: 345 0.063 - 0.094: 133 0.094 - 0.126: 65 0.126 - 0.157: 12 Chirality restraints: 1111 Sorted by residual: chirality pdb=" CB ILE R 173 " pdb=" CA ILE R 173 " pdb=" CG1 ILE R 173 " pdb=" CG2 ILE R 173 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA PRO R 299 " pdb=" N PRO R 299 " pdb=" C PRO R 299 " pdb=" CB PRO R 299 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA VAL A 225 " pdb=" N VAL A 225 " pdb=" C VAL A 225 " pdb=" CB VAL A 225 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 1108 not shown) Planarity restraints: 1181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO G 49 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 274 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO R 275 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 275 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 275 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 169 " 0.017 2.00e-02 2.50e+03 1.31e-02 4.27e+00 pdb=" CG TRP B 169 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 169 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 169 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 169 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 169 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 169 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 169 " 0.003 2.00e-02 2.50e+03 ... (remaining 1178 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 111 2.64 - 3.21: 6749 3.21 - 3.77: 10543 3.77 - 4.34: 14694 4.34 - 4.90: 24271 Nonbonded interactions: 56368 Sorted by model distance: nonbonded pdb=" OD1 ASP R 146 " pdb=" OH TYR R 157 " model vdw 2.080 3.040 nonbonded pdb=" OE2 GLU A 297 " pdb=" OG1 THR A 302 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR A 181 " pdb=" O HIS B 142 " model vdw 2.142 3.040 nonbonded pdb=" O TYR R 187 " pdb=" OG SER R 190 " model vdw 2.154 3.040 nonbonded pdb=" O SER R 85 " pdb=" OG SER R 139 " model vdw 2.162 3.040 ... (remaining 56363 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.980 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.008 0.060 6883 Z= 0.337 Angle : 0.766 12.490 9366 Z= 0.432 Chirality : 0.049 0.157 1111 Planarity : 0.004 0.061 1179 Dihedral : 12.980 80.916 2362 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.29), residues: 868 helix: 0.46 (0.27), residues: 383 sheet: -0.47 (0.40), residues: 162 loop : -0.74 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 68 TYR 0.024 0.002 TYR R 187 PHE 0.017 0.002 PHE B 235 TRP 0.035 0.003 TRP B 169 HIS 0.010 0.002 HIS R 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00768 / 0.34 ( 6878) covalent geometry : angle 0.76508 / 0.43 ( 9354) SS BOND : bond 0.00514 / 0.26 ( 3) SS BOND : angle 1.54497 / 0.79 ( 6) hydrogen bonds : bond 0.14498 / 9.20 ( 380) hydrogen bonds : angle 6.66761 / 4.95 ( 1107) link_TRANS : bond 0.00419 / 0.20 ( 2) link_TRANS : angle 0.80053 / 0.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 357 GLU cc_start: 0.7379 (tp30) cc_final: 0.7111 (tp30) REVERT: B 258 ASP cc_start: 0.6449 (m-30) cc_final: 0.6068 (t0) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.0668 time to fit residues: 9.0564 Evaluate side-chains 88 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 72 ASN R 123 ASN R 294 ASN A 190 GLN A 197 HIS B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.121810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.095503 restraints weight = 13243.954| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.27 r_work: 0.3439 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6883 Z= 0.164 Angle : 0.583 5.947 9366 Z= 0.316 Chirality : 0.043 0.150 1111 Planarity : 0.004 0.054 1179 Dihedral : 5.097 28.165 950 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.57 % Allowed : 6.59 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.29), residues: 868 helix: 1.10 (0.27), residues: 394 sheet: -0.49 (0.38), residues: 177 loop : -0.62 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 310 TYR 0.010 0.001 TYR R 187 PHE 0.014 0.002 PHE A 189 TRP 0.026 0.002 TRP B 169 HIS 0.008 0.001 HIS R 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 6878) covalent geometry : angle 0.58281 / 0.32 ( 9354) SS BOND : bond 0.00432 / 0.22 ( 3) SS BOND : angle 0.86953 / 0.45 ( 6) hydrogen bonds : bond 0.04576 / 2.97 ( 380) hydrogen bonds : angle 4.93818 / 3.66 ( 1107) link_TRANS : bond 0.00154 / 0.08 ( 2) link_TRANS : angle 0.52666 / 0.