Starting phenix.real_space_refine on Fri Sep 11 08:05:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jhj_22338/09_2026/7jhj_22338.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jhj_22338/09_2026/7jhj_22338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7jhj_22338/09_2026/7jhj_22338.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jhj_22338/09_2026/7jhj_22338.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jhj_22338/09_2026/7jhj_22338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jhj_22338/09_2026/7jhj_22338.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jhj_22338/09_2026/7jhj_22338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jhj_22338/09_2026/7jhj_22338.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 66 5.16 5 C 5420 2.51 5 N 1434 2.21 5 O 1566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8486 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1715 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2532 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 364 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1757 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2083 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 268} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.83, per 1000 atoms: 0.22 Number of scatterers: 8486 At special positions: 0 Unit cell: (104.94, 115.54, 108.12, 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 66 16.00 O 1566 8.00 N 1434 7.00 C 5420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 28 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 97 " - pdb=" SG CYS R 174 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 353.7 milliseconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 14 sheets defined 33.3% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 9 through 30 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.808A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.504A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.680A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.751A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 330 through 351 removed outlier: 4.003A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.529A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.522A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.606A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'R' and resid 33 through 60 removed outlier: 3.946A pdb=" N LEU R 44 " --> pdb=" O THR R 40 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU R 49 " --> pdb=" O VAL R 45 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR R 51 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY R 54 " --> pdb=" O LEU R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 92 removed outlier: 3.629A pdb=" N VAL R 70 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP R 82 " --> pdb=" O GLU R 78 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 127 removed outlier: 3.631A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 161 removed outlier: 3.665A pdb=" N GLY R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 212 removed outlier: 3.667A pdb=" N LEU R 189 " --> pdb=" O ALA R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 220 removed outlier: 3.915A pdb=" N ARG R 219 " --> pdb=" O LYS R 216 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS R 220 " --> pdb=" O PHE R 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 216 through 220' Processing helix chain 'R' and resid 221 through 240 removed outlier: 4.067A pdb=" N VAL R 227 " --> pdb=" O LEU R 223 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE R 233 " --> pdb=" O PHE R 229 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N CYS R 234 " --> pdb=" O THR R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 246 Processing helix chain 'R' and resid 267 through 285 removed outlier: 3.623A pdb=" N ALA R 271 " --> pdb=" O TYR R 267 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER R 285 " --> pdb=" O LEU R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 301 removed outlier: 3.544A pdb=" N SER R 292 " --> pdb=" O HIS R 288 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR R 298 " --> pdb=" O LYS R 294 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA R 301 " --> pdb=" O VAL R 297 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.798A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.248A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.713A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.130A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.862A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.694A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.787A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.787A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'D' and resid 182 through 183 removed outlier: 5.583A pdb=" N LEU D 175 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU D 166 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 177 " --> pdb=" O TRP D 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 168 through 170 410 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1408 1.32 - 1.44: 2340 1.44 - 1.57: 4812 1.57 - 1.69: 4 1.69 - 1.82: 95 Bond restraints: 8659 Sorted by residual: bond pdb=" CAY Y01 R 401 " pdb=" OAW Y01 R 401 " ideal model delta sigma weight residual 1.332 1.427 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" CAP Y01 R 401 " pdb=" CAQ Y01 R 401 " ideal model delta sigma weight residual 1.541 1.606 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" CBE Y01 R 401 " pdb=" CBI Y01 R 401 " ideal model delta sigma weight residual 1.550 1.497 0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" CAS Y01 R 401 " pdb=" CBF Y01 R 401 " ideal model delta sigma weight residual 1.533 1.486 0.047 2.00e-02 2.50e+03 5.55e+00 bond pdb=" CBB Y01 R 401 " pdb=" CBE Y01 R 401 " ideal model delta sigma weight residual 1.535 1.582 -0.047 2.00e-02 2.50e+03 5.47e+00 ... (remaining 8654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 11331 2.00 - 3.99: 357 3.99 - 5.99: 53 5.99 - 7.99: 16 7.99 - 9.99: 3 Bond angle restraints: 11760 Sorted by residual: angle pdb=" C ASN A 269 " pdb=" N LYS A 270 " pdb=" CA LYS A 270 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.63e+01 angle pdb=" CA GLU B 130 " pdb=" CB GLU B 130 " pdb=" CG GLU B 130 " ideal model delta sigma weight residual 114.10 122.02 -7.92 2.00e+00 2.50e-01 1.57e+01 angle pdb=" N TYR R 267 " pdb=" CA TYR R 267 " pdb=" C TYR R 267 " ideal model delta sigma weight residual 109.81 117.34 -7.53 2.21e+00 2.05e-01 1.16e+01 angle pdb=" CAM Y01 R 401 " pdb=" CAY Y01 R 401 " pdb=" OAW Y01 R 401 " ideal model delta sigma weight residual 111.19 121.18 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" C ARG B 129 " pdb=" N GLU B 130 " pdb=" CA GLU B 130 " ideal model delta sigma weight residual 122.08 126.82 -4.74 1.47e+00 4.63e-01 1.04e+01 ... (remaining 11755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.08: 4388 14.08 - 28.16: 545 28.16 - 42.23: 134 42.23 - 56.31: 26 56.31 - 70.39: 5 Dihedral angle restraints: 5098 sinusoidal: 1880 harmonic: 3218 Sorted by residual: dihedral pdb=" CA TYR R 267 " pdb=" C TYR R 267 " pdb=" N PRO R 268 " pdb=" CA PRO R 268 " ideal model delta harmonic sigma weight residual -180.00 -153.97 -26.03 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA GLU A 8 " pdb=" C GLU A 8 " pdb=" N ASP A 9 " pdb=" CA ASP A 9 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 5095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1077 0.067 - 0.134: 259 0.134 - 0.201: 29 0.201 - 0.268: 7 0.268 - 0.335: 1 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CBG Y01 R 401 " pdb=" CAQ Y01 R 401 " pdb=" CBD Y01 R 401 " pdb=" CBI Y01 R 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.67 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB ILE D 100 " pdb=" CA ILE D 