Starting phenix.real_space_refine on Mon May 12 07:45:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hvi_35044/05_2025/8hvi_35044_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hvi_35044/05_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_35044/05_2025/8hvi_35044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hvi_35044/05_2025/8hvi_35044.map" model { file = "/net/cci-nas-00/data/ceres_data/8hvi_35044/05_2025/8hvi_35044_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hvi_35044/05_2025/8hvi_35044_neut.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'PHE:plan': 1, 'HIS: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: 5.12, per 1000 atoms: 0.57 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: 2.14 Conformation dependent library (CDL) restraints added in 875.4 milliseconds 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: 1.03 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: 2.43 Time building geometry restraints manager: 2.45 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.930 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- 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 : 9.87 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (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 TRP 0.019 0.002 TRP C 169 HIS 0.005 0.001 HIS R 323 PHE 0.020 0.002 PHE H 227 TYR 0.016 0.002 TYR H 223 ARG 0.005 0.001 ARG R 140 Details of bonding type rmsd hydrogen bonds : bond 0.15966 ( 418) hydrogen bonds : angle 6.68727 ( 1194) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.98655 ( 4) covalent geometry : bond 0.00478 ( 9165) covalent geometry : angle 0.91946 (12411) *********************** 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 : 1.024 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: 0.2706 time to fit residues: 19.3522 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 : 0.970 ------------------------------------------------------------------------------- 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 94 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.2361 r_free = 0.2361 target = 0.032209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2043 r_free = 0.2043 target = 0.025981 restraints weight = 82600.066| |-----------------------------------------------------------------------------| r_work (start): 0.2024 rms_B_bonded: 3.14 r_work: 0.1942 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.1942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9192 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 9167 Z= 0.205 Angle : 0.556 6.632 12415 Z= 0.295 Chirality : 0.039 0.126 1412 Planarity : 0.004 0.044 1570 Dihedral : 5.611 58.641 1272 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.57 % Allowed : 19.51 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1130 helix: 0.99 (0.26), residues: 410 sheet: -0.75 (0.33), residues: 257 loop : -1.91 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS R 106 PHE 0.014 0.001 PHE H 29 TYR 0.009 0.001 TYR R 287 ARG 0.003 0.000 ARG R 224 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 418) hydrogen bonds : angle 4.98578 ( 1194) SS BOND : bond 0.00228 ( 2) SS BOND : angle 1.21448 ( 4) covalent geometry : bond 0.00451 ( 9165) covalent geometry : angle 0.55555 (12411) *********************** 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 69 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 1.076 Fit side-chains REVERT: R 192 MET cc_start: 0.9570 (tpt) cc_final: 0.9235 (tpt) REVERT: B 243 MET cc_start: 0.9611 (OUTLIER) cc_final: 0.8103 (mmm) REVERT: D 26 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7436 (p0) REVERT: H 180 MET cc_start: 0.9560 (OUTLIER) cc_final: 0.7394 (tmm) outliers start: 25 outliers final: 12 residues processed: 64 average time/residue: 0.2073 time to fit residues: 19.3827 Evaluate side-chains 56 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 C residue 276 VAL Chi-restraints excluded: chain C residue 327 VAL 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 180 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.2364 r_free = 0.2364 target = 0.032244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2048 r_free = 0.2048 target = 0.025932 restraints weight = 83495.206| |-----------------------------------------------------------------------------| r_work (start): 0.2033 rms_B_bonded: 3.29 r_work: 0.1952 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.1952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9203 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9167 Z= 0.170 Angle : 0.513 5.603 12415 Z= 0.272 Chirality : 0.039 0.145 1412 Planarity : 0.003 0.043 1570 Dihedral : 5.070 52.079 1266 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.18 % Allowed : 19.10 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.25), residues: 1130 helix: 1.38 (0.26), residues: 409 sheet: -0.68 (0.33), residues: 257 loop : -1.80 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.002 0.001 HIS R 106 PHE 0.010 0.001 PHE B 189 TYR 0.008 0.001 TYR H 178 ARG 0.003 0.000 ARG R 154 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 