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: R 76 HIS cc_start: 0.8496 (OUTLIER) cc_final: 0.8230 (m-70) REVERT: A 14 GLU cc_start: 0.8044 (pp20) cc_final: 0.7651 (pp20) REVERT: B 258 ASP cc_start: 0.7160 (m-30) cc_final: 0.6711 (t0) outliers start: 4 outliers final: 1 residues processed: 99 average time/residue: 0.0624 time to fit residues: 8.8278 Evaluate side-chains 93 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 HIS Chi-restraints excluded: chain A residue 331 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 0.0570 chunk 85 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.122367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.093471 restraints weight = 13138.274| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.49 r_work: 0.3447 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6883 Z= 0.151 Angle : 0.544 5.532 9366 Z= 0.295 Chirality : 0.042 0.146 1111 Planarity : 0.004 0.049 1179 Dihedral : 4.827 30.804 950 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.00 % Allowed : 10.89 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.29), residues: 868 helix: 1.47 (0.27), residues: 393 sheet: -0.29 (0.38), residues: 176 loop : -0.63 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 310 TYR 0.011 0.001 TYR A 278 PHE 0.015 0.002 PHE A 189 TRP 0.022 0.002 TRP B 169 HIS 0.007 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 6878) covalent geometry : angle 0.54344 / 0.29 ( 9354) SS BOND : bond 0.00403 / 0.20 ( 3) SS BOND : angle 0.68386 / 0.35 ( 6) hydrogen bonds : bond 0.04194 / 2.72 ( 380) hydrogen bonds : angle 4.66626 / 3.46 ( 1107) link_TRANS : bond 0.00167 / 0.08 ( 2) link_TRANS : angle 0.51550 / 0.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: R 153 TYR cc_start: 0.7568 (m-80) cc_final: 0.7244 (m-80) REVERT: A 311 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6435 (mp0) REVERT: B 61 MET cc_start: 0.8347 (ptm) cc_final: 0.8019 (ptm) REVERT: B 258 ASP cc_start: 0.7128 (m-30) cc_final: 0.6727 (t0) REVERT: G 50 LEU cc_start: 0.8651 (mm) cc_final: 0.8366 (mp) outliers start: 7 outliers final: 0 residues processed: 106 average time/residue: 0.0677 time to fit residues: 10.1154 Evaluate side-chains 95 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 66 optimal weight: 0.1980 chunk 22 optimal weight: 0.0170 chunk 82 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.122152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.093500 restraints weight = 13267.298| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.42 r_work: 0.3446 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6883 Z= 0.149 Angle : 0.533 5.322 9366 Z= 0.288 Chirality : 0.042 0.145 1111 Planarity : 0.004 0.045 1179 Dihedral : 4.739 32.133 950 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.86 % Allowed : 12.18 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.29), residues: 868 helix: 1.62 (0.27), residues: 393 sheet: -0.26 (0.38), residues: 178 loop : -0.52 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.012 0.001 TYR A 278 PHE 0.015 0.002 PHE A 307 TRP 0.020 0.002 TRP B 169 HIS 0.005 0.001 HIS R 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 6878) covalent geometry : angle 0.53304 / 0.29 ( 9354) SS BOND : bond 0.00435 / 0.22 ( 3) SS BOND : angle 0.59758 / 0.30 ( 6) hydrogen bonds : bond 0.04060 / 2.63 ( 380) hydrogen bonds : angle 4.55308 / 3.38 ( 1107) link_TRANS : bond 0.00166 / 0.08 ( 2) link_TRANS : angle 0.51457 / 0.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: R 153 TYR cc_start: 0.7517 (m-80) cc_final: 0.7274 (m-80) REVERT: A 311 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6405 (mp0) REVERT: B 61 MET cc_start: 0.8328 (ptm) cc_final: 0.7974 (ptm) REVERT: B 258 ASP cc_start: 0.7152 (m-30) cc_final: 0.6721 (t0) REVERT: B 336 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8192 (tp) outliers start: 13 outliers final: 5 residues processed: 110 average time/residue: 0.0726 time to fit residues: 11.2293 Evaluate side-chains 100 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.122774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.094197 restraints weight = 13269.457| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.43 r_work: 0.3456 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6883 Z= 0.133 Angle : 0.532 7.758 9366 Z= 0.285 Chirality : 0.041 0.144 1111 Planarity : 0.004 0.044 1179 Dihedral : 4.602 31.227 950 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.29 % Allowed : 12.89 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.29), residues: 868 helix: 1.71 (0.27), residues: 395 sheet: -0.21 (0.38), residues: 178 loop : -0.51 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.012 0.001 TYR A 278 PHE 0.017 0.001 PHE A 307 TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS R 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 6878) covalent geometry : angle 0.53242 / 0.28 ( 9354) SS BOND : bond 0.00413 / 0.21 ( 3) SS BOND : angle 0.50805 / 0.25 ( 6) hydrogen bonds : bond 0.03896 / 2.53 ( 380) hydrogen bonds : angle 4.45422 / 3.29 ( 1107) link_TRANS : bond 0.00161 / 0.08 ( 2) link_TRANS : angle 0.54721 / 0.