100 " pdb=" CG1 ILE D 100 " pdb=" CG2 ILE D 100 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CBF Y01 R 401 " pdb=" CAS Y01 R 401 " pdb=" CBD Y01 R 401 " pdb=" CBH Y01 R 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.67 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1370 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 243 " -0.057 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO R 244 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO R 244 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 244 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 269 " -0.049 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO R 270 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO R 270 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO R 270 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 199 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C PHE A 199 " -0.051 2.00e-02 2.50e+03 pdb=" O PHE A 199 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP A 200 " 0.017 2.00e-02 2.50e+03 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2406 2.80 - 3.32: 7200 3.32 - 3.85: 13980 3.85 - 4.37: 16549 4.37 - 4.90: 29452 Nonbonded interactions: 69587 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.273 3.040 nonbonded pdb=" OG SER D 7 " pdb=" OG SER D 21 " model vdw 2.281 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.309 3.040 nonbonded pdb=" O TYR R 32 " pdb=" OH TYR R 266 " model vdw 2.310 3.040 ... (remaining 69582 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: 0.720 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.580 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.009 0.095 8663 Z= 0.387 Angle : 0.871 9.985 11768 Z= 0.463 Chirality : 0.057 0.335 1373 Planarity : 0.007 0.086 1474 Dihedral : 13.449 70.389 3012 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.45 % Allowed : 8.38 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.21), residues: 1101 helix: -2.24 (0.20), residues: 360 sheet: -1.96 (0.27), residues: 288 loop : -2.46 (0.24), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 175 TYR 0.024 0.003 TYR B 105 PHE 0.024 0.003 PHE D 27 TRP 0.020 0.003 TRP R 113 HIS 0.008 0.002 HIS R 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00905 / 0.39 ( 8659) covalent geometry : angle 0.87052 / 0.46 (11760) SS BOND : bond 0.00512 / 0.24 ( 4) SS BOND : angle 1.18896 / 0.65 ( 8) hydrogen bonds : bond 0.12624 / 8.50 ( 406) hydrogen bonds : angle 6.13275 / 4.31 ( 1137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 0.311 Fit side-chains REVERT: A 247 MET cc_start: 0.8311 (mtp) cc_final: 0.8107 (mtm) REVERT: A 251 ASP cc_start: 0.7728 (t70) cc_final: 0.7427 (t0) REVERT: B 30 LEU cc_start: 0.8432 (tp) cc_final: 0.8084 (tp) REVERT: B 101 MET cc_start: 0.8886 (mtp) cc_final: 0.8634 (mtp) REVERT: B 127 LYS cc_start: 0.8884 (mttp) cc_final: 0.8627 (mtpt) REVERT: B 228 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7820 (p0) REVERT: B 301 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8489 (mtpp) outliers start: 4 outliers final: 1 residues processed: 167 average time/residue: 0.1083 time to fit residues: 23.4552 Evaluate side-chains 136 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.0570 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.110763 restraints weight = 11349.321| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.41 r_work: 0.3055 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8663 Z= 0.109 Angle : 0.525 6.111 11768 Z= 0.281 Chirality : 0.041 0.134 1373 Planarity : 0.004 0.063 1474 Dihedral : 5.153 51.699 1211 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.13 % Allowed : 14.16 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.23), residues: 1101 helix: -0.16 (0.27), residues: 364 sheet: -1.79 (0.28), residues: 281 loop : -1.90 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 313 TYR 0.016 0.001 TYR D 178 PHE 0.018 0.001 PHE R 57 TRP 0.016 