Starting phenix.real_space_refine on Sat Aug 23 00:45:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hvi_35044/08_2025/8hvi_35044_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hvi_35044/08_2025/8hvi_35044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hvi_35044/08_2025/8hvi_35044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hvi_35044/08_2025/8hvi_35044.map" model { file = "/net/cci-nas-00/data/ceres_data/8hvi_35044/08_2025/8hvi_35044_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hvi_35044/08_2025/8hvi_35044_neut.cif" } resolution = 3.04 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5697 2.51 5 N 1537 2.21 5 O 1689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8988 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2439 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 301} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1713 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 212} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2601 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'NFI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.67, per 1000 atoms: 0.19 Number of scatterers: 8988 At special positions: 0 Unit cell: (115.132, 118.36, 125.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 1689 8.00 N 1537 7.00 C 5697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 207.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 37.1% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'R' and resid 39 through 72 removed outlier: 3.580A pdb=" N ILE R 43 " --> pdb=" O GLU R 39 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL R 52 " --> pdb=" O VAL R 48 " (cutoff:3.500A) Proline residue: R 58 - end of helix removed outlier: 3.590A pdb=" N LEU R 72 " --> pdb=" O LEU R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 91 Processing helix chain 'R' and resid 94 through 102 removed outlier: 3.824A pdb=" N TRP R 98 " --> pdb=" O THR R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 146 removed outlier: 3.836A pdb=" N LYS R 116 " --> pdb=" O LEU R 112 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL R 117 " --> pdb=" O LEU R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 153 Processing helix chain 'R' and resid 157 through 181 Proline residue: R 176 - end of helix Processing helix chain 'R' and resid 193 through 229 Proline residue: R 211 - end of helix Processing helix chain 'R' and resid 233 through 271 Proline residue: R 257 - end of helix Processing helix chain 'R' and resid 286 through 302 Processing helix chain 'R' and resid 303 through 313 Processing helix chain 'R' and resid 316 through 331 removed outlier: 4.100A pdb=" N SER R 320 " --> pdb=" O ARG R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 344 Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.650A pdb=" N LYS B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 removed outlier: 4.327A pdb=" N TRP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.703A pdb=" N LYS B 248 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 249 " --> pdb=" O GLU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 295 through 310 removed outlier: 3.606A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 352 removed outlier: 3.660A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 338 " --> pdb=" O PHE B 334 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP B 350 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 26 removed outlier: 3.646A pdb=" N LEU C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 4.055A pdb=" N THR C 34 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 22 removed outlier: 3.655A pdb=" N LYS D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.511A pdb=" N SER H 31 " --> pdb=" O ALA H 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 6.761A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 52 removed outlier: 4.155A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 338 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 331 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 327 " --> pdb=" O TRP C 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.783A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.370A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.513A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.660A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 