418) hydrogen bonds : angle 4.79725 ( 1194) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.98879 ( 4) covalent geometry : bond 0.00376 ( 9165) covalent geometry : angle 0.51256 (12411) *********************** 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 74 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 43 time to evaluate : 1.048 Fit side-chains REVERT: R 192 MET cc_start: 0.9610 (tpt) cc_final: 0.9228 (tpt) REVERT: B 33 GLU cc_start: 0.9685 (OUTLIER) cc_final: 0.8892 (mm-30) REVERT: B 243 MET cc_start: 0.9630 (OUTLIER) cc_final: 0.8091 (mmm) REVERT: C 61 MET cc_start: 0.9397 (ppp) cc_final: 0.9078 (ppp) REVERT: C 171 ILE cc_start: 0.9799 (OUTLIER) cc_final: 0.9559 (mp) REVERT: D 26 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7631 (p0) outliers start: 31 outliers final: 14 residues processed: 71 average time/residue: 0.1961 time to fit residues: 20.2683 Evaluate side-chains 59 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 266 LEU 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 184 THR 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 H residue 2 VAL Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 203 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.2369 r_free = 0.2369 target = 0.032282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2051 r_free = 0.2051 target = 0.025968 restraints weight = 83129.146| |-----------------------------------------------------------------------------| r_work (start): 0.2037 rms_B_bonded: 3.25 r_work: 0.1959 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.1959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9197 moved from start: 0.1547 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= 0.158 Angle : 0.495 5.497 12415 Z= 0.264 Chirality : 0.038 0.123 1412 Planarity : 0.003 0.042 1570 Dihedral : 4.704 42.193 1264 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.59 % Allowed : 18.89 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.25), residues: 1130 helix: 1.50 (0.26), residues: 411 sheet: -0.71 (0.33), residues: 261 loop : -1.72 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.002 0.001 HIS C 54 PHE 0.009 0.001 PHE B 189 TYR 0.007 0.001 TYR H 178 ARG 0.002 0.000 ARG R 154 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 418) hydrogen bonds : angle 4.67420 ( 1194) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.82986 ( 4) covalent geometry : bond 0.00351 ( 9165) covalent geometry : angle 0.49468 (12411) *********************** 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 77 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 42 time to evaluate : 0.997 Fit side-chains REVERT: R 192 MET cc_start: 0.9618 (tpt) cc_final: 0.9188 (tpt) REVERT: B 24 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8351 (ptm160) REVERT: B 33 GLU cc_start: 0.9676 (OUTLIER) cc_final: 0.8899 (mm-30) REVERT: B 243 MET cc_start: 0.9608 (OUTLIER) cc_final: 0.8125 (mmm) REVERT: B 266 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9147 (tp) REVERT: C 171 ILE cc_start: 0.9799 (OUTLIER) cc_final: 0.9549 (mp) REVERT: D 26 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7715 (p0) outliers start: 35 outliers final: 18 residues processed: 71 average time/residue: 0.2040 time to fit residues: 20.9439 Evaluate side-chains 63 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 39 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 24 ARG Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 266 LEU 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 276 VAL 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 2 VAL Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 0.3980 chunk 89 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- 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 = 0.2376 r_free = 0.2376 target = 0.032427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2059 r_free = 0.2059 target = 0.026118 restraints weight = 82575.531| |-----------------------------------------------------------------------------| r_work (start): 0.2044 rms_B_bonded: 3.27 r_work: 0.1966 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.1966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9197 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9167 Z= 0.141 Angle : 0.495 7.588 12415 Z= 0.260 Chirality : 0.038 0.121 1412 Planarity : 0.003 0.041 1570 Dihedral : 4.565 39.254 1264 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.00 % Allowed : 18.69 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1130 helix: 1.58 (0.26), residues: 411 sheet: -0.65 (0.33), residues: 261 loop : -1.65 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.002 0.001 HIS C 54 PHE 0.009 0.001 PHE B 189 TYR 0.007 0.001 TYR H 178 ARG 0.003 0.000 ARG R 154 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 418) hydrogen bonds : angle 4.58234 ( 1194) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.80091 ( 4) covalent geometry : bond 0.00312 ( 9165) covalent geometry : angle 0.49491 (12411) *********************** 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 79 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 