0.001 TRP R 113 HIS 0.004 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 8659) covalent geometry : angle 0.52505 / 0.28 (11760) SS BOND : bond 0.00293 / 0.14 ( 4) SS BOND : angle 0.60415 / 0.33 ( 8) hydrogen bonds : bond 0.03281 / 2.22 ( 406) hydrogen bonds : angle 4.47782 / 3.18 ( 1137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.256 Fit side-chains REVERT: A 24 ARG cc_start: 0.8258 (ttp-110) cc_final: 0.7811 (mtm110) REVERT: A 247 MET cc_start: 0.8538 (mtp) cc_final: 0.8334 (mtm) REVERT: A 251 ASP cc_start: 0.8189 (t70) cc_final: 0.7771 (t0) REVERT: A 304 GLN cc_start: 0.8758 (tt0) cc_final: 0.8502 (tt0) REVERT: A 345 LYS cc_start: 0.8577 (tttt) cc_final: 0.8164 (ttmt) REVERT: B 127 LYS cc_start: 0.8953 (mttp) cc_final: 0.8635 (mtpt) REVERT: B 186 ASP cc_start: 0.8225 (m-30) cc_final: 0.7989 (m-30) REVERT: B 301 LYS cc_start: 0.9066 (mtpp) cc_final: 0.8570 (mtpp) REVERT: R 240 MET cc_start: 0.6580 (tmm) cc_final: 0.6288 (tmm) outliers start: 10 outliers final: 7 residues processed: 158 average time/residue: 0.0942 time to fit residues: 20.0971 Evaluate side-chains 145 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 0.0170 chunk 49 optimal weight: 3.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.111229 restraints weight = 11231.381| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.37 r_work: 0.3026 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8663 Z= 0.112 Angle : 0.500 5.927 11768 Z= 0.266 Chirality : 0.041 0.142 1373 Planarity : 0.004 0.060 1474 Dihedral : 4.756 49.902 1209 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.04 % Allowed : 14.95 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.25), residues: 1101 helix: 0.57 (0.29), residues: 370 sheet: -1.54 (0.28), residues: 287 loop : -1.67 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.012 0.001 TYR D 178 PHE 0.019 0.001 PHE R 57 TRP 0.016 0.001 TRP R 113 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8659) covalent geometry : angle 0.49986 / 0.27 (11760) SS BOND : bond 0.00293 / 0.14 ( 4) SS BOND : angle 0.55350 / 0.30 ( 8) hydrogen bonds : bond 0.02992 / 2.02 ( 406) hydrogen bonds : angle 4.13045 / 2.95 ( 1137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.309 Fit side-chains REVERT: A 24 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7781 (mtm110) REVERT: A 247 MET cc_start: 0.8461 (mtp) cc_final: 0.8227 (mtm) REVERT: A 251 ASP cc_start: 0.8139 (t70) cc_final: 0.7756 (t0) REVERT: A 304 GLN cc_start: 0.8689 (tt0) cc_final: 0.8442 (tt0) REVERT: A 313 ARG cc_start: 0.8423 (mpt-90) cc_final: 0.7933 (ptp-170) REVERT: A 345 LYS cc_start: 0.8575 (tttt) cc_final: 0.8122 (ttmt) REVERT: B 127 LYS cc_start: 0.8986 (mttp) cc_final: 0.8629 (mtpt) REVERT: B 186 ASP cc_start: 0.8254 (m-30) cc_final: 0.8001 (m-30) REVERT: C 48 ASP cc_start: 0.8786 (t0) cc_final: 0.8524 (t0) REVERT: R 167 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6744 (pp) outliers start: 18 outliers final: 10 residues processed: 159 average time/residue: 0.0854 time to fit residues: 18.7907 Evaluate side-chains 148 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 7 optimal weight: 0.0670 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 21 optimal weight: 8.9990 chunk 24 optimal weight: 0.1980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.145574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110007 restraints weight = 11410.376| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.19 r_work: 0.3104 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8663 Z= 0.092 Angle : 0.491 9.846 11768 Z= 0.257 Chirality : 0.041 0.133 1373 Planarity : 0.004 0.059 1474 Dihedral : 4.492 48.031 1209 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.49 % Allowed : 16.53 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.25), residues: 1101 helix: 0.98 (0.29), residues: 370 sheet: -1.43 (0.27), residues: 287 loop : -1.50 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.013 