4.038A pdb=" N LEU C 252 " --> pdb=" O MET C 262 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 275 through 277 removed outlier: 3.762A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN C 295 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 17 through 23 removed outlier: 3.592A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 47 through 51 removed outlier: 3.651A pdb=" N TRP H 36 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'H' and resid 134 through 136 removed outlier: 3.807A pdb=" N VAL H 135 " --> pdb=" O LYS H 232 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU H 234 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY H 213 " --> pdb=" O LEU H 233 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL H 214 " --> pdb=" O GLN H 167 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR H 216 " --> pdb=" O PHE H 165 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE H 165 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP H 164 " --> pdb=" O LEU H 176 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1194 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: 1.05 Time building geometry restraints manager: 0.76 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: 2745 1.34 - 1.46: 2103 1.46 - 1.58: 4227 1.58 - 1.70: 0 1.70 - 1.83: 90 Bond restraints: 9165 Sorted by residual: bond pdb=" C ILE R 210 " pdb=" N PRO R 211 " ideal model delta sigma weight residual 1.335 1.401 -0.066 1.36e-02 5.41e+03 2.35e+01 bond pdb=" N LEU B 348 " pdb=" CA LEU B 348 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.20e-02 6.94e+03 9.62e+00 bond pdb=" N TYR R 287 " pdb=" CA TYR R 287 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.25e-02 6.40e+03 5.98e+00 bond pdb=" N MET C 61 " pdb=" CA MET C 61 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.54e+00 bond pdb=" N LEU C 286 " pdb=" CA LEU C 286 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.27e-02 6.20e+03 5.21e+00 ... (remaining 9160 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 12120 2.60 - 5.21: 242 5.21 - 7.81: 42 7.81 - 10.41: 4 10.41 - 13.01: 3 Bond angle restraints: 12411 Sorted by residual: angle pdb=" N ILE C 270 " pdb=" CA ILE C 270 " pdb=" C ILE C 270 " ideal model delta sigma weight residual 113.47 107.08 6.39 1.01e+00 9.80e-01 4.00e+01 angle pdb=" C ALA B 338 " pdb=" N VAL B 339 " pdb=" CA VAL B 339 " ideal model delta sigma weight residual 122.35 115.91 6.44 1.18e+00 7.18e-01 2.98e+01 angle pdb=" CB MET H 218 " pdb=" CG MET H 218 " pdb=" SD MET H 218 " ideal model delta sigma weight residual 112.70 125.71 -13.01 3.00e+00 1.11e-01 1.88e+01 angle pdb=" CB MET C 188 " pdb=" CG MET C 188 " pdb=" SD MET C 188 " ideal model delta sigma weight residual 112.70 125.43 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" CA ILE R 214 " pdb=" CB ILE R 214 " pdb=" CG1 ILE R 214 " ideal model delta sigma weight residual 110.40 117.48 -7.08 1.70e+00 3.46e-01 1.73e+01 ... (remaining 12406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4784 17.94 - 35.87: 518 35.87 - 53.81: 116 53.81 - 71.75: 20 71.75 - 89.68: 5 Dihedral angle restraints: 5443 sinusoidal: 2109 harmonic: 3334 Sorted by residual: dihedral pdb=" CB CYS H 147 " pdb=" SG CYS H 147 " pdb=" SG CYS H 217 " pdb=" CB CYS H 217 " ideal model delta sinusoidal sigma weight residual 93.00 37.82 55.18 1 1.00e+01 1.00e-02 4.12e+01 dihedral pdb=" CA LYS C 78 " pdb=" C LYS C 78 " pdb=" N LEU C 79 " pdb=" CA LEU C 79 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -121.96 35.96 1 1.00e+01 1.00e-02 1.83e+01 ... (remaining 5440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1156 0.063 - 0.126: 226 0.126 - 0.189: 28 0.189 - 0.252: 1 0.252 - 0.315: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA LEU C 286 " pdb=" N LEU C 286 " pdb=" C LEU C 286 " pdb=" CB LEU C 286 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB THR C 47 " pdb=" CA THR C 47 " pdb=" OG1 THR C 47 " pdb=" CG2 THR C 47 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA MET R 279 " pdb=" N MET R 279 " pdb=" C MET R 279 " pdb=" CB MET R 279 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 1409 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 NFI R 401 " -0.068 2.00e-02 2.50e+03 2.32e-01 6.72e+02 pdb=" C11 NFI R 401 " 0.274 