Starting phenix.real_space_refine on Thu Jul 2 06:06:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/20zd_67427/07_2026/20zd_67427.cif Found real_map, /net/cci-nas-00/data/ceres_data/20zd_67427/07_2026/20zd_67427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/20zd_67427/07_2026/20zd_67427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/20zd_67427/07_2026/20zd_67427.map" model { file = "/net/cci-nas-00/data/ceres_data/20zd_67427/07_2026/20zd_67427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/20zd_67427/07_2026/20zd_67427.cif" } resolution = 2.8 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= -0.001 sd= 0.025 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 49 5.16 5 C 4386 2.51 5 N 1171 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6878 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2585 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 410 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2072 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 258} Chain breaks: 4 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 1.31, per 1000 atoms: 0.19 Number of scatterers: 6878 At special positions: 0 Unit cell: (93.275, 94.71, 130.585, 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 49 16.00 O 1272 8.00 N 1171 7.00 C 4386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.39 Conformation dependent library (CDL) restraints added in 269.3 milliseconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 49.7% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.613A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.174A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.653A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.851A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.092A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.139A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.526A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 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 removed outlier: 3.631A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'R' and resid 62 through 91 removed outlier: 3.633A pdb=" N LYS R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 118 Processing helix chain 'R' and resid 119 through 128 Processing helix chain 'R' and resid 140 through 172 Processing helix chain 'R' and resid 172 through 178 removed outlier: 3.508A pdb=" N ALA R 176 " --> pdb=" O HIS R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 201 removed outlier: 4.131A pdb=" N ARG R 184 " --> pdb=" O MET R 180 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE R 189 " --> pdb=" O THR R 185 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER R 190 " --> pdb=" O LYS R 186 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE R 192 " --> pdb=" O PHE R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 273 Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 293 through 329 removed outlier: 4.296A pdb=" N VAL R 313 " --> pdb=" O VAL R 309 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 368 removed outlier: 3.690A pdb=" N SER R 356 " --> pdb=" O LEU R 352 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR R 358 " --> pdb=" O TYR R 354 " (cutoff:3.500A) Proline residue: R 361 - end of helix removed outlier: 4.034A pdb=" N ASN R 365 " --> pdb=" O PRO R 361 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU R 366 " --> pdb=" O ILE R 362 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL R 367 " --> pdb=" O LEU R 363 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER R 368 " --> pdb=" O TYR R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 383 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.773A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.608A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.796A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.161A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.667A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.635A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.271A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.556A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 