Starting phenix.real_space_refine on Sat Jun 7 15:37:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hvi_35044/06_2025/8hvi_35044_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hvi_35044/06_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_35044/06_2025/8hvi_35044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hvi_35044/06_2025/8hvi_35044.map" model { file = "/net/cci-nas-00/data/ceres_data/8hvi_35044/06_2025/8hvi_35044_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hvi_35044/06_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-5710/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: 5.36, per 1000 atoms: 0.60 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: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.83 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: 2.17 Time building geometry restraints manager: 2.75 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 22.220 Find NCS groups from input model: 0.090 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- 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 : 1.037 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: 0.3041 time to fit residues: 21.8752 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 : 2.330 ------------------------------------------------------------------------------- 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 = 0.2357 r_free = 0.2357 target = 0.032219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2037 r_free = 0.2037 target = 0.025966 restraints weight = 82705.896| |-----------------------------------------------------------------------------| r_work (start): 0.2023 rms_B_bonded: 3.15 r_work: 0.1942 rms_B_bonded: 3.42 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 : 1.089 Fit side-chains REVERT: R 192 MET cc_start: 0.9571 (tpt) cc_final: 0.9237 (tpt) REVERT: B 243 MET cc_start: 0.9611 (OUTLIER) cc_final: 0.8100 (mmm) REVERT: D 26 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7432 (p0) REVERT: H 180 MET cc_start: 0.9562 (OUTLIER) cc_final: 0.7394 (tmm) outliers start: 25 outliers final: 12 residues processed: 64 average time/residue: 0.2201 time to fit residues: 20.6023 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 : 1.107 ------------------------------------------------------------------------------- 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: 1.9990 chunk 7 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.2371 r_free = 0.2371 target = 0.032472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2057 r_free = 0.2057 target = 0.026141 restraints weight = 83227.367| |-----------------------------------------------------------------------------| r_work (start): 0.2040 rms_B_bonded: 3.31 r_work: 0.1959 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.1959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9198 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9167 Z= 0.145 Angle : 0.506 5.662 12415 Z= 0.268 Chirality : 0.039 0.134 1412 Planarity : 0.003 0.044 1570 Dihedral : 5.041 50.897 1266 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.18 % Allowed : 18.79 % 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 (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: -0.54 (0.25), residues: 1130 helix: 1.39 (0.26), residues: 409 sheet: -0.65 (0.33), residues: 257 loop : -1.79 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 169 HIS 0.002 0.001 HIS C 54 PHE 0.010 0.001 PHE B 189 TYR 0.007 0.001 TYR H 178 ARG 0.004 0.000 ARG R 154 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 418) hydrogen bonds : angle 4.76176 ( 1194) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.96999 ( 4) covalent geometry : bond 0.00321 ( 9165) covalent geometry : angle 0.50616 (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 : 1.078 Fit side-chains REVERT: R 192 MET cc_start: 0.9602 (tpt) cc_final: 0.9217 (tpt) REVERT: B 33 GLU cc_start: 0.9678 (OUTLIER) cc_final: 0.8909 (mm-30) REVERT: B 243 MET cc_start: 0.9609 (OUTLIER) cc_final: 0.8020 (mmm) REVERT: C 61 MET cc_start: 0.9381 (ppp) cc_final: 0.9050 (ppp) REVERT: C 171 ILE cc_start: 0.9795 (OUTLIER) cc_final: 0.9553 (mp) REVERT: D 26 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7570 (p0) outliers start: 31 outliers final: 13 residues processed: 71 average time/residue: 0.2044 time to fit residues: 21.1813 Evaluate side-chains 59 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 216 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 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 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: 0.5980 chunk 57 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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 = 0.2368 r_free = 0.2368 target = 0.032266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2047 r_free = 0.2047 target = 0.025955 restraints weight = 83411.346| |-----------------------------------------------------------------------------| r_work (start): 0.2033 rms_B_bonded: 3.26 r_work: 0.1955 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.1955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9200 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9167 Z= 0.169 Angle : 0.501 5.744 12415 Z= 0.266 Chirality : 0.039 0.123 1412 Planarity : 0.003 0.042 1570 Dihedral : 4.726 43.372 1264 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.18 % Allowed : 19.20 % 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: -0.46 (0.25), residues: 1130 helix: 1.51 (0.26), residues: 410 sheet: -0.71 (0.33), residues: 261 loop : -1.75 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.002 0.001 HIS H 35 PHE 