Starting phenix.real_space_refine on Thu Mar 13 09:49:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xk2_33241/03_2025/7xk2_33241.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk2_33241/03_2025/7xk2_33241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xk2_33241/03_2025/7xk2_33241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk2_33241/03_2025/7xk2_33241.map" model { file = "/net/cci-nas-00/data/ceres_data/7xk2_33241/03_2025/7xk2_33241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk2_33241/03_2025/7xk2_33241.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.085 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 5594 2.51 5 N 1509 2.21 5 O 1622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8791 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1798 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2596 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2229 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 274} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "S" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1711 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 429 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'FI7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.35, per 1000 atoms: 0.61 Number of scatterers: 8791 At special positions: 0 Unit cell: (87.36, 116.48, 132.08, 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 1622 8.00 N 1509 7.00 C 5594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 34.9% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.608A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.650A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.747A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 273 through 281 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.715A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'R' and resid 25 through 53 Proline residue: R 31 - end of helix removed outlier: 3.966A pdb=" N LEU R 43 " --> pdb=" O ILE R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 80 removed outlier: 3.894A pdb=" N PHE R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 86 Processing helix chain 'R' and resid 97 through 130 removed outlier: 3.996A pdb=" N ARG R 101 " --> pdb=" O ASP R 97 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU R 104 " --> pdb=" O CYS R 100 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE R 105 " --> pdb=" O ARG R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 158 removed outlier: 3.650A pdb=" N LEU R 158 " --> pdb=" O ILE R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 165 removed outlier: 3.935A pdb=" N LYS R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS R 165 " --> pdb=" O HIS R 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 160 through 165' Processing helix chain 'R' and resid 188 through 218 removed outlier: 3.560A pdb=" N MET R 192 " --> pdb=" O TRP R 188 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 3.589A pdb=" N LEU R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA R 209 " --> pdb=" O LEU R 205 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG R 210 " --> pdb=" O PHE R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 261 removed outlier: 3.843A pdb=" N ILE R 233 " --> pdb=" O ALA R 229 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 271 through 290 Processing helix chain 'R' and resid 291 through 294 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.614A pdb=" N ASP S 223 " --> pdb=" O GLU S 220 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 220 through 224' Processing helix chain 'C' and resid 8 through 24 removed outlier: 4.198A pdb=" N ALA C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) removed outlier: 3.844A 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 'C' and resid 45 through 48 removed outlier: 3.814A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 187 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 187 removed outlier: 7.133A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.266A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.749A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.007A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.954A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.630A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.836A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.620A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 6 through 7 removed outlier: 3.728A pdb=" N SER S 7 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 Processing sheet with id=AB3, first strand: chain 'S' and resid 38 through 39 Processing