0.001 TYR D 178 PHE 0.020 0.001 PHE R 57 TRP 0.014 0.001 TRP R 113 HIS 0.001 0.000 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 ( 8659) covalent geometry : angle 0.49051 / 0.26 (11760) SS BOND : bond 0.00270 / 0.13 ( 4) SS BOND : angle 0.47559 / 0.26 ( 8) hydrogen bonds : bond 0.02730 / 1.85 ( 406) hydrogen bonds : angle 3.94171 / 2.83 ( 1137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.242 Fit side-chains REVERT: A 24 ARG cc_start: 0.8310 (ttp-110) cc_final: 0.7905 (mtm110) REVERT: A 247 MET cc_start: 0.8556 (mtp) cc_final: 0.8330 (mtm) REVERT: A 251 ASP cc_start: 0.8231 (t70) cc_final: 0.7950 (t0) REVERT: A 304 GLN cc_start: 0.8710 (tt0) cc_final: 0.8408 (tt0) REVERT: A 313 ARG cc_start: 0.8443 (mpt-90) cc_final: 0.7945 (ptp-170) REVERT: A 345 LYS cc_start: 0.8722 (tttt) cc_final: 0.8291 (ttmt) REVERT: B 22 ARG cc_start: 0.7524 (ptp-170) cc_final: 0.7316 (ptp-170) REVERT: B 59 TYR cc_start: 0.8656 (m-80) cc_final: 0.8430 (m-80) REVERT: B 127 LYS cc_start: 0.9037 (mttp) cc_final: 0.8670 (mtpt) REVERT: B 217 MET cc_start: 0.7814 (ptt) cc_final: 0.7599 (ptt) REVERT: B 301 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8652 (mtpp) REVERT: R 81 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8219 (tt) REVERT: R 167 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6634 (pp) outliers start: 22 outliers final: 14 residues processed: 164 average time/residue: 0.0834 time to fit residues: 18.8928 Evaluate side-chains 152 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.144054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.111237 restraints weight = 11356.770| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.34 r_work: 0.3050 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8663 Z= 0.121 Angle : 0.507 6.133 11768 Z= 0.265 Chirality : 0.042 0.143 1373 Planarity : 0.004 0.058 1474 Dihedral : 4.508 47.229 1209 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.17 % Allowed : 16.99 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.25), residues: 1101 helix: 1.21 (0.29), residues: 370 sheet: -1.36 (0.27), residues: 296 loop : -1.37 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.011 0.001 TYR D 223 PHE 0.022 0.001 PHE R 57 TRP 0.019 0.001 TRP R 82 HIS 0.002 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 8659) covalent geometry : angle 0.50672 / 0.27 (11760) SS BOND : bond 0.00281 / 0.14 ( 4) SS BOND : angle 0.54490 / 0.29 ( 8) hydrogen bonds : bond 0.02970 / 2.00 ( 406) hydrogen bonds : angle 3.90909 / 2.81 ( 1137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.223 Fit side-chains REVERT: A 24 ARG cc_start: 0.8370 (ttp-110) cc_final: 0.7934 (mtm110) REVERT: A 247 MET cc_start: 0.8615 (mtp) cc_final: 0.8384 (mtm) REVERT: A 251 ASP cc_start: 0.8313 (t70) cc_final: 0.7952 (t0) REVERT: A 304 GLN cc_start: 0.8742 (tt0) cc_final: 0.8471 (tt0) REVERT: A 313 ARG cc_start: 0.8442 (mpt-90) cc_final: 0.8023 (ptp-170) REVERT: A 345 LYS cc_start: 0.8755 (tttt) cc_final: 0.8320 (ttmt) REVERT: B 22 ARG cc_start: 0.7593 (ptp-170) cc_final: 0.7382 (ptp-170) REVERT: B 127 LYS cc_start: 0.9096 (mttp) cc_final: 0.8725 (mtpt) REVERT: B 186 ASP cc_start: 0.8483 (m-30) cc_final: 0.8153 (m-30) REVERT: B 301 LYS cc_start: 0.9112 (mtpp) cc_final: 0.8699 (mtpp) REVERT: R 167 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6528 (pp) outliers start: 28 outliers final: 18 residues processed: 153 average time/residue: 0.0922 time to fit residues: 19.3014 Evaluate side-chains 149 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 242 SER Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.143394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.110540 restraints weight = 11244.274| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.32 r_work: 0.3041 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8663 Z= 0.138 Angle : 0.527 8.689 11768 Z= 0.273 Chirality : 0.042 0.144 1373 Planarity : 0.004 0.058 1474 Dihedral : 4.535 47.152 1209 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.17 % Allowed : 17.10 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.26), residues: 1101 helix: 1.33 (0.29), residues: 371 sheet: -1.37 (0.28), residues: 286 loop : -1.28 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.013 0.001 TYR D 223 PHE 0.022 0.001 PHE R 57 TRP 0.017 0.001 TRP R 82 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8659) covalent geometry : angle 0.52728 / 0.27 (11760) SS BOND : bond 0.00293 / 0.14 ( 4) SS BOND : angle 0.58055 / 0.31 ( 8) hydrogen bonds : bond 0.03111 / 2.10 ( 406) hydrogen bonds : angle 3.93072 / 2.82 ( 1137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.272 Fit side-chains REVERT: A 24 ARG cc_start: 0.8368 (ttp-110) cc_final: 0.7915 (mtm110) REVERT: A 247 MET cc_start: 0.8592 (mtp) cc_final: 0.8360 (mtm) REVERT: A 251 ASP cc_start: 0.8335 (t70) cc_final: 0.7986 (t0) REVERT: A 304 GLN cc_start: 0.8794 (tt0) cc_final: 0.8529 (tt0) REVERT: A 313 ARG cc_start: 0.8469 (mpt-90) cc_final: 0.7924 (ptp-170) REVERT: A 345 LYS cc_start: 0.8772 (tttt) cc_final: 0.8328 (ttmt) REVERT: B 105 TYR cc_start: 0.9284 (OUTLIER) cc_final: 0.8990 (t80) REVERT: B 127 LYS cc_start: 0.9087 (mttp) cc_final: 0.8711 (mtpt) REVERT: B 186 ASP cc_start: 0.8483 (m-30) cc_final: 0.8157 (m-30) REVERT: B 301 LYS cc_start: 0.9106 (mtpp) cc_final: 0.8696 (mttp) REVERT: D 59 TYR cc_start: 0.8708 (m-10) cc_final: 0.8506 (m-10) REVERT: R 167 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6617 (pp) outliers start: 28 outliers final: 17 residues processed: 150 average time/residue: 0.0918 time to fit residues: 18.6920 Evaluate side-chains 147 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 242 SER Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.144250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.105464 restraints weight = 11366.635| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.20 r_work: 0.3074 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8663 Z= 0.124 Angle : 0.519 7.534 11768 Z= 0.270 Chirality : 0.042 0.141 1373 Planarity : 0.003 0.058 1474 Dihedral : 4.439 46.323 1209 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.83 % Allowed : 17.89 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.26), residues: 1101 helix: 1.46 (0.29), residues: 372 sheet: -1.20 (0.27), residues: 302 loop : -1.27 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.012 0.001 TYR D 223 PHE 0.019 0.001 PHE R 57 TRP 0.015 0.001 TRP R 82 HIS 0.002 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 8659) covalent geometry : angle 0.51856 / 0.27 (11760) SS BOND : bond 0.00294 / 0.14 ( 4) SS BOND : angle 0.53460 / 0.28 ( 8) hydrogen bonds : bond 0.03008 / 2.03 ( 406) hydrogen bonds : angle 3.92707 / 2.82 ( 1137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.300 Fit side-chains REVERT: A 24 ARG cc_start: 0.8335 (ttp-110) cc_final: 0.7895 (mtm110) REVERT: A 247 MET cc_start: 0.8650 (mtp) cc_final: 0.8413 (mtm) REVERT: A 251 ASP cc_start: 0.8290 (t70) cc_final: 0.7951 (t0) REVERT: A 304 GLN cc_start: 0.8773 (tt0) cc_final: 0.8508 (tt0) REVERT: A 313 ARG cc_start: 0.8441 (mpt-90) cc_final: 0.7899 (ptp-170) REVERT: A 345 LYS cc_start: 0.8727 (tttt) cc_final: 0.8295 (ttmt) REVERT: B 105 TYR cc_start: 0.9270 (OUTLIER) cc_final: 0.8985 (t80) REVERT: B 127 LYS cc_start: 0.9051 (mttp) cc_final: 0.8677 (mtpt) REVERT: B 186 ASP cc_start: 0.8421 (m-30) cc_final: 0.8096 (m-30) REVERT: B 268 ASN cc_start: 0.8670 (t0) cc_final: 0.8464 (t0) REVERT: B 301 LYS cc_start: 0.9069 (mtpp) cc_final: 0.8700 (mtpp) REVERT: D 59 TYR cc_start: 0.8662 (m-10) cc_final: 0.8457 (m-10) REVERT: R 167 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6577 (pp) outliers start: 25 outliers final: 16 residues processed: 153 average time/residue: 0.0894 time to fit residues: 18.9472 Evaluate side-chains 146 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 104 