0.009 0.001 PHE B 189 TYR 0.008 0.001 TYR H 178 ARG 0.002 0.000 ARG R 154 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 418) hydrogen bonds : angle 4.68309 ( 1194) SS BOND : bond 0.00166 ( 2) SS BOND : angle 0.76216 ( 4) covalent geometry : bond 0.00376 ( 9165) covalent geometry : angle 0.50076 (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 73 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 42 time to evaluate : 1.016 Fit side-chains REVERT: R 192 MET cc_start: 0.9615 (tpt) cc_final: 0.9191 (tpt) REVERT: B 24 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8359 (ptm160) REVERT: B 33 GLU cc_start: 0.9684 (OUTLIER) cc_final: 0.8900 (mm-30) REVERT: B 243 MET cc_start: 0.9610 (OUTLIER) cc_final: 0.8115 (mmm) REVERT: B 266 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9133 (tp) REVERT: C 171 ILE cc_start: 0.9803 (OUTLIER) cc_final: 0.9544 (mp) REVERT: D 26 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7671 (p0) outliers start: 31 outliers final: 18 residues processed: 68 average time/residue: 0.2185 time to fit residues: 21.5453 Evaluate side-chains 64 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 40 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 232 LEU Chi-restraints excluded: chain B residue 24 ARG 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 178 THR 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 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: 5.9990 chunk 89 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 104 optimal weight: 0.3980 chunk 99 optimal weight: 9.9990 chunk 71 optimal weight: 0.1980 chunk 39 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.033287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2098 r_free = 0.2098 target = 0.026937 restraints weight = 81595.702| |-----------------------------------------------------------------------------| r_work (start): 0.2082 rms_B_bonded: 3.32 r_work: 0.2000 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.1672 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= 0.092 Angle : 0.480 9.218 12415 Z= 0.252 Chirality : 0.038 0.124 1412 Planarity : 0.003 0.042 1570 Dihedral : 4.393 39.942 1264 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.08 % Allowed : 19.82 % Favored : 77.10 % 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: -0.23 (0.26), residues: 1130 helix: 1.62 (0.26), residues: 411 sheet: -0.52 (0.34), residues: 255 loop : -1.57 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 169 HIS 0.002 0.000 HIS R 323 PHE 0.010 0.001 PHE B 189 TYR 0.008 0.001 TYR H 102 ARG 0.007 0.000 ARG R 154 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 418) hydrogen bonds : angle 4.41832 ( 1194) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.84383 ( 4) covalent geometry : bond 0.00194 ( 9165) covalent geometry : angle 0.48007 (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 72 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 42 time to evaluate : 1.107 Fit side-chains REVERT: R 192 MET cc_start: 0.9637 (tpt) cc_final: 0.9257 (tpt) REVERT: B 243 MET cc_start: 0.9507 (OUTLIER) cc_final: 0.7804 (mmm) REVERT: C 158 VAL cc_start: 0.9390 (OUTLIER) cc_final: 0.9111 (p) REVERT: C 171 ILE cc_start: 0.9793 (OUTLIER) cc_final: 0.9543 (mp) REVERT: C 271 CYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8984 (p) REVERT: D 26 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7717 (p0) outliers start: 30 outliers final: 14 residues processed: 68 average time/residue: 0.2072 time to fit residues: 20.7375 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 : 1.159 ------------------------------------------------------------------------------- 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 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 58 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER 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 184 THR Chi-restraints excluded: chain C residue 271 CYS 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 83 MET 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: 10.0000 chunk 63 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.2355 r_free = 0.2355 target = 0.031615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2039 r_free = 0.2039 target = 0.025395 restraints weight = 82934.860| |-----------------------------------------------------------------------------| r_work (start): 0.2021 rms_B_bonded: 3.18 r_work: 0.1942 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.1942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9203 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 9167 Z= 0.259 Angle : 0.535 6.351 12415 Z= 0.281 Chirality : 0.040 0.123 1412 Planarity : 0.003 0.039 1570 Dihedral : 4.591 43.024 1262 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.29 % Allowed : 19.40 % 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: -0.33 (0.26), residues: 1130 helix: 1.58 (0.27), residues: 411 sheet: -0.62 (0.33), residues: 260 loop : -1.66 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 169 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE H 29 TYR 0.011 0.001 TYR H 178 ARG 0.004 0.000 ARG R 140 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 418) hydrogen bonds : angle 4.69457 ( 1194) SS BOND : bond 0.00301 ( 2) SS BOND : angle 0.71689 ( 4) covalent geometry : bond 0.00574 ( 9165) covalent geometry : angle 0.53542 (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 68 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 36 time to evaluate : 1.102 Fit side-chains REVERT: B 24 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8414 (ptm160) REVERT: B 243 MET