40 time to evaluate : 1.065 Fit side-chains REVERT: R 192 MET cc_start: 0.9606 (tpt) cc_final: 0.9174 (tpt) REVERT: B 24 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8294 (ptm160) REVERT: B 33 GLU cc_start: 0.9666 (OUTLIER) cc_final: 0.8915 (mm-30) REVERT: B 243 MET cc_start: 0.9594 (OUTLIER) cc_final: 0.8108 (mmm) REVERT: C 171 ILE cc_start: 0.9806 (OUTLIER) cc_final: 0.9552 (mp) REVERT: C 271 CYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9020 (p) REVERT: D 26 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8235 (p0) outliers start: 39 outliers final: 19 residues processed: 72 average time/residue: 0.2759 time to fit residues: 28.6699 Evaluate side-chains 63 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 38 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 24 ARG Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR 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 327 VAL 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 129 THR 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 3 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.2363 r_free = 0.2363 target = 0.031922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2047 r_free = 0.2047 target = 0.025647 restraints weight = 82377.398| |-----------------------------------------------------------------------------| r_work (start): 0.2034 rms_B_bonded: 3.25 r_work: 0.1954 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.1954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9206 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 : 0.004 0.029 9167 Z= 0.189 Angle : 0.515 6.583 12415 Z= 0.268 Chirality : 0.039 0.121 1412 Planarity : 0.003 0.040 1570 Dihedral : 4.532 43.756 1262 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.39 % Allowed : 19.30 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1130 helix: 1.58 (0.26), residues: 411 sheet: -0.63 (0.33), residues: 261 loop : -1.66 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.002 0.001 HIS H 35 PHE 0.008 0.001 PHE B 189 TYR 0.009 0.001 TYR H 178 ARG 0.004 0.000 ARG R 154 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 418) hydrogen bonds : angle 4.62311 ( 1194) SS BOND : bond 0.00171 ( 2) SS BOND : angle 0.70206 ( 4) covalent geometry : bond 0.00419 ( 9165) covalent geometry : angle 0.51540 (12411) *********************** 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 73 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 40 time to evaluate : 1.077 Fit side-chains REVERT: R 192 MET cc_start: 0.9582 (tpt) cc_final: 0.9121 (tpt) REVERT: B 24 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8380 (ptm160) REVERT: B 33 GLU cc_start: 0.9687 (OUTLIER) cc_final: 0.8881 (mm-30) REVERT: B 243 MET cc_start: 0.9622 (OUTLIER) cc_final: 0.8154 (mmm) REVERT: C 171 ILE cc_start: 0.9809 (OUTLIER) cc_final: 0.9556 (mp) REVERT: C 271 CYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9041 (p) REVERT: D 26 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.7997 (p0) outliers start: 33 outliers final: 21 residues processed: 68 average time/residue: 0.2138 time to fit residues: 21.0773 Evaluate side-chains 65 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 38 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 R residue 232 LEU Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR 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 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 129 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 177 ILE 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 53 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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 = 0.2363 r_free = 0.2363 target = 0.031875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2047 r_free = 0.2047 target = 0.025596 restraints weight = 83445.896| |-----------------------------------------------------------------------------| r_work (start): 0.2033 rms_B_bonded: 3.26 r_work: 0.1953 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.1953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9167 Z= 0.188 Angle : 0.513 6.755 12415 Z= 0.267 Chirality : 0.039 0.121 1412 Planarity : 0.003 0.039 1570 Dihedral : 4.562 47.190 1262 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.59 % Allowed : 19.10 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.26), residues: 1130 helix: 1.60 (0.27), residues: 411 sheet: -0.62 (0.33), residues: 261 loop : -1.63 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.002 0.001 HIS C 54 PHE 0.008 0.001 PHE B 189 TYR 0.008 0.001 TYR H 178 ARG 0.004 0.000 ARG R 154 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 418) hydrogen bonds : angle 4.61244 ( 1194) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.70145 ( 4) covalent geometry : bond 0.00417 ( 9165) covalent geometry : angle 0.51296 (12411) *********************** 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 73 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 38 time to evaluate : 1.000 Fit side-chains REVERT: R 192 MET cc_start: 0.9579 (tpt) cc_final: 0.9121 (tpt) REVERT: B 24 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8383 (ptm160) REVERT: B 33 GLU cc_start: 0.9682 (OUTLIER) cc_final: 0.8870 (mm-30) REVERT: B 243 MET cc_start: 0.9613 (OUTLIER) cc_final: 0.8168 (mmm) REVERT: C 171 ILE cc_start: 0.9815 (OUTLIER) cc_final: 0.9583 (mp) REVERT: C 271 CYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9054 (p) REVERT: D 26 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7939 (p0) outliers start: 35 outliers final: 23 residues processed: 69 average time/residue: 0.2066 time to fit residues: 20.6155 Evaluate side-chains 67 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 38 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 R residue 232 LEU Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR 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 327 VAL 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 67 ARG Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 177 ILE 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 100 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 chunk 91 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- 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 = 0.2381 r_free = 0.2381 target = 0.032406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2068 r_free = 0.2068 target = 0.026112 restraints weight = 83422.401| |-----------------------------------------------------------------------------| r_work (start): 0.2053 rms_B_bonded: 3.29 r_work: 0.1972 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.1972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9197 moved from start: 0.1806 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= 0.128 Angle : 0.494 7.281 12415 Z= 0.257 Chirality : 0.038 0.122 1412 Planarity : 0.003 0.040 1570 Dihedral : 4.492 49.114 1262 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.39 % Allowed : 18.99 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1130 helix: 1.63 (0.27), residues: 412 sheet: -0.63 (0.33), residues: 263 loop : -1.51 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.002 0.000 HIS C 54 PHE 0.009 0.001 PHE B 189 TYR 0.007 0.001 TYR H 102 ARG 0.004 0.000 ARG R 154 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 418) hydrogen bonds : angle 4.47458 ( 1194) SS BOND : bond 0.00130 ( 2) SS BOND : angle 0.75292 ( 4) covalent geometry : bond 0.00282 ( 9165) covalent geometry : angle 0.49392 (12411) *********************** 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 73 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 40 time to evaluate : 1.087 Fit side-chains REVERT: R 192 MET cc_start: 0.9573 (tpt) cc_final: 0.9100 (tpt) REVERT: B 24 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8301 (ptm160) REVERT: B 33 GLU cc_start: 0.9672 (OUTLIER) cc_final: 0.8899 (mm-30) REVERT: B 243 MET cc_start: 0.9562 (OUTLIER) cc_final: 0.8030 (mmm) REVERT: C 171 ILE cc_start: 0.9807 (OUTLIER) cc_final: 0.9547 (mp) REVERT: C 271 CYS cc_start: 0.9379 (OUTLIER) cc_final: 0.9028 (p) REVERT: D 26 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8013 (p0) REVERT: H 141 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8046 (pp20) outliers start: 33 outliers final: 21 residues processed: 69 average time/residue: 0.2181 time to fit residues: 21.5463 Evaluate side-chains 66 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 39 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 R residue 232 LEU Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 321 THR 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 178 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 VAL 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 83 MET Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 177 ILE 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 67 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 0.4980 chunk 81 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 overall best weight: 6.0988 ------------------------------------------------------------------------------- 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 = 0.2357 r_free = 0.2357 target = 0.031668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2040 r_free = 0.2040 target = 0.025399 restraints weight = 83211.280| |-----------------------------------------------------------------------------| r_work (start): 0.2027 rms_B_bonded: 3.24 r_work: 0.1947 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.1947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9211 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 9167 Z= 0.225 Angle : 0.539 8.455 12415 Z= 0.277 Chirality : 0.039 0.122 1412 Planarity : 0.003 0.039 1570 Dihedral : 4.642 52.860 1262 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.29 % Allowed : 19.30 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1130 helix: 1.60 (0.27), residues: 411 sheet: -0.64 (0.33), residues: 261 loop : -1.58 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.003 0.001 HIS H 35 PHE 0.009 0.001 PHE H 29 TYR 0.009 0.001 TYR H 178 ARG 0.003 0.000 ARG R 140 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 418) hydrogen bonds : angle 4.62376 ( 1194) SS BOND : bond 0.00246 ( 2) SS BOND : angle 0.62305 ( 4) covalent geometry : bond 0.00500 ( 9165) covalent geometry : angle 0.53866 (12411) *********************** 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 70 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 38 time to evaluate : 1.050 Fit side-chains REVERT: R 192 MET cc_start: 0.9576 (tpt) cc_final: 0.9102 (tpt) REVERT: B 24 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8373 (ptm160) REVERT: B 33 GLU cc_start: 0.9690 (OUTLIER) cc_final: 0.8853 (mm-30) REVERT: B 243 MET cc_start: 0.9615 (OUTLIER) cc_final: 0.8250 (mmm) REVERT: C 171 ILE cc_start: 0.9816 (OUTLIER) cc_final: 0.9580 (mp) REVERT: C 271 CYS cc_start: 0.9443 (OUTLIER) cc_final: 0.9067 (p) REVERT: D 26 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.7887 (p0) outliers start: 32 outliers final: 22 residues processed: 66 average time/residue: 0.2251 time to fit residues: 21.3168 Evaluate side-chains 65 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 37 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 R residue 232 LEU Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR 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 327 VAL 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 129 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 177 ILE 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 76 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 81 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.2398 r_free = 0.2398 target = 0.032870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2078 r_free = 0.2078 target = 0.026603 restraints weight = 82629.969| |-----------------------------------------------------------------------------| r_work (start): 0.2064 rms_B_bonded: 3.14 r_work: 0.2011 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9167 Z= 0.101 Angle : 0.515 8.997 12415 Z= 0.263 Chirality : 0.038 0.124 1412 Planarity : 0.003 0.040 1570 Dihedral : 4.482 53.076 1262 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.57 % Allowed : 20.12 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1130 helix: 1.71 (0.27), residues: 412 sheet: -0.62 (0.32), residues: 269 loop : -1.41 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 169 HIS 0.002 0.000 HIS C 311 PHE 0.009 0.001 PHE B 189 TYR 0.008 0.001 TYR H 102 ARG 0.004 0.000 ARG R 154 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 418) hydrogen bonds : angle 4.38301 ( 1194) SS BOND : bond 0.00189 ( 2) SS BOND : angle 0.76660 ( 4) covalent geometry : bond 0.00221 ( 9165) covalent geometry : angle 0.51525 (12411) ********************** 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 66 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 41 time to evaluate : 1.023 Fit side-chains REVERT: R 192 MET cc_start: 0.9606 (tpt) cc_final: 0.9173 (tpt) REVERT: B 24 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8186 (ptm160) REVERT: B 243 MET cc_start: 0.9512 (OUTLIER) cc_final: 0.7804 (mmm) REVERT: C 171 ILE cc_start: 0.9801 (OUTLIER) cc_final: 0.9550 (mp) REVERT: C 271 CYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8896 (p) REVERT: D 26 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.7996 (p0) outliers start: 25 outliers final: 15 residues processed: 62 average time/residue: 0.2335 time to fit residues: 20.4568 Evaluate side-chains 58 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 LEU 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 243 MET 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 178 THR Chi-restraints excluded: chain C residue 271 CYS 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 83 MET Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 177 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 49 optimal weight: 0.0000 chunk 92 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.032786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2079 r_free = 0.2079 target = 0.026464 restraints weight = 82929.840| |-----------------------------------------------------------------------------| r_work (start): 0.2065 rms_B_bonded: 3.25 r_work: 0.1988 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.1988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9187 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9167 Z= 0.115 Angle : 0.518 9.156 12415 Z= 0.265 Chirality : 0.038 0.126 1412 Planarity : 0.003 0.040 1570 Dihedral : 4.496 54.481 1262 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.36 % Allowed : 20.43 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.26), residues: 1130 helix: 1.72 (0.26), residues: 412 sheet: -0.58 (0.32), residues: 267 loop : -1.38 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.002 0.000 HIS C 54 PHE 0.009 0.001 PHE B 189 TYR 0.007 0.001 TYR H 50 ARG 0.009 0.000 ARG R 154 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 418) hydrogen bonds : angle 4.39159 ( 1194) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.62369 ( 4) covalent geometry : bond 0.00253 ( 9165) covalent geometry : angle 0.51791 (12411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4328.82 seconds wall clock time: 75 minutes 55.86 seconds (4555.86 seconds total)