2.00e-02 2.50e+03 pdb=" C9 NFI R 401 " 0.161 2.00e-02 2.50e+03 pdb=" N1 NFI R 401 " -0.402 2.00e-02 2.50e+03 pdb=" O2 NFI R 401 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 337 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C ASP B 337 " 0.044 2.00e-02 2.50e+03 pdb=" O ASP B 337 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA B 338 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 201 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C VAL B 201 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL B 201 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY B 202 " 0.014 2.00e-02 2.50e+03 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2081 2.78 - 3.31: 8268 3.31 - 3.84: 14220 3.84 - 4.37: 15713 4.37 - 4.90: 27510 Nonbonded interactions: 67792 Sorted by model distance: nonbonded pdb=" O VAL R 335 " pdb=" OG1 THR R 339 " model vdw 2.255 3.040 nonbonded pdb=" OG SER D 8 " pdb=" OE1 GLN D 11 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR B 182 " pdb=" OD1 ASN C 119 " model vdw 2.302 3.040 nonbonded pdb=" OG SER C 227 " pdb=" OD1 ASP C 228 " model vdw 2.312 3.040 nonbonded pdb=" NE2 GLN C 220 " pdb=" O LEU C 255 " model vdw 2.322 3.120 ... (remaining 67787 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.140 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9167 Z= 0.245 Angle : 0.919 13.014 12415 Z= 0.498 Chirality : 0.051 0.315 1412 Planarity : 0.008 0.232 1570 Dihedral : 15.477 89.683 3287 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 0.62 % Allowed : 20.84 % Favored : 78.54 % 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 aren not related in a simple way. whole: -1.79 (0.23), residues: 1130 helix: -0.29 (0.24), residues: 398 sheet: -0.98 (0.33), residues: 256 loop : -2.03 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 140 TYR 0.016 0.002 TYR H 223 PHE 0.020 0.002 PHE H 227 TRP 0.019 0.002 TRP C 169 HIS 0.005 0.001 HIS R 323 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 9165) covalent geometry : angle 0.91946 (12411) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.98655 ( 4) hydrogen bonds : bond 0.15966 ( 418) hydrogen bonds : angle 6.68727 ( 1194) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.299 Fit side-chains REVERT: B 312 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8671 (mmmt) REVERT: H 189 ASP cc_start: 0.7370 (p0) cc_final: 0.7150 (p0) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.0936 time to fit residues: 6.5923 Evaluate side-chains 46 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 312 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN C 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.037758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2292 r_free = 0.2292 target = 0.030793 restraints weight = 79904.301| |-----------------------------------------------------------------------------| r_work (start): 0.2068 rms_B_bonded: 3.12 r_work: 0.2013 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9167 Z= 0.107 Angle : 0.533 5.882 12415 Z= 0.282 Chirality : 0.038 0.131 1412 Planarity : 0.004 0.045 1570 Dihedral : 5.498 51.761 1272 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.67 % Allowed : 18.69 % Favored : 78.64 % 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 aren not related in a simple way. whole: -0.72 (0.25), residues: 1130 helix: 1.06 (0.26), residues: 403 sheet: -0.61 (0.33), residues: 251 loop : -1.76 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 224 TYR 0.011 0.001 TYR R 287 PHE 0.011 0.001 PHE B 189 TRP 0.018 0.001 TRP C 169 HIS 0.003 0.001 HIS R 106 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 9165) covalent geometry : angle 0.53286 (12411) SS BOND : bond 0.00480 ( 2) SS BOND : angle 1.33224 ( 4) hydrogen bonds : bond 0.03926 ( 418) hydrogen bonds : angle 4.83754 ( 1194) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 44 time to evaluate : 0.269 Fit side-chains REVERT: R 192 MET cc_start: 0.9586 (tpt) cc_final: 0.9291 (tpt) REVERT: B 243 MET cc_start: 0.9581 (OUTLIER) cc_final: 0.7840 (mmm) REVERT: D 26 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7705 (p0) REVERT: H 180 MET cc_start: 0.9545 (OUTLIER) cc_final: 0.7368 (tmm) outliers start: 26 outliers final: 11 residues processed: 65 average time/residue: 0.0830 time to fit residues: 7.7755 