Starting phenix.real_space_refine on Fri Aug 22 23:31:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jhj_22338/08_2025/7jhj_22338.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jhj_22338/08_2025/7jhj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7jhj_22338/08_2025/7jhj_22338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jhj_22338/08_2025/7jhj_22338.map" model { file = "/net/cci-nas-00/data/ceres_data/7jhj_22338/08_2025/7jhj_22338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jhj_22338/08_2025/7jhj_22338.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.69, per 1000 atoms: 0.20 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: 0.46 Conformation dependent library (CDL) restraints added in 283.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.28 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: 1.16 Time building geometry restraints manager: 0.62 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: 4434 14.08 - 28.16: 551 28.16 - 42.23: 140 42.23 - 56.31: 26 56.31 - 70.39: 5 Dihedral angle restraints: 5156 sinusoidal: 1938 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 5153 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.000 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 13.452 70.389 3070 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 aren 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 covalent geometry : bond 0.00905 ( 8659) covalent geometry : angle 0.87052 (11760) SS BOND : bond 0.00512 ( 4) SS BOND : angle 1.18896 ( 8) hydrogen bonds : bond 0.12624 ( 406) hydrogen bonds : angle 6.13275 ( 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 : 0.348 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: 0.1331 time to fit residues: 28.5341 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 : 0.363 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3708 r_free = 0.3708 target = 0.143971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.111074 restraints weight = 11344.162| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.42 r_work: 0.3059 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1512 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= 0.107 Angle : 0.519 5.973 11768 Z= 0.278 Chirality : 0.041 0.134 1373 Planarity : 0.004 0.063 1474 Dihedral : 5.372 51.470 1269 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.25 % Allowed : 14.38 % Favored : 84.37 % 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 aren not related in a simple way. whole: -1.98 (0.24), residues: 1101 helix: -0.12 (0.27), residues: 364 sheet: -1.77 (0.28), residues: 281 loop : -1.89 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 175 TYR 0.015 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 covalent geometry : bond 0.00229 ( 8659) covalent geometry : angle 0.51935 (11760) SS BOND : bond 0.00299 ( 4) SS BOND : angle 0.61014 ( 8) hydrogen bonds : bond 0.03183 ( 406) hydrogen bonds : angle 4.44196 ( 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 163 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.344 Fit side-chains REVERT: A 24 ARG cc_start: 0.8260 (ttp-110) cc_final: 0.7855 (mtm110) REVERT: A 247 MET cc_start: 0.8540 (mtp) cc_final: 0.8339 (mtm) REVERT: A 251 ASP cc_start: 0.8181 (t70) cc_final: 0.7770 (t0) REVERT: A 304 GLN cc_start: 0.8752 (tt0) cc_final: 0.8473 (tt0) REVERT: A 345 LYS cc_start: 0.8592 (tttt) cc_final: 0.8175 (ttmt) REVERT: B 127 LYS cc_start: 0.8950 (mttp) cc_final: 0.8631 (mtpt) REVERT: B 186 ASP cc_start: 0.8222 (m-30) cc_final: 0.8001 (m-30) REVERT: B 301 LYS cc_start: 0.9069 (mtpp) cc_final: 0.8552 (mtpp) REVERT: R 240 MET cc_start: 0.6570 (tmm) cc_final: 0.6287 (tmm) outliers start: 11 outliers final: 8 residues processed: 159 average time/residue: 0.1123 time to fit residues: 24.0064 Evaluate side-chains 146 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 293 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: 0.7980 chunk 39 optimal weight: 0.0970 chunk 74 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 18 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3716 r_free = 0.3716 target = 0.144670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111937 restraints weight = 11222.042| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.34 r_work: 0.3043 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8663 Z= 0.102 Angle : 0.492 6.061 11768 Z= 0.261 Chirality : 0.041 0.142 1373 Planarity : 0.004 0.060 1474 Dihedral : 4.916 49.439 1267 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.93 % Allowed : 15.52 % Favored : 82.56 % 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 aren not related in a simple way. whole: -1.35 (0.25), residues: 1101 helix: 0.60 (0.29), residues: 370 sheet: -1.52 (0.28), residues: 287 loop : -1.65 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.012 0.001 TYR D 178 PHE 0.019 0.001 PHE R 57 TRP 0.015 0.001 TRP R 113 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 8659) covalent geometry : angle 0.49191 (11760) SS BOND : bond 0.00279 ( 4) SS BOND : angle 0.50831 ( 8) hydrogen bonds : bond 0.02907 ( 406) hydrogen bonds : angle 4.09006 ( 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 163 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.355 Fit side-chains REVERT: A 24 ARG cc_start: 0.8389 (ttp-110) cc_final: 0.7965 (mtm110) REVERT: A 247 MET cc_start: 0.8552 (mtp) cc_final: 0.8343 (mtm) REVERT: A 251 ASP cc_start: 0.8297 (t70) cc_final: 0.7954 (t0) REVERT: A 304 GLN cc_start: 0.8772 (tt0) cc_final: 0.8465 (tt0) REVERT: A 313 ARG cc_start: 0.8437 (mpt-90) cc_final: 0.7944 (ptp-170) REVERT: A 345 LYS cc_start: 0.8753 (tttt) cc_final: 0.8297 (ttmt) REVERT: B 30 LEU cc_start: 0.8359 (tp) cc_final: 0.8009 (tp) REVERT: B 127 LYS cc_start: 0.9062 (mttp) cc_final: 0.8680 (mtpt) REVERT: B 262 MET cc_start: 0.8766 (tpp) cc_final: 0.8512 (tpp) REVERT: B 301 LYS cc_start: 0.9150 (mtpp) cc_final: 0.8679 (mtpp) REVERT: C 48 ASP cc_start: 0.8869 (t0) cc_final: 0.8622 (t0) REVERT: D 83 MET cc_start: 0.9186 (mtm) cc_final: 0.8974 (mtm) REVERT: R 167 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6709 (pp) outliers start: 17 outliers final: 8 residues processed: 157 average time/residue: 0.1079 time to fit residues: 23.0186 Evaluate side-chains 145 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 24 optimal weight: 0.0270 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 32 GLN R 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.108160 restraints weight = 11488.994| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.09 r_work: 0.3079 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8663 Z= 0.124 Angle : 0.517 9.510 11768 Z= 0.269 Chirality : 0.042 0.136 1373 Planarity : 0.004 0.059 1474 Dihedral : 4.861 48.492 1267 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.60 % Allowed : 16.08 % Favored : 81.31 % 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 aren not related in a simple way. whole: -1.04 (0.25), residues: 1101 helix: 0.96 (0.29), residues: 370 sheet: -1.48 (0.28), residues: 286 loop : -1.48 (0.28), residues: 445 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 0.019 0.001 PHE R 57 TRP 0.018 0.001 TRP R 82 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8659) covalent geometry : angle 0.51667 (11760) SS BOND : bond 0.00283 ( 4) SS BOND : angle 0.54005 ( 8) hydrogen bonds : bond 0.02987 ( 406) hydrogen bonds : angle 3.99140 ( 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 164 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.399 Fit side-chains REVERT: A 24 ARG cc_start: 0.8330 (ttp-110) cc_final: 0.7890 (mtm110) REVERT: A 247 MET cc_start: 0.8578 (mtp) cc_final: 0.8344 (mtm) REVERT: A 251 ASP cc_start: 0.8209 (t70) cc_final: 0.7939 (t0) REVERT: A 304 GLN cc_start: 0.8728 (tt0) cc_final: 0.8487 (tt0) REVERT: A 313 ARG cc_start: 0.8445 (mpt-90) cc_final: 0.7930 (ptp-170) REVERT: A 345 LYS cc_start: 0.8721 (tttt) cc_final: 0.8274 (ttmt) REVERT: B 127 LYS cc_start: 0.9045 (mttp) cc_final: 0.8681 (mtpt) REVERT: B 186 ASP cc_start: 0.8396 (m-30) cc_final: 0.8117 (m-30) REVERT: B 301 LYS cc_start: 0.9147 (mtpp) cc_final: 0.8773 (mtpp) REVERT: R 167 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6705 (pp) outliers start: 23 outliers final: 16 residues processed: 154 average time/residue: 0.1091 time to fit residues: 22.8011 Evaluate side-chains 150 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 A residue 297 GLU Chi-restraints excluded: chain A residue 305 CYS 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 211 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain R residue 52 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 72 optimal weight: 0.0040 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.145415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.112749 restraints weight = 11321.013| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.35 r_work: 0.3090 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2190 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= 0.098 Angle : 0.492 7.869 11768 Z= 0.257 