1155 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: 1.06 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1130 1.31 - 1.44: 1890 1.44 - 1.57: 3911 1.57 - 1.70: 9 1.70 - 1.83: 70 Bond restraints: 7010 Sorted by residual: bond pdb=" CG PHE R 174 " pdb=" CD2 PHE R 174 " ideal model delta sigma weight residual 1.384 1.583 -0.199 2.10e-02 2.27e+03 9.01e+01 bond pdb=" CG PHE R 174 " pdb=" CD1 PHE R 174 " ideal model delta sigma weight residual 1.384 1.188 0.196 2.10e-02 2.27e+03 8.74e+01 bond pdb=" CG LEU A 234 " pdb=" CD1 LEU A 234 " ideal model delta sigma weight residual 1.521 1.262 0.259 3.30e-02 9.18e+02 6.16e+01 bond pdb=" C SER R 244 " pdb=" O SER R 244 " ideal model delta sigma weight residual 1.236 1.185 0.052 1.15e-02 7.56e+03 2.03e+01 bond pdb=" CA SER R 181 " pdb=" CB SER R 181 " ideal model delta sigma weight residual 1.529 1.461 0.068 1.55e-02 4.16e+03 1.93e+01 ... (remaining 7005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 8768 3.75 - 7.50: 670 7.50 - 11.25: 57 11.25 - 15.00: 5 15.00 - 18.75: 2 Bond angle restraints: 9502 Sorted by residual: angle pdb=" CA PHE A 354 " pdb=" CB PHE A 354 " pdb=" CG PHE A 354 " ideal model delta sigma weight residual 113.80 123.58 -9.78 1.00e+00 1.00e+00 9.57e+01 angle pdb=" NE ARG R 322 " pdb=" CZ ARG R 322 " pdb=" NH2 ARG R 322 " ideal model delta sigma weight residual 119.20 110.96 8.24 9.00e-01 1.23e+00 8.38e+01 angle pdb=" CA PHE B 151 " pdb=" CB PHE B 151 " pdb=" CG PHE B 151 " ideal model delta sigma weight residual 113.80 122.85 -9.05 1.00e+00 1.00e+00 8.20e+01 angle pdb=" CG ARG B 49 " pdb=" CD ARG B 49 " pdb=" NE ARG B 49 " ideal model delta sigma weight residual 112.00 130.75 -18.75 2.20e+00 2.07e-01 7.26e+01 angle pdb=" CG ARG C 27 " pdb=" CD ARG C 27 " pdb=" NE ARG C 27 " ideal model delta sigma weight residual 112.00 129.26 -17.26 2.20e+00 2.07e-01 6.16e+01 ... (remaining 9497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 3722 17.11 - 34.22: 314 34.22 - 51.33: 103 51.33 - 68.44: 19 68.44 - 85.55: 8 Dihedral angle restraints: 4166 sinusoidal: 1581 harmonic: 2585 Sorted by residual: dihedral pdb=" C ASN B 119 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " ideal model delta harmonic sigma weight residual -122.60 -140.05 17.45 0 2.50e+00 1.60e-01 4.87e+01 dihedral pdb=" C ASN R 360 " pdb=" N ASN R 360 " pdb=" CA ASN R 360 " pdb=" CB ASN R 360 " ideal model delta harmonic sigma weight residual -122.60 -138.56 15.96 0 2.50e+00 1.60e-01 4.07e+01 dihedral pdb=" CD ARG R 322 " pdb=" NE ARG R 322 " pdb=" CZ ARG R 322 " pdb=" NH1 ARG R 322 " ideal model delta sinusoidal sigma weight residual 0.00 54.74 -54.74 1 1.00e+01 1.00e-02 4.06e+01 ... (remaining 4163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 823 0.130 - 0.260: 251 0.260 - 0.389: 29 0.389 - 0.519: 5 0.519 - 0.649: 3 Chirality restraints: 1111 Sorted by residual: chirality pdb=" CG LEU A 234 " pdb=" CB LEU A 234 " pdb=" CD1 LEU A 234 " pdb=" CD2 LEU A 234 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.45e+00 chirality pdb=" CA ASN R 360 " pdb=" N ASN R 360 " pdb=" C ASN R 360 " pdb=" CB ASN R 360 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.36e+00 ... (remaining 1108 not shown) Planarity restraints: 1191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 322 " -0.671 9.50e-02 1.11e+02 3.03e-01 7.55e+01 pdb=" NE ARG R 322 " 0.069 2.00e-02 2.50e+03 pdb=" CZ ARG R 322 " -0.069 2.00e-02 2.50e+03 pdb=" NH1 ARG R 322 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG R 322 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 299 " 0.522 9.50e-02 1.11e+02 2.41e-01 7.25e+01 pdb=" NE ARG R 299 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARG R 299 " -0.114 2.00e-02 2.50e+03 pdb=" NH1 ARG R 299 " 0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG R 299 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 49 " 0.320 9.50e-02 1.11e+02 1.49e-01 3.15e+01 pdb=" NE ARG B 49 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG B 49 " 0.071 2.00e-02 2.50e+03 pdb=" NH1 ARG B 49 " -0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG B 49 " -0.012 2.00e-02 2.50e+03 ... (remaining 1188 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 18 2.50 - 3.10: 4548 3.10 - 3.70: 10338 3.70 - 4.30: 14365 4.30 - 4.90: 23828 Nonbonded interactions: 53097 Sorted by model distance: nonbonded pdb=" OG SER A 6 " pdb=" OD1 ASP A 9 " model vdw 1.905 3.040 nonbonded pdb=" O SER R 244 " pdb=" CG PRO R 248 " model vdw 2.134 3.440 nonbonded pdb=" O SER R 357 " pdb=" CD PRO R 361 " model vdw 2.158 3.