sheet with id=AB4, first strand: chain 'S' and resid 92 through 93 Processing sheet with id=AB5, first strand: chain 'S' and resid 156 through 159 removed outlier: 3.748A pdb=" N THR S 215 " --> pdb=" O SER S 204 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER S 204 " --> pdb=" O THR S 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 186 through 189 removed outlier: 6.623A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2528 1.34 - 1.46: 1693 1.46 - 1.57: 4662 1.57 - 1.69: 2 1.69 - 1.81: 96 Bond restraints: 8981 Sorted by residual: bond pdb=" C02 FI7 R 401 " pdb=" C17 FI7 R 401 " ideal model delta sigma weight residual 1.545 1.627 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C17 FI7 R 401 " pdb=" N19 FI7 R 401 " ideal model delta sigma weight residual 1.348 1.414 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C07 FI7 R 401 " pdb=" N15 FI7 R 401 " ideal model delta sigma weight residual 1.300 1.365 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C02 FI7 R 401 " pdb=" C04 FI7 R 401 " ideal model delta sigma weight residual 1.546 1.606 -0.060 2.00e-02 2.50e+03 9.14e+00 bond pdb=" C05 FI7 R 401 " pdb=" O16 FI7 R 401 " ideal model delta sigma weight residual 1.330 1.390 -0.060 2.00e-02 2.50e+03 8.96e+00 ... (remaining 8976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 11871 2.76 - 5.52: 220 5.52 - 8.28: 46 8.28 - 11.04: 15 11.04 - 13.80: 9 Bond angle restraints: 12161 Sorted by residual: angle pdb=" CA GLN A 52 " pdb=" CB GLN A 52 " pdb=" CG GLN A 52 " ideal model delta sigma weight residual 114.10 124.36 -10.26 2.00e+00 2.50e-01 2.63e+01 angle pdb=" C ALA R 174 " pdb=" N ASN R 175 " pdb=" CA ASN R 175 " ideal model delta sigma weight residual 122.46 129.13 -6.67 1.41e+00 5.03e-01 2.23e+01 angle pdb=" CA LYS C 20 " pdb=" CB LYS C 20 " pdb=" CG LYS C 20 " ideal model delta sigma weight residual 114.10 123.43 -9.33 2.00e+00 2.50e-01 2.18e+01 angle pdb=" C THR R 283 " pdb=" N TYR R 284 " pdb=" CA TYR R 284 " ideal model delta sigma weight residual 121.58 112.72 8.86 1.95e+00 2.63e-01 2.07e+01 angle pdb=" CA TYR R 284 " pdb=" CB TYR R 284 " pdb=" CG TYR R 284 " ideal model delta sigma weight residual 113.90 121.60 -7.70 1.80e+00 3.09e-01 1.83e+01 ... (remaining 12156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4590 17.63 - 35.25: 579 35.25 - 52.88: 133 52.88 - 70.51: 20 70.51 - 88.14: 7 Dihedral angle restraints: 5329 sinusoidal: 2063 harmonic: 3266 Sorted by residual: dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual 93.00 160.11 -67.11 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CB CYS R 18 " pdb=" SG CYS R 18 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual -86.00 -35.39 -50.61 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CA TYR S 94 " pdb=" C TYR S 94 " pdb=" N TYR S 95 " pdb=" CA TYR S 95 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 5326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1255 0.100 - 0.199: 99 0.199 - 0.298: 8 0.298 - 0.398: 1 0.398 - 0.497: 1 Chirality restraints: 1364 Sorted by residual: chirality pdb=" CB ILE R 238 " pdb=" CA ILE R 238 " pdb=" CG1 ILE R 238 " pdb=" CG2 ILE R 238 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CG LEU R 80 " pdb=" CB LEU R 80 " pdb=" CD1 LEU R 80 " pdb=" CD2 LEU R 80 " both_signs ideal model delta sigma weight residual False -2.59 -2.91 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA TYR R 284 " pdb=" N TYR R 284 " pdb=" C TYR R 284 " pdb=" CB TYR R 284 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1361 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 265 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C ILE A 265 " -0.049 2.00e-02 2.50e+03 pdb=" O ILE A 265 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 266 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 134 " 0.191 9.50e-02 1.11e+02 8.64e-02 5.90e+00 pdb=" NE ARG B 134 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 134 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 134 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 134 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 197 " -0.181 9.50e-02 1.11e+02 8.18e-02 5.17e+00 pdb=" NE ARG B 197 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 197 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 197 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 197 " -0.001 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1903 2.78 - 3.31: 7739 3.31 - 3.84: 14840 3.84 - 4.37: 17084 4.37 - 4.90: 29646 Nonbonded interactions: 71212 Sorted by model distance: nonbonded pdb=" O ILE R 278 " pdb=" OG SER R 281 " model vdw 2.251 3.040 