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107247 restraints weight = 11294.714| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.19 r_work: 0.3049 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8663 Z= 0.150 Angle : 0.536 7.017 11768 Z= 0.280 Chirality : 0.043 0.143 1373 Planarity : 0.004 0.058 1474 Dihedral : 4.534 46.933 1209 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.60 % Allowed : 18.91 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.26), residues: 1101 helix: 1.48 (0.29), residues: 372 sheet: -1.16 (0.27), residues: 302 loop : -1.31 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.014 0.001 TYR D 223 PHE 0.021 0.001 PHE R 57 TRP 0.014 0.001 TRP R 82 HIS 0.002 0.001 HIS R 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 8659) covalent geometry : angle 0.53575 / 0.28 (11760) SS BOND : bond 0.00292 / 0.14 ( 4) SS BOND : angle 0.57424 / 0.31 ( 8) hydrogen bonds : bond 0.03181 / 2.15 ( 406) hydrogen bonds : angle 3.97670 / 2.85 ( 1137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.309 Fit side-chains REVERT: A 24 ARG cc_start: 0.8337 (ttp-110) cc_final: 0.7881 (mtm110) REVERT: A 247 MET cc_start: 0.8610 (mtp) cc_final: 0.8368 (mtm) REVERT: A 251 ASP cc_start: 0.8284 (t70) cc_final: 0.7960 (t0) REVERT: A 304 GLN cc_start: 0.8783 (tt0) cc_final: 0.8536 (tt0) REVERT: B 105 TYR cc_start: 0.9279 (OUTLIER) cc_final: 0.9027 (t80) REVERT: B 127 LYS cc_start: 0.9050 (mttp) cc_final: 0.8652 (mtpt) REVERT: B 186 ASP cc_start: 0.8465 (m-30) cc_final: 0.8150 (m-30) REVERT: B 268 ASN cc_start: 0.8646 (t0) cc_final: 0.8436 (t0) REVERT: B 301 LYS cc_start: 0.9084 (mtpp) cc_final: 0.8659 (mtpp) REVERT: B 338 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8916 (mm) REVERT: R 167 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6585 (pp) outliers start: 23 outliers final: 18 residues processed: 149 average time/residue: 0.0981 time to fit residues: 19.6348 Evaluate side-chains 151 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 20 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.144030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.105194 restraints weight = 11301.229| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.18 r_work: 0.2983 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8663 Z= 0.131 Angle : 0.531 8.510 11768 Z= 0.276 Chirality : 0.042 0.143 1373 Planarity : 0.004 0.057 1474 Dihedral : 4.462 46.267 1209 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.72 % Allowed : 19.37 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.26), residues: 1101 helix: 1.46 (0.29), residues: 378 sheet: -1.10 (0.28), residues: 301 loop : -1.26 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.013 0.001 TYR D 223 PHE 0.021 0.001 PHE R 57 TRP 0.014 0.001 TRP R 82 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 8659) covalent geometry : angle 0.53057 / 0.28 (11760) SS BOND : bond 0.00290 / 0.14 ( 4) SS BOND : angle 0.54536 / 0.29 ( 8) hydrogen bonds : bond 0.03084 / 2.08 ( 406) hydrogen bonds : angle 3.97591 / 2.85 ( 1137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.253 Fit side-chains REVERT: A 24 ARG cc_start: 0.8308 (ttp-110) cc_final: 0.7852 (mtm110) REVERT: A 247 MET cc_start: 0.8551 (mtp) cc_final: 0.8308 (mtm) REVERT: A 251 ASP cc_start: 0.8279 (t70) cc_final: 0.7987 (t0) REVERT: A 304 GLN cc_start: 0.8747 (tt0) cc_final: 0.8504 (tt0) REVERT: A 345 LYS cc_start: 0.8710 (tttt) cc_final: 0.8253 (ttmt) REVERT: B 105 TYR cc_start: 0.9281 (OUTLIER) cc_final: 0.9012 (t80) REVERT: B 127 LYS cc_start: 0.9069 (mttp) cc_final: 0.8681 (mtpt) REVERT: B 186 ASP cc_start: 0.8471 (m-30) cc_final: 0.8154 (m-30) REVERT: B 268 ASN cc_start: 0.8678 (t0) cc_final: 0.8477 (t0) REVERT: B 301 LYS cc_start: 0.9085 (mtpp) cc_final: 0.8753 (mtpp) REVERT: B 338 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8919 (mm) REVERT: R 167 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6479 (pp) outliers start: 24 outliers