cc_start: 0.9631 (OUTLIER) cc_final: 0.8294 (mmm) REVERT: C 171 ILE cc_start: 0.9812 (OUTLIER) cc_final: 0.9567 (mp) REVERT: C 271 CYS cc_start: 0.9490 (OUTLIER) cc_final: 0.9143 (p) REVERT: D 26 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8024 (p0) outliers start: 32 outliers final: 18 residues processed: 65 average time/residue: 0.1931 time to fit residues: 18.9020 Evaluate side-chains 58 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 35 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 88 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 80 optimal weight: 0.0370 chunk 90 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- 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 = 0.032443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2060 r_free = 0.2060 target = 0.026117 restraints weight = 83057.314| |-----------------------------------------------------------------------------| r_work (start): 0.2046 rms_B_bonded: 3.24 r_work: 0.1970 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.1970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9192 moved from start: 0.1756 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= 0.124 Angle : 0.495 6.546 12415 Z= 0.258 Chirality : 0.038 0.121 1412 Planarity : 0.003 0.040 1570 Dihedral : 4.446 43.900 1262 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.77 % Allowed : 19.82 % 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: -0.21 (0.26), residues: 1130 helix: 1.67 (0.27), residues: 411 sheet: -0.60 (0.33), residues: 262 loop : -1.55 (0.28), residues: 457 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 178 ARG 0.005 0.000 ARG R 154 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 418) hydrogen bonds : angle 4.49345 ( 1194) SS BOND : bond 0.00138 ( 2) SS BOND : angle 0.71789 ( 4) covalent geometry : bond 0.00272 ( 9165) covalent geometry : angle 0.49472 (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 68 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 41 time to evaluate : 1.270 Fit side-chains REVERT: R 192 MET cc_start: 0.9677 (tpt) cc_final: 0.9378 (tpt) REVERT: B 24 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8267 (ptm160) REVERT: B 243 MET cc_start: 0.9586 (OUTLIER) cc_final: 0.8009 (mmm) REVERT: C 171 ILE cc_start: 0.9811 (OUTLIER) cc_final: 0.9579 (mp) REVERT: C 271 CYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9033 (p) REVERT: D 26 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8146 (p0) outliers start: 27 outliers final: 17 residues processed: 65 average time/residue: 0.2228 time to fit residues: 21.1991 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 : 0.990 ------------------------------------------------------------------------------- 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 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 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 26 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.2370 r_free = 0.2370 target = 0.032146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2050 r_free = 0.2050 target = 0.025799 restraints weight = 83531.741| |-----------------------------------------------------------------------------| r_work (start): 0.2036 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: 0.9200 moved from start: 0.1793 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= 0.176 Angle : 0.513 8.305 12415 Z= 0.266 Chirality : 0.038 0.122 1412 Planarity : 0.003 0.039 1570 Dihedral : 4.513 47.311 1262 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.87 % Allowed : 19.20 % 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: -0.22 (0.26), residues: 1130 helix: 1.64 (0.26), residues: 411 sheet: -0.58 (0.33), residues: 260 loop : -1.55 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.006 0.000 ARG R 154 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 418) hydrogen bonds : angle 4.53950 ( 1194) SS BOND : bond 0.00144 ( 2) SS BOND : angle 0.66497 ( 4) covalent geometry : bond 0.00391 ( 9165) covalent geometry : angle 0.51310 (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 66 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 38 time to evaluate : 1.204 Fit side-chains REVERT: R 192 MET cc_start: 0.9691 (tpt) cc_final: 0.9389 (tpt) REVERT: B 24 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8277 (ptm160) REVERT: B 243 MET cc_start: 0.9596 (OUTLIER) cc_final: 0.8112 (mmm) REVERT: C 171 ILE cc_start: 0.9813 (OUTLIER) cc_final: 0.9581 (mp) REVERT: C 271 CYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9139 (p) REVERT: D 26 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7941 (p0) REVERT: H 141 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8099 (pp20) outliers start: 28 outliers final: 20 residues processed: 63 average time/residue: 0.2606 time to fit residues: 24.4151 Evaluate side-chains 62 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 37 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 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 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 83 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 56 optimal weight: 0.2980 chunk 73 optimal weight: 0.0670 chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.2724 ------------------------------------------------------------------------------- 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 = 0.2412 r_free = 0.2412 target = 0.033310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2095 r_free = 0.2095 target = 0.027021 restraints weight = 81756.911| |-----------------------------------------------------------------------------| r_work (start): 0.2081 rms_B_bonded: 3.15 r_work: 0.2027 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9166 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9167 Z= 0.090 Angle : 0.494 7.554 12415 Z= 0.253 Chirality : 0.038 0.126 1412 Planarity : 0.003 0.040 1570 Dihedral : 4.358 48.092 1262 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.36 % Allowed : 19.92 % 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: -0.09 (0.26), residues: 1130 helix: 1.72 (0.27), residues: 412 sheet: -0.58 (0.32), residues: 269 loop : -1.40 (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 R 259 PHE 0.009 0.001 PHE B 189 TYR 0.008 0.001 TYR H 102 ARG 0.007 0.000 ARG R 154 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 418) hydrogen bonds : angle 4.29365 ( 1194) SS BOND : bond 0.00187 ( 2) SS BOND : angle 0.80002 ( 4) covalent geometry : bond 0.00189 ( 9165) covalent geometry : angle 0.49372 (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 63 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 40 time to evaluate : 1.091 Fit side-chains REVERT: R 192 MET cc_start: 0.9678 (tpt) cc_final: 0.9462 (tpt) REVERT: B 24 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8183 (ptm160) REVERT: B 243 MET cc_start: 0.9459 (OUTLIER) cc_final: 0.7658 (mmm) REVERT: C 271 CYS cc_start: 0.9323 (OUTLIER) cc_final: 0.8990 (p) REVERT: D 26 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8184 (p0) REVERT: H 141 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8139 (pp20) outliers start: 23 outliers final: 17 residues processed: 60 average time/residue: 0.2289 time to fit residues: 19.8510 Evaluate side-chains 61 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 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 177 THR 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 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 = 0.032298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2056 r_free = 0.2056 target = 0.025975 restraints weight = 83544.811| |-----------------------------------------------------------------------------| r_work (start): 0.2043 rms_B_bonded: 3.25 r_work: 0.1965 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.1965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9199 moved from start: 0.1864 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= 0.173 Angle : 0.520 8.180 12415 Z= 0.267 Chirality : 0.038 0.122 1412 Planarity : 0.003 0.039 1570 Dihedral : 4.490 51.138 1262 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.77 % Allowed : 19.40 % Favored : 77.82 % 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: 1.67 (0.27), residues: 412 sheet: -0.54 (0.33), residues: 266 loop : -1.43 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS C 54 PHE 0.008 0.001 PHE B 189 TYR 0.008 0.001 TYR H 178 ARG 0.006 0.000 ARG R 154 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 418) hydrogen bonds : angle 4.48161 ( 1194) SS BOND : bond 0.00188 ( 2) SS BOND : angle 0.61905 ( 4) covalent geometry : bond 0.00385 ( 9165) covalent geometry : angle 0.52025 (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 65 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 38 time to evaluate : 1.178 Fit side-chains REVERT: R 192 MET cc_start: 0.9680 (tpt) cc_final: 0.9379 (tpt) REVERT: B 24 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8286 (ptm160) REVERT: B 243 MET cc_start: 0.9571 (OUTLIER) cc_final: 0.8053 (mmm) REVERT: C 171 ILE cc_start: 0.9812 (OUTLIER) cc_final: 0.9571 (mp) REVERT: C 271 CYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9045 (p) REVERT: D 26 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.7991 (p0) outliers start: 27 outliers final: 18 residues processed: 61 average time/residue: 0.2163 time to fit residues: 19.7191 Evaluate side-chains 60 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 37 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 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 177 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 6.9990 chunk 66 optimal weight: 0.0770 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 overall best weight: 2.4144 ------------------------------------------------------------------------------- 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 = 0.2394 r_free = 0.2394 target = 0.032781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2076 r_free = 0.2076 target = 0.026441 restraints weight = 82703.706| |-----------------------------------------------------------------------------| r_work (start): 0.2062 rms_B_bonded: 3.26 r_work: 0.1985 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.1985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9186 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9167 Z= 0.115 Angle : 0.515 9.229 12415 Z= 0.263 Chirality : 0.038 0.124 1412 Planarity : 0.003 0.039 1570 Dihedral : 4.451 51.566 1262 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.26 % Allowed : 20.12 % 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: -0.08 (0.26), residues: 1130 helix: 1.69 (0.26), residues: 412 sheet: -0.57 (0.32), residues: 269 loop : -1.37 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.002 0.000 HIS H 35 PHE 0.009 0.001 PHE B 189 TYR 0.007 0.001 TYR H 50 ARG 0.007 0.000 ARG R 154 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 418) hydrogen bonds : angle 4.39874 ( 1194) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.61123 ( 4) covalent geometry : bond 0.00252 ( 9165) covalent geometry : angle 0.51533 (12411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4223.21 seconds wall clock time: 74 minutes 8.70 seconds (4448.70 seconds total)