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.291 3.040 nonbonded pdb=" OE1 GLN S 142 " pdb=" OG1 THR S 243 " model vdw 2.297 3.040 nonbonded pdb=" OG SER S 206 " pdb=" O THR S 213 " model vdw 2.313 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.329 3.040 ... (remaining 71207 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: 1.530 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.010 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 8981 Z= 0.328 Angle : 1.022 13.801 12161 Z= 0.515 Chirality : 0.056 0.497 1364 Planarity : 0.007 0.086 1542 Dihedral : 16.480 88.136 3210 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.32 % Allowed : 22.03 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.23), residues: 1114 helix: -1.04 (0.25), residues: 355 sheet: -1.11 (0.30), residues: 265 loop : -2.24 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS R 223 PHE 0.036 0.002 PHE A 334 TYR 0.035 0.002 TYR S 235 ARG 0.021 0.001 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: B 301 LYS cc_start: 0.7031 (ptmm) cc_final: 0.6631 (pttt) REVERT: S 80 PHE cc_start: 0.8645 (m-80) cc_final: 0.8348 (m-80) REVERT: C 18 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7645 (tp-100) outliers start: 3 outliers final: 2 residues processed: 172 average time/residue: 0.2390 time to fit residues: 55.0743 Evaluate side-chains 169 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 280 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN R 110 ASN S 142 GLN C 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.189529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126190 restraints weight = 10198.660| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.60 r_work: 0.3182 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8981 Z= 0.195 Angle : 0.626 8.426 12161 Z= 0.324 Chirality : 0.042 0.209 1364 Planarity : 0.005 0.046 1542 Dihedral : 5.662 43.535 1247 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.25 % Allowed : 21.93 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.24), residues: 1114 helix: 0.29 (0.27), residues: 359 sheet: -1.15 (0.30), residues: 274 loop : -2.04 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.005 0.001 HIS A 188 PHE 0.016 0.001 PHE A 196 TYR 0.028 0.001 TYR S 235 ARG 0.008 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 336 PHE cc_start: 0.8524 (t80) cc_final: 0.8314 (t80) REVERT: B 45 MET cc_start: 0.8380 (mtt) cc_final: 0.8149 (mtt) REVERT: B 214 ARG cc_start: 0.8319 (mpp80) cc_final: 0.7973 (mmt90) REVERT: B 301 LYS cc_start: 0.7138 (ptmm) cc_final: 0.6728 (pttt) REVERT: R 282 PHE cc_start: 0.8525 (m-80) cc_final: 0.8316 (m-80) REVERT: R 284 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6938 (p90) REVERT: S 43 LYS cc_start: 0.8232 (mppt) cc_final: 0.7939 (mmtm) REVERT: S 180 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.8228 (mtt-85) REVERT: C 18 GLN cc_start: 0.7870 (tp40) cc_final: 0.7633 (tp-100) outliers start: 21 outliers final: 13 residues processed: 188 average time/residue: 0.2272 time to fit residues: 57.6294 Evaluate side-chains 178 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.1163 > 50: distance: 74 - 131: 32.224 distance: 100 - 107: 30.778 distance: 107 - 108: 57.212 distance: 108 - 109: 57.706 distance: 108 - 111: 39.525 distance: 109 - 110: 60.536 distance: 113 - 114: 56.734 distance: 113 - 116: 11.951 distance: 114 - 115: 39.818 distance: 114 - 120: 56.033 distance: 116 - 117: 42.211 distance: 117 - 118: 56.141 distance: 117 - 119: 40.484 distance: 121 - 122: 40.418 distance: 121 - 124: 56.757 distance: 122 - 123: 69.252 distance: 122 - 131: 56.286 distance: 124 - 125: 69.598 distance: 125 - 126: 39.861 distance: 128 - 130: 57.125 distance: 131 - 132: 13.321 distance: 132 - 133: 57.555 distance: 132 - 135: 28.141 distance: 133 - 134: 41.049 distance: 133 - 136: 64.097 distance: 136 - 137: 32.011 distance: 137 - 138: 28.735 distance: 138 - 139: 11.511 distance: 138 - 140: 12.001 distance: 141 - 142: 40.235 distance: 141 - 144: 39.524 distance: 142 - 147: 67.813 distance: 144 - 146: 8.066 distance: 147 - 148: 37.040 distance: 148 - 149: 57.728 distance: 148 - 151: 40.569 distance: 149 - 155: 56.295 distance: 152 - 154: 40.153 distance: 155 - 156: 40.278 distance: 156 - 159: 40.479 distance: 157 - 158: 40.425 distance: 160 - 161: 56.529 distance: 161 - 162: 16.924 distance: 162 - 163: 46.486 distance: 162 - 164: 22.328 distance: 164 - 165: 40.535 distance: 165 - 166: 40.925 distance: 166 - 174: 34.220 distance: 168 - 169: 49.321 distance: 169 - 170: 51.109 distance: 169 - 171: 40.275 distance: 171 - 173: 56.501 distance: 172 - 173: 41.089