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: R 153 TYR cc_start: 0.7504 (m-80) cc_final: 0.7225 (m-80) REVERT: A 52 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 307 PHE cc_start: 0.7058 (t80) cc_final: 0.6346 (t80) REVERT: A 311 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6411 (mp0) REVERT: B 61 MET cc_start: 0.8317 (ptm) cc_final: 0.7996 (ptm) REVERT: B 164 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8260 (m) REVERT: B 258 ASP cc_start: 0.7129 (m-30) cc_final: 0.6695 (t0) REVERT: B 336 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8123 (tp) REVERT: G 50 LEU cc_start: 0.8680 (mm) cc_final: 0.8353 (mt) outliers start: 16 outliers final: 6 residues processed: 113 average time/residue: 0.0676 time to fit residues: 10.8810 Evaluate side-chains 100 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 42 optimal weight: 0.0870 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.123336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.094685 restraints weight = 13318.016| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.44 r_work: 0.3470 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6883 Z= 0.125 Angle : 0.527 6.951 9366 Z= 0.283 Chirality : 0.041 0.140 1111 Planarity : 0.004 0.043 1179 Dihedral : 4.499 29.907 950 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.15 % Allowed : 14.18 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.29), residues: 868 helix: 1.75 (0.27), residues: 398 sheet: 0.01 (0.38), residues: 174 loop : -0.44 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.012 0.001 TYR A 278 PHE 0.015 0.001 PHE A 189 TRP 0.018 0.002 TRP B 169 HIS 0.004 0.001 HIS R 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 6878) covalent geometry : angle 0.52667 / 0.28 ( 9354) SS BOND : bond 0.00385 / 0.19 ( 3) SS BOND : angle 0.43435 / 0.21 ( 6) hydrogen bonds : bond 0.03790 / 2.47 ( 380) hydrogen bonds : angle 4.37283 / 3.22 ( 1107) link_TRANS : bond 0.00149 / 0.08 ( 2) link_TRANS : angle 0.55777 / 0.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: R 153 TYR cc_start: 0.7455 (m-80) cc_final: 0.7198 (m-80) REVERT: R 173 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8049 (mp) REVERT: A 52 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 311 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6332 (mp0) REVERT: B 61 MET cc_start: 0.8261 (ptm) cc_final: 0.7996 (ptm) REVERT: B 164 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8207 (m) REVERT: B 234 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7922 (m-80) REVERT: B 258 ASP cc_start: 0.7119 (m-30) cc_final: 0.6648 (t0) REVERT: B 336 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8127 (tp) REVERT: G 50 LEU cc_start: 0.8702 (mm) cc_final: 0.8345 (mt) outliers start: 15 outliers final: 7 residues processed: 109 average time/residue: 0.0718 time to fit residues: 11.1160 Evaluate side-chains 102 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 57 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.123005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.094404 restraints weight = 13083.661| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.40 r_work: 0.3468 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6883 Z= 0.135 Angle : 0.527 6.578 9366 Z= 0.285 Chirality : 0.042 0.141 1111 Planarity : 0.004 0.041 1179 Dihedral : 4.473 31.215 950 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.01 % Allowed : 14.04 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.29), residues: 868 helix: 1.80 (0.27), residues: 396 sheet: -0.06 (0.38), residues: 176 loop : -0.40 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.014 0.001 TYR A 278 PHE 0.022 0.002 PHE A 307 TRP 0.017 0.002 TRP B 169 HIS 0.004 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 6878) covalent geometry : angle 0.52747 / 0.28 ( 9354) SS BOND : bond 0.00404 / 0.20 ( 3) SS BOND : angle 0.49365 / 0.24 ( 6) hydrogen bonds : bond 0.03790 / 2.47 ( 380) hydrogen bonds : angle 4.35408 / 3.21 ( 1107) link_TRANS : bond 0.00149 / 0.08 ( 2) link_TRANS : angle 0.53693 / 0.