Evaluate side-chains 56 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 180 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 85 optimal weight: 0.0970 chunk 89 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.034644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2138 r_free = 0.2138 target = 0.028269 restraints weight = 80792.750| |-----------------------------------------------------------------------------| r_work (start): 0.2122 rms_B_bonded: 3.32 r_work: 0.2047 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 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 : 0.002 0.025 9167 Z= 0.087 Angle : 0.485 6.103 12415 Z= 0.255 Chirality : 0.038 0.143 1412 Planarity : 0.003 0.041 1570 Dihedral : 4.639 51.548 1266 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.77 % Allowed : 18.17 % Favored : 79.06 % 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 aren not related in a simple way. whole: -0.31 (0.25), residues: 1130 helix: 1.49 (0.26), residues: 405 sheet: -0.55 (0.33), residues: 255 loop : -1.52 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 154 TYR 0.008 0.001 TYR R 49 PHE 0.012 0.001 PHE B 189 TRP 0.018 0.001 TRP C 169 HIS 0.002 0.000 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00173 ( 9165) covalent geometry : angle 0.48505 (12411) SS BOND : bond 0.00353 ( 2) SS BOND : angle 1.06484 ( 4) hydrogen bonds : bond 0.03466 ( 418) hydrogen bonds : angle 4.41650 ( 1194) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 46 time to evaluate : 0.247 Fit side-chains REVERT: R 192 MET cc_start: 0.9611 (tpt) cc_final: 0.9308 (tpt) REVERT: B 243 MET cc_start: 0.9405 (OUTLIER) cc_final: 0.7504 (mmm) REVERT: B 256 ASN cc_start: 0.9827 (m-40) cc_final: 0.9568 (m-40) REVERT: C 171 ILE cc_start: 0.9750 (OUTLIER) cc_final: 0.9512 (mp) REVERT: D 26 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7482 (p0) REVERT: H 141 GLU cc_start: 0.7353 (tm-30) cc_final: 0.7097 (pp20) REVERT: H 180 MET cc_start: 0.9514 (OUTLIER) cc_final: 0.7326 (tmm) outliers start: 27 outliers final: 8 residues processed: 70 average time/residue: 0.0752 time to fit residues: 7.5093 Evaluate side-chains 56 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 125 ASN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain H residue 180 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 5.9990 chunk 70 optimal weight: 0.0270 chunk 76 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 55 optimal weight: 0.1980 chunk 98 optimal weight: 10.0000 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN C 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.035115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2160 r_free = 0.2160 target = 0.028810 restraints weight = 82175.184| |-----------------------------------------------------------------------------| r_work (start): 0.2145 rms_B_bonded: 3.25 r_work: 0.2089 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9167 Z= 0.083 Angle : 0.475 7.152 12415 Z= 0.246 Chirality : 0.038 0.127 1412 Planarity : 0.003 0.039 1570 Dihedral : 4.072 42.719 1262 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.57 % Allowed : 18.89 % Favored : 78.54 % 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 aren not related in a simple way. whole: -0.00 (0.26), residues: 1130 helix: 1.68 (0.26), residues: 407 sheet: -0.41 (0.34), residues: 254 loop : -1.27 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 206 TYR 0.008 0.001 TYR R 49 PHE 0.010 0.001 PHE B 189 TRP 0.016 0.001 TRP C 169 HIS 0.002 0.000 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00165 ( 9165) covalent geometry : angle 0.47454 (12411) SS BOND : bond 0.00272 ( 2) SS BOND : angle 0.85792 ( 4) hydrogen bonds : bond 0.03107 ( 418) hydrogen bonds : angle 4.17786 ( 1194) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 0.216 Fit side-chains REVERT: R 192 MET cc_start: 0.9604 (tpt) cc_final: 0.9216 (tpt) REVERT: B 256 ASN cc_start: 0.9818 (m-40) cc_final: 0.9542 (m-40) REVERT: C 158 VAL cc_start: 0.9406 (OUTLIER) cc_final: 0.9191 (p) REVERT: D 26 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7555 (p0) REVERT: H 180 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.7231 (tmm) outliers start: 25 outliers final: 9 residues processed: 65 average time/residue: 0.0719 time to fit residues: 6.7931 