final: 18 residues processed: 152 average time/residue: 0.0882 time to fit residues: 18.0910 Evaluate side-chains 152 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 2 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 chunk 15 optimal weight: 0.0470 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 0.0670 chunk 1 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.147052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.111536 restraints weight = 11211.122| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.21 r_work: 0.3122 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8663 Z= 0.093 Angle : 0.502 7.239 11768 Z= 0.263 Chirality : 0.041 0.147 1373 Planarity : 0.003 0.057 1474 Dihedral : 4.209 43.057 1209 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.04 % Allowed : 20.39 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.26), residues: 1101 helix: 1.62 (0.29), residues: 377 sheet: -1.01 (0.28), residues: 301 loop : -1.23 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 62 TYR 0.014 0.001 TYR D 178 PHE 0.025 0.001 PHE R 57 TRP 0.016 0.001 TRP R 82 HIS 0.001 0.000 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 ( 8659) covalent geometry : angle 0.50154 / 0.26 (11760) SS BOND : bond 0.00251 / 0.12 ( 4) SS BOND : angle 0.52725 / 0.28 ( 8) hydrogen bonds : bond 0.02767 / 1.88 ( 406) hydrogen bonds : angle 3.88910 / 2.79 ( 1137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.289 Fit side-chains REVERT: A 24 ARG cc_start: 0.8315 (ttp-110) cc_final: 0.7911 (mtm110) REVERT: A 247 MET cc_start: 0.8660 (mtp) cc_final: 0.8446 (mtm) REVERT: A 251 ASP cc_start: 0.8240 (t70) cc_final: 0.7929 (t0) REVERT: A 304 GLN cc_start: 0.8724 (tt0) cc_final: 0.8437 (tt0) REVERT: A 313 ARG cc_start: 0.8459 (mpt-90) cc_final: 0.7911 (ptp-170) REVERT: A 345 LYS cc_start: 0.8723 (tttt) cc_final: 0.8327 (ttmt) REVERT: B 22 ARG cc_start: 0.7430 (ptp-170) cc_final: 0.6939 (mtm180) REVERT: B 127 LYS cc_start: 0.9017 (mttp) cc_final: 0.8655 (mtpt) REVERT: B 175 GLN cc_start: 0.8771 (pt0) cc_final: 0.8564 (mm-40) REVERT: B 301 LYS cc_start: 0.9055 (mtpp) cc_final: 0.8770 (mtpp) REVERT: B 338 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8898 (mm) REVERT: D 180 MET cc_start: 0.8930 (ttp) cc_final: 0.8719 (tmm) REVERT: R 68 MET cc_start: 0.8863 (tpt) cc_final: 0.8467 (tpt) REVERT: R 167 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6450 (pp) REVERT: R 284 TRP cc_start: 0.8543 (t60) cc_final: 0.8157 (t-100) outliers start: 18 outliers final: 13 residues processed: 158 average time/residue: 0.0884 time to fit residues: 19.0877 Evaluate side-chains 153 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 229 PHE Chi-restraints excluded: chain R residue 293 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 93 optimal weight: 0.0570 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113370 restraints weight = 11166.143| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.31 r_work: 0.3079 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8663 Z= 0.112 Angle : 0.519 7.788 11768 Z= 0.272 Chirality : 0.042 0.148 1373 Planarity : 0.003 0.057 1474 Dihedral : 4.238 43.052 1209 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.15 % Allowed : 20.61 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.26), residues: 1101 helix: 1.64 (0.29), residues: 377 sheet: -0.99 (0.28), residues: 301 loop : -1.22 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 256 TYR 0.011 0.001 TYR D 178 PHE 0.024 0.001 PHE R 57 TRP 0.016 0.001 TRP R 82 HIS 0.002 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 8659) covalent geometry : angle 0.51942 / 0.27 (11760) SS BOND : bond 0.00262 / 0.13 ( 4) SS BOND : angle 0.52622 / 0.28 ( 8) hydrogen bonds : bond 0.02863 / 1.94 ( 406) hydrogen bonds : angle 3.88630 / 2.78 ( 1137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2177.92 seconds wall clock time: 38 minutes 3.63 seconds (2283.63 seconds total)