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: R 153 TYR cc_start: 0.7465 (m-80) cc_final: 0.7239 (m-80) REVERT: R 173 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8112 (mp) REVERT: R 292 MET cc_start: 0.7888 (mmm) cc_final: 0.7362 (mtt) REVERT: A 52 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8112 (tm-30) REVERT: A 307 PHE cc_start: 0.7027 (t80) cc_final: 0.6386 (t80) REVERT: A 311 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6429 (mp0) REVERT: B 164 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8185 (m) REVERT: B 234 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: B 258 ASP cc_start: 0.7133 (m-30) cc_final: 0.6641 (t0) outliers start: 14 outliers final: 8 residues processed: 105 average time/residue: 0.0647 time to fit residues: 9.6230 Evaluate side-chains 103 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 64 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 15 optimal weight: 0.0870 chunk 6 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 264 HIS ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.123932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.098034 restraints weight = 13108.865| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.35 r_work: 0.3489 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6883 Z= 0.116 Angle : 0.516 5.668 9366 Z= 0.279 Chirality : 0.041 0.140 1111 Planarity : 0.004 0.043 1179 Dihedral : 4.334 28.466 950 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.15 % Allowed : 13.61 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.29), residues: 868 helix: 1.90 (0.27), residues: 398 sheet: -0.05 (0.38), residues: 176 loop : -0.40 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.014 0.001 TYR A 278 PHE 0.019 0.001 PHE A 307 TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 6878) covalent geometry : angle 0.51621 / 0.28 ( 9354) SS BOND : bond 0.00358 / 0.18 ( 3) SS BOND : angle 0.39537 / 0.19 ( 6) hydrogen bonds : bond 0.03598 / 2.36 ( 380) hydrogen bonds : angle 4.26568 / 3.14 ( 1107) link_TRANS : bond 0.00135 / 0.07 ( 2) link_TRANS : angle 0.57269 / 0.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: R 84 CYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7583 (t) REVERT: R 153 TYR cc_start: 0.7436 (m-80) cc_final: 0.7163 (m-80) REVERT: R 173 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7981 (mp) REVERT: R 289 ILE cc_start: 0.8542 (mm) cc_final: 0.8299 (mt) REVERT: R 292 MET cc_start: 0.7880 (mmm) cc_final: 0.7534 (mtt) REVERT: A 52 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8111 (tm-30) REVERT: A 197 HIS cc_start: 0.8511 (t-170) cc_final: 0.7857 (t-170) REVERT: A 279 PHE cc_start: 0.8077 (m-10) cc_final: 0.7710 (m-80) REVERT: A 311 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: B 164 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8011 (m) REVERT: B 234 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: B 258 ASP cc_start: 0.7066 (m-30) cc_final: 0.6609 (t0) REVERT: G 50 LEU cc_start: 0.8682 (mm) cc_final: 0.8358 (mt) outliers start: 15 outliers final: 8 residues processed: 111 average time/residue: 0.0675 time to fit residues: 10.7120 Evaluate side-chains 106 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 25 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.122276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.093083 restraints weight = 13289.791| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.50 r_work: 0.3439 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6883 Z= 0.164 Angle : 0.555 6.749 9366 Z= 0.298 Chirality : 0.042 0.144 1111 Planarity : 0.004 0.044 1179 Dihedral : 4.524 34.466 950 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.01 % Allowed : 14.47 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.29), residues: 868 helix: 1.76 (0.27), residues: 396 sheet: -0.14 (0.37), residues: 181 loop : -0.33 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 22 TYR 0.015 0.001 TYR A 278 PHE 0.025 0.002 PHE A 307 TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS R 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 6878) covalent geometry : angle 0.55520 / 0.30 ( 9354) SS BOND : bond 0.00442 / 0.22 ( 3) SS BOND : angle 0.60030 / 0.30 ( 6) hydrogen bonds : bond 0.03942 / 2.55 ( 380) hydrogen bonds : angle 4.43401 / 3.29 ( 1107) link_TRANS : bond 0.00169 / 0.08 ( 2) link_TRANS : angle 0.50133 / 0.