Evaluate side-chains 56 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 180 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.0040 chunk 31 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.034259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2133 r_free = 0.2133 target = 0.027875 restraints weight = 81800.187| |-----------------------------------------------------------------------------| r_work (start): 0.2117 rms_B_bonded: 3.37 r_work: 0.2053 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9152 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9167 Z= 0.105 Angle : 0.482 8.518 12415 Z= 0.247 Chirality : 0.038 0.124 1412 Planarity : 0.003 0.038 1570 Dihedral : 4.080 41.654 1262 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.77 % Allowed : 18.89 % Favored : 78.34 % 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 aren not related in a simple way. whole: 0.04 (0.26), residues: 1130 helix: 1.77 (0.27), residues: 407 sheet: -0.52 (0.33), residues: 264 loop : -1.22 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 154 TYR 0.009 0.001 TYR H 178 PHE 0.009 0.001 PHE B 189 TRP 0.012 0.001 TRP C 169 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9165) covalent geometry : angle 0.48171 (12411) SS BOND : bond 0.00162 ( 2) SS BOND : angle 0.65763 ( 4) hydrogen bonds : bond 0.03207 ( 418) hydrogen bonds : angle 4.20443 ( 1194) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 43 time to evaluate : 0.312 Fit side-chains REVERT: R 192 MET cc_start: 0.9604 (tpt) cc_final: 0.9234 (tpt) REVERT: B 256 ASN cc_start: 0.9825 (m-40) cc_final: 0.9552 (m-40) REVERT: C 158 VAL cc_start: 0.9399 (OUTLIER) cc_final: 0.9160 (p) REVERT: C 171 ILE cc_start: 0.9748 (OUTLIER) cc_final: 0.9504 (mp) REVERT: D 26 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7459 (p0) REVERT: H 141 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7455 (pp20) REVERT: H 180 MET cc_start: 0.9493 (OUTLIER) cc_final: 0.7196 (tmm) outliers start: 27 outliers final: 12 residues processed: 67 average time/residue: 0.0707 time to fit residues: 7.0528 Evaluate side-chains 59 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 180 MET Chi-restraints excluded: chain H residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0670 chunk 105 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 overall best weight: 3.9724 ------------------------------------------------------------------------------- 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 = 0.2396 r_free = 0.2396 target = 0.032987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2083 r_free = 0.2083 target = 0.026656 restraints weight = 83090.200| |-----------------------------------------------------------------------------| r_work (start): 0.2068 rms_B_bonded: 3.31 r_work: 0.2003 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9184 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9167 Z= 0.157 Angle : 0.495 6.699 12415 Z= 0.258 Chirality : 0.038 0.135 1412 Planarity : 0.003 0.037 1570 Dihedral : 4.229 40.229 1262 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.57 % Allowed : 18.99 % Favored : 78.44 % 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 aren not related in a simple way. whole: -0.03 (0.26), residues: 1130 helix: 1.69 (0.27), residues: 412 sheet: -0.46 (0.33), residues: 260 loop : -1.33 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 154 TYR 0.009 0.001 TYR H 178 PHE 0.009 0.001 PHE H 29 TRP 0.010 0.001 TRP C 169 HIS 0.003 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9165) covalent geometry : angle 0.49538 (12411) SS BOND : bond 0.00096 ( 2) SS BOND : angle 0.46789 ( 4) hydrogen bonds : bond 0.03482 ( 418) hydrogen bonds : angle 4.37655 ( 1194) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 40 time to evaluate : 0.323 Fit side-chains REVERT: R 192 MET cc_start: 0.9648 (tpt) cc_final: 0.9173 (tpt) REVERT: C 171 ILE cc_start: 0.9786 (OUTLIER) cc_final: 0.9547 (mp) REVERT: C 271 CYS cc_start: 0.9369 (OUTLIER) cc_final: 0.8824 (p) REVERT: D 26 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7700 (p0) outliers start: 25 outliers final: 16 residues processed: 63 average time/residue: 0.0728 time to fit residues: 6.7920 Evaluate side-chains 58 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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 = 0.2389 r_free = 0.2389 target = 0.032737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2073 r_free = 0.2073 target = 0.026421 restraints weight = 83627.154| |-----------------------------------------------------------------------------| r_work (start): 0.2058 rms_B_bonded: 3.30 r_work: 0.1998 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.1998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9186 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9167 Z= 0.159 Angle : 0.501 7.169 12415 Z= 0.259 Chirality : 0.038 0.122 1412 Planarity : 0.003 0.037 1570 Dihedral : 4.299 38.586 1262 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.98 % Allowed : 18.48 % Favored : 78.54 % 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 aren not related in a simple way. whole: -0.03 (0.26), residues: 1130 helix: 1.68 (0.26), residues: 412 sheet: -0.47 (0.33), residues: 260 loop : -1.33 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 154 TYR 0.010 0.001 TYR H 178 PHE 0.008 0.001 PHE H 29 TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9165) covalent geometry : angle 0.50078 (12411) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.58677 ( 4) hydrogen bonds : bond 0.03491 ( 418) hydrogen bonds : angle 4.41704 ( 1194) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 40 time to evaluate : 0.220 Fit side-chains REVERT: R 192 MET cc_start: 0.9629 (tpt) cc_final: 0.9162 (tpt) REVERT: C 171 ILE cc_start: 0.9798 (OUTLIER) cc_final: 0.9559 (mp) REVERT: C 271 CYS cc_start: 0.9370 (OUTLIER) cc_final: 0.8943 (p) outliers start: 29 outliers final: 20 residues processed: 67 average time/residue: 0.0804 time to fit residues: 7.8036 Evaluate side-chains 60 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 38 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 203 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.2374 r_free = 0.2374 target = 0.032234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2059 r_free = 0.2059 target = 0.025963 restraints weight = 83132.193| |-----------------------------------------------------------------------------| r_work (start): 0.2044 rms_B_bonded: 3.24 r_work: 0.1985 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.1985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9193 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9167 Z= 0.197 Angle : 0.531 8.564 12415 Z= 0.272 Chirality : 0.039 0.123 1412 Planarity : 0.003 0.038 1570 Dihedral : 4.439 42.668 1262 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.57 % Allowed : 19.40 % Favored : 78.03 % 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 aren not related in a simple way. whole: -0.10 (0.26), residues: 1130 helix: 1.64 (0.26), residues: 412 sheet: -0.50 (0.33), residues: 260 loop : -1.39 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 154 TYR 0.011 0.001 TYR H 178 PHE 0.010 0.001 PHE H 29 TRP 0.010 0.001 TRP C 169 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9165) covalent geometry : angle 0.53091 (12411) SS BOND : bond 0.00175 ( 2) SS BOND : angle 0.41092 ( 4) hydrogen bonds : bond 0.03689 ( 418) hydrogen bonds : angle 4.52847 ( 1194) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 39 time to evaluate : 0.338 Fit side-chains REVERT: B 24 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8296 (ptm160) REVERT: C 171 ILE cc_start: 0.9804 (OUTLIER) cc_final: 0.9565 (mp) REVERT: C 271 CYS cc_start: 0.9448 (OUTLIER) cc_final: 0.9089 (p) outliers start: 25 outliers final: 20 residues processed: 61 average time/residue: 0.0855 time to fit residues: 7.5330 Evaluate side-chains 62 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 39 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.033045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2089 r_free = 0.2089 target = 0.026695 restraints weight = 83301.381| |-----------------------------------------------------------------------------| r_work (start): 0.2073 rms_B_bonded: 3.30 r_work: 0.2013 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9178 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9167 Z= 0.114 Angle : 0.502 8.412 12415 Z= 0.257 Chirality : 0.038 0.120 1412 Planarity : 0.003 0.039 1570 Dihedral : 4.353 44.323 1262 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.16 % Allowed : 19.82 % Favored : 78.03 % 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 aren not related in a simple way. whole: -0.01 (0.26), residues: 1130 helix: 1.71 (0.26), residues: 412 sheet: -0.51 (0.33), residues: 262 loop : -1.28 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 154 TYR 0.008 0.001 TYR H 178 PHE 0.009 0.001 PHE B 189 TRP 0.015 0.001 TRP C 169 HIS 0.002 0.000 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9165) covalent geometry : angle 0.50161 (12411) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.55290 ( 4) hydrogen bonds : bond 0.03376 ( 418) hydrogen bonds : angle 4.37872 ( 1194) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.226 Fit side-chains REVERT: R 192 MET cc_start: 0.9634 (tpt) cc_final: 0.9350 (tpt) REVERT: B 24 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8212 (ptm160) REVERT: C 171 ILE cc_start: 0.9802 (OUTLIER) cc_final: 0.9551 (mp) REVERT: C 271 CYS cc_start: 0.9346 (OUTLIER) cc_final: 0.8842 (p) outliers start: 21 outliers final: 14 residues processed: 58 average time/residue: 0.0831 time to fit residues: 6.9925 Evaluate side-chains 56 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.2411 r_free = 0.2411 target = 0.033291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2104 r_free = 0.2104 target = 0.026940 restraints weight = 82500.811| |-----------------------------------------------------------------------------| r_work (start): 0.2087 rms_B_bonded: 3.33 r_work: 0.2025 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9167 Z= 0.108 Angle : 0.503 9.064 12415 Z= 0.256 Chirality : 0.038 0.123 1412 Planarity : 0.003 0.039 1570 Dihedral : 4.330 47.075 1262 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.26 % Allowed : 19.61 % Favored : 78.13 % 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 aren not related in a simple way. whole: 0.06 (0.26), residues: 1130 helix: 1.73 (0.26), residues: 412 sheet: -0.46 (0.33), residues: 262 loop : -1.22 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 154 TYR 0.008 0.001 TYR H 178 PHE 0.009 0.001 PHE B 189 TRP 0.014 0.001 TRP C 169 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9165) covalent geometry : angle 0.50281 (12411) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.50438 ( 4) hydrogen bonds : bond 0.03285 ( 418) hydrogen bonds : angle 4.30778 ( 1194) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 40 time to evaluate : 0.289 Fit side-chains REVERT: R 192 MET cc_start: 0.9644 (tpt) cc_final: 0.9324 (tpt) REVERT: B 24 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8219 (ptm160) REVERT: C 171 ILE cc_start: 0.9798 (OUTLIER) cc_final: 0.9549 (mp) REVERT: C 271 CYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8831 (p) REVERT: H 141 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8107 (pp20) outliers start: 22 outliers final: 16 residues processed: 59 average time/residue: 0.0955 time to fit residues: 7.9442 Evaluate side-chains 59 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.2405 r_free = 0.2405 target = 0.033084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2094 r_free = 0.2094 target = 0.026724 restraints weight = 81652.701| |-----------------------------------------------------------------------------| r_work (start): 0.2079 rms_B_bonded: 3.28 r_work: 0.2019 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9167 Z= 0.121 Angle : 0.509 8.967 12415 Z= 0.258 Chirality : 0.038 0.121 1412 Planarity : 0.003 0.038 1570 Dihedral : 4.362 48.552 1262 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.05 % Allowed : 19.71 % Favored : 78.23 % 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 aren not related in a simple way. whole: 0.06 (0.26), residues: 1130 helix: 1.75 (0.26), residues: 412 sheet: -0.46 (0.33), residues: 262 loop : -1.24 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 154 TYR 0.008 0.001 TYR H 178 PHE 0.009 0.001 PHE B 189 TRP 0.013 0.001 TRP C 169 HIS 0.002 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9165) covalent geometry : angle 0.50884 (12411) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.47128 ( 4) hydrogen bonds : bond 0.03332 ( 418) hydrogen bonds : angle 4.32744 ( 1194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1617.43 seconds wall clock time: 28 minutes 36.23 seconds (1716.23 seconds total)