Chirality : 0.041 0.139 1373 Planarity : 0.004 0.059 1474 Dihedral : 4.642 46.151 1267 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.06 % Allowed : 16.76 % Favored : 80.18 % 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 aren not related in a simple way. whole: -0.79 (0.25), residues: 1101 helix: 1.26 (0.29), residues: 371 sheet: -1.35 (0.27), residues: 296 loop : -1.41 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.011 0.001 TYR D 178 PHE 0.019 0.001 PHE R 57 TRP 0.015 0.001 TRP R 82 HIS 0.001 0.000 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 8659) covalent geometry : angle 0.49217 (11760) SS BOND : bond 0.00285 ( 4) SS BOND : angle 0.47613 ( 8) hydrogen bonds : bond 0.02762 ( 406) hydrogen bonds : angle 3.86887 ( 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 178 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.352 Fit side-chains REVERT: A 24 ARG cc_start: 0.8401 (ttp-110) cc_final: 0.7998 (mtm110) REVERT: A 247 MET cc_start: 0.8654 (mtp) cc_final: 0.8433 (mtm) REVERT: A 251 ASP cc_start: 0.8239 (t70) cc_final: 0.7897 (t0) REVERT: A 304 GLN cc_start: 0.8755 (tt0) cc_final: 0.8482 (tt0) REVERT: A 313 ARG cc_start: 0.8415 (mpt-90) cc_final: 0.8057 (ptp-170) REVERT: A 333 GLN cc_start: 0.8683 (tp-100) cc_final: 0.8266 (tp-100) REVERT: A 345 LYS cc_start: 0.8785 (tttt) cc_final: 0.8386 (ttmt) REVERT: B 105 TYR cc_start: 0.9185 (OUTLIER) cc_final: 0.8901 (t80) REVERT: B 127 LYS cc_start: 0.9031 (mttp) cc_final: 0.8679 (mtpt) REVERT: B 186 ASP cc_start: 0.8392 (m-30) cc_final: 0.8173 (m-30) REVERT: B 220 GLN cc_start: 0.8400 (mt0) cc_final: 0.8131 (mt0) REVERT: B 301 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8786 (mttp) REVERT: R 167 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6745 (pp) outliers start: 27 outliers final: 19 residues processed: 167 average time/residue: 0.1072 time to fit residues: 24.1656 Evaluate side-chains 163 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 A residue 297 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 37 ILE 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 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: 3.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.109339 restraints weight = 11250.148| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.34 r_work: 0.3031 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8663 Z= 0.167 Angle : 0.546 5.956 11768 Z= 0.286 Chirality : 0.043 0.146 1373 Planarity : 0.004 0.058 1474 Dihedral : 4.852 47.575 1267 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.28 % Allowed : 17.21 % Favored : 79.50 % 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 aren not related in a simple way. whole: -0.78 (0.25), residues: 1101 helix: 1.27 (0.29), residues: 370 sheet: -1.37 (0.27), residues: 292 loop : -1.38 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.016 0.002 TYR D 223 PHE 0.019 0.002 PHE R 57 TRP 0.019 0.001 TRP R 82 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8659) covalent geometry : angle 0.54611 (11760) SS BOND : bond 0.00300 ( 4) SS BOND : angle 0.61903 ( 8) hydrogen bonds : bond 0.03280 ( 406) hydrogen bonds : angle 4.02768 ( 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 168 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.335 Fit side-chains REVERT: A 24 ARG cc_start: 0.8403 (ttp-110) cc_final: 0.7945 (mtm110) REVERT: A 247 MET cc_start: 0.8624 (mtp) cc_final: 0.8375 (mtm) REVERT: A 251 ASP cc_start: 0.8298 (t70) cc_final: 0.8003 (t0) REVERT: A 304 GLN cc_start: 0.8779 (tt0) cc_final: 0.8556 (tt0) REVERT: A 313 ARG cc_start: 0.8442 (mpt-90) cc_final: 0.7911 (ptp-170) REVERT: B 105 TYR cc_start: 0.9304 (OUTLIER) cc_final: 0.8995 (t80) REVERT: B 127 LYS cc_start: 0.9119 (mttp) cc_final: 0.8723 (mtpt) REVERT: B 186 ASP cc_start: 0.8506 (m-30) cc_final: 0.8213 (m-30) REVERT: B 301 LYS cc_start: 0.9155 (mtpp) cc_final: 0.8648 (mtpp) REVERT: R 103 MET cc_start: 0.8030 (ptp) cc_final: 0.7824 (ptm) REVERT: R 167 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6676 (pp) outliers start: 29 outliers final: 18 residues processed: 158 average time/residue: 0.1196 time to fit residues: 25.1662 Evaluate side-chains 155 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 A residue 305 CYS 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 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 130 THR 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: 3.9990 chunk 74 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 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 = 0.3705 r_free = 0.3705 target = 0.143842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107955 restraints weight = 11399.118| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.22 r_work: 0.3094 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8663 Z= 0.125 Angle : 0.514 6.123 11768 Z= 0.270 Chirality : 0.042 0.143 1373 Planarity : 0.003 0.058 1474 Dihedral : 4.691 46.810 1267 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.72 % Allowed : 18.46 % Favored : 78.82 % 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 aren not related in a simple way. whole: -0.61 (0.25), residues: 1101 helix: 1.42 (0.29), residues: 372 sheet: -1.28 (0.28), residues: 291 loop : -1.32 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.014 0.001 TYR D 223 PHE 0.021 0.001 PHE R 57 TRP 0.019 0.001 TRP R 82 HIS 0.002 0.001 HIS R 136 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8659) covalent geometry : angle 0.51348 (11760) SS BOND : bond 0.00291 ( 4) SS BOND : angle 0.56157 ( 8) hydrogen bonds : bond 0.03075 ( 406) hydrogen bonds : angle 3.95431 ( 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 161 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.359 Fit side-chains REVERT: A 24 ARG cc_start: 0.8349 (ttp-110) cc_final: 0.7906 (mtm110) REVERT: A 247 MET cc_start: 0.8613 (mtp) cc_final: 0.8381 (mtm) REVERT: A 251 ASP cc_start: 0.8231 (t70) cc_final: 0.7934 (t0) REVERT: A 304 GLN cc_start: 0.8744 (tt0) cc_final: 0.8496 (tt0) REVERT: A 313 ARG cc_start: 0.8415 (mpt-90) cc_final: 0.7904 (ptp-170) REVERT: A 345 LYS cc_start: 0.8718 (tttt) cc_final: 0.8289 (ttmt) REVERT: B 105 TYR cc_start: 0.9265 (OUTLIER) cc_final: 0.9004 (t80) REVERT: B 127 LYS cc_start: 0.9041 (mttp) cc_final: 0.8668 (mtpt) REVERT: B 186 ASP cc_start: 0.8394 (m-30) cc_final: 0.8081 (m-30) REVERT: B 262 MET cc_start: 0.8727 (tpp) cc_final: 0.8525 (tpp) REVERT: B 301 LYS cc_start: 0.9090 (mtpp) cc_final: 0.8603 (mtpp) REVERT: B 338 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8922 (mm) REVERT: R 167 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6624 (pp) outliers start: 24 outliers final: 17 residues processed: 154 average time/residue: 0.1086 time to fit residues: 22.3295 Evaluate side-chains 153 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 A residue 297 GLU Chi-restraints excluded: chain A residue 305 CYS 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 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 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.1986 > 50: distance: 54 - 128: 6.045 distance: 57 - 125: 5.413 distance: 70 - 73: 4.421 distance: 73 - 74: 14.107 distance: 73 - 79: 15.099 distance: 74 - 77: 13.709 distance: 75 - 76: 28.601 distance: 75 - 80: 22.020 distance: 77 - 78: 11.455 distance: 78 - 79: 8.511 distance: 80 - 81: 3.874 distance: 81 - 82: 21.873 distance: 81 - 84: 14.301 distance: 82 - 83: 16.261 distance: 82 - 88: 12.783 distance: 84 - 85: 17.174 distance: 85 - 86: 5.113 distance: 85 - 87: 8.619 distance: 88 - 89: 12.452 distance: 89 - 90: 8.897 distance: 89 - 92: 14.207 distance: 90 - 91: 8.882 distance: 90 - 95: 6.310 distance: 92 - 93: 7.087 distance: 92 - 94: 5.772 distance: 95 - 96: 3.164 distance: 96 - 97: 3.196 distance: 96 - 99: 6.716 distance: 97 - 98: 16.872 distance: 97 - 106: 9.530 distance: 99 - 100: 10.998 distance: 100 - 101: 9.826 distance: 101 - 102: 3.960 distance: 102 - 103: 12.410 distance: 103 - 104: 11.811 distance: 103 - 105: 11.538 distance: 106 - 107: 5.757 distance: 107 - 108: 7.227 distance: 107 - 110: 3.957 distance: 108 - 114: 4.786 distance: 110 - 111: 5.250 distance: 111 - 112: 3.478 distance: 111 - 113: 10.494 distance: 114 - 115: 4.792 distance: 115 - 116: 5.890 distance: 115 - 118: 7.948 distance: 116 - 117: 5.573 distance: 116 - 125: 5.812 distance: 118 - 119: 9.833 distance: 119 - 120: 9.012 distance: 119 - 121: 5.479 distance: 120 - 122: 9.778 distance: 121 - 123: 5.031 distance: 122 - 124: 7.100 distance: 123 - 124: 9.975 distance: 127 - 128: 7.661 distance: 127 - 132: 5.498 distance: 129 - 130: 15.305 distance: 129 - 131: 8.787 distance: 132 - 133: 3.831 distance: 132 - 173: 11.499 distance: 133 - 134: 5.793 distance: 133 - 136: 9.441 distance: 134 - 135: 9.469 distance: 134 - 138: 6.348 distance: 135 - 170: 5.037 distance: 136 - 137: 12.286 distance: 138 - 139: 6.569 distance: 139 - 140: 4.424 distance: 140 - 141: 7.415 distance: 140 - 142: 6.595 distance: 142 - 143: 6.594 distance: 143 - 144: 4.901 distance: 143 - 146: 6.644 distance: 144 - 145: 5.148