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: R 153 TYR cc_start: 0.7569 (m-80) cc_final: 0.7297 (m-80) REVERT: R 292 MET cc_start: 0.7909 (mmm) cc_final: 0.7331 (mtt) REVERT: A 52 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8101 (tm-30) REVERT: A 197 HIS cc_start: 0.8546 (t-170) cc_final: 0.7910 (t-170) REVERT: A 307 PHE cc_start: 0.7045 (t80) cc_final: 0.6378 (t80) REVERT: A 311 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: B 234 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: B 258 ASP cc_start: 0.7121 (m-30) cc_final: 0.6637 (t0) REVERT: B 336 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8037 (tp) REVERT: G 50 LEU cc_start: 0.8630 (mm) cc_final: 0.8327 (mt) outliers start: 14 outliers final: 7 residues processed: 107 average time/residue: 0.0674 time to fit residues: 10.3793 Evaluate side-chains 103 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.124233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.095495 restraints weight = 13272.810| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.44 r_work: 0.3485 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6883 Z= 0.119 Angle : 0.532 6.893 9366 Z= 0.287 Chirality : 0.041 0.184 1111 Planarity : 0.004 0.044 1179 Dihedral : 4.327 28.641 950 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.86 % Allowed : 15.19 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.29), residues: 868 helix: 1.90 (0.27), residues: 397 sheet: -0.09 (0.38), residues: 176 loop : -0.39 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 22 TYR 0.014 0.001 TYR A 278 PHE 0.025 0.001 PHE A 307 TRP 0.014 0.002 TRP R 174 HIS 0.004 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 6878) covalent geometry : angle 0.53178 / 0.29 ( 9354) SS BOND : bond 0.00368 / 0.18 ( 3) SS BOND : angle 0.37394 / 0.19 ( 6) hydrogen bonds : bond 0.03643 / 2.38 ( 380) hydrogen bonds : angle 4.30724 / 3.17 ( 1107) link_TRANS : bond 0.00148 / 0.08 ( 2) link_TRANS : angle 0.58790 / 0.38 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: R 84 CYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7656 (t) REVERT: R 153 TYR cc_start: 0.7438 (m-80) cc_final: 0.7197 (m-80) REVERT: R 289 ILE cc_start: 0.8562 (mm) cc_final: 0.8310 (mt) REVERT: R 292 MET cc_start: 0.7919 (mmm) cc_final: 0.7262 (mtt) REVERT: A 52 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8097 (tm-30) REVERT: A 197 HIS cc_start: 0.8454 (t-170) cc_final: 0.7770 (t-170) REVERT: A 235 GLU cc_start: 0.8199 (pm20) cc_final: 0.7993 (pm20) REVERT: A 279 PHE cc_start: 0.7733 (m-80) cc_final: 0.7345 (m-80) REVERT: A 307 PHE cc_start: 0.6959 (t80) cc_final: 0.6361 (t80) REVERT: A 311 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6454 (mp0) REVERT: B 164 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8069 (m) REVERT: B 234 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: B 258 ASP cc_start: 0.7108 (m-30) cc_final: 0.6627 (t0) REVERT: G 50 LEU cc_start: 0.8672 (mm) cc_final: 0.8354 (mt) outliers start: 13 outliers final: 7 residues processed: 106 average time/residue: 0.0678 time to fit residues: 10.2158 Evaluate side-chains 104 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 CYS Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 0.0670 chunk 21 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 64 optimal weight: 0.0270 chunk 75 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 74 ASN ** R 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.124368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.095617 restraints weight = 13228.726| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.44 r_work: 0.3488 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6883 Z= 0.118 Angle : 0.529 5.922 9366 Z= 0.286 Chirality : 0.041 0.158 1111 Planarity : 0.004 0.043 1179 Dihedral : 4.303 28.793 950 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.86 % Allowed : 15.04 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.29), residues: 868 helix: 1.87 (0.27), residues: 399 sheet: -0.05 (0.38), residues: 170 loop : -0.40 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.014 0.001 TYR A 278 PHE 0.023 0.001 PHE A 307 TRP 0.012 0.001 TRP R 174 HIS 0.004 0.001 HIS R 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 6878) covalent geometry : angle 0.52870 / 0.29 ( 9354) SS BOND : bond 0.00373 / 0.19 ( 3) SS BOND : angle 0.42173 / 0.21 ( 6) hydrogen bonds : bond 0.03604 / 2.35 ( 380) hydrogen bonds : angle 4.27389 / 3.15 ( 1107) link_TRANS : bond 0.00142 / 0.07 ( 2) link_TRANS : angle 0.56437 / 0.36 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2201.54 seconds wall clock time: 38 minutes 14.02 seconds (2294.02 seconds total)