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR A 182 " pdb=" ND2 ASN B 119 " model vdw 2.309 3.120 ... (remaining 53092 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: 0.360 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.420 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:5.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 : 0.013 0.259 7010 Z= 0.809 Angle : 2.181 18.745 9502 Z= 1.478 Chirality : 0.123 0.649 1111 Planarity : 0.019 0.303 1191 Dihedral : 15.358 85.555 2486 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.46 % Allowed : 8.92 % Favored : 86.62 % Cbeta Deviations : 2.50 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.26), residues: 862 helix: 0.76 (0.25), residues: 397 sheet: 0.84 (0.49), residues: 104 loop : -1.55 (0.27), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.108 0.011 ARG R 299 TYR 0.047 0.008 TYR B 59 PHE 0.061 0.008 PHE R 174 TRP 0.045 0.010 TRP B 169 HIS 0.028 0.006 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.01333 / 0.81 ( 7010) covalent geometry : angle 2.18082 / 1.48 ( 9502) hydrogen bonds : bond 0.22491 / 14.73 ( 395) hydrogen bonds : angle 7.23868 / 5.13 ( 1155) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: A 193 ASP cc_start: 0.9688 (m-30) cc_final: 0.9305 (p0) REVERT: A 195 HIS cc_start: 0.7952 (m90) cc_final: 0.7513 (m90) REVERT: A 280 LYS cc_start: 0.9311 (mppt) cc_final: 0.8843 (mppt) REVERT: A 330 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8897 (tptt) REVERT: B 9 GLN cc_start: 0.9526 (tp40) cc_final: 0.9180 (tm-30) REVERT: B 14 LEU cc_start: 0.9300 (mt) cc_final: 0.8957 (mt) REVERT: B 15 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8415 (tptt) REVERT: B 118 ASP cc_start: 0.8536 (t0) cc_final: 0.8280 (p0) REVERT: B 142 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.7938 (m-70) REVERT: C 22 GLU cc_start: 0.9247 (tt0) cc_final: 0.8753 (tp30) REVERT: C 28 ILE cc_start: 0.8694 (tt) cc_final: 0.8224 (tt) REVERT: R 120 MET cc_start: 0.7755 (mmm) cc_final: 0.7076 (tpt) REVERT: R 194 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7695 (mm) REVERT: R 234 LYS cc_start: 0.6653 (tttt) cc_final: 0.6296 (ttmm) outliers start: 33 outliers final: 8 residues processed: 260 average time/residue: 0.5096 time to fit residues: 138.6605 Evaluate side-chains 147 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 321 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 256 ASN A 346 ASN B 44 GLN B 75 GLN B 88 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS R 256 ASN ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.125933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.081248 restraints weight = 14377.932| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.07 r_work: 0.3050 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7010 Z= 0.191 Angle : 0.816 13.607 9502 Z= 0.423 Chirality : 0.048 0.217 1111 Planarity : 0.005 0.041 1191 Dihedral : 7.169 72.208 969 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.59 % Allowed : 21.62 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.27), residues: 862 helix: 1.94 (0.24), residues: 407 sheet: 0.89 (0.41), residues: 142 loop : -1.75 (0.29), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 322 TYR 0.022 0.002 TYR R 339 PHE 0.018 0.002 PHE B 292 TRP 0.022 0.002 TRP B 82 HIS 0.006 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 ( 7010) covalent geometry : angle 0.81613 / 0.42 ( 9502) hydrogen bonds : bond 0.06484 / 4.21 ( 395) hydrogen bonds : angle 5.01864 / 3.52 ( 1155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: A 195 HIS cc_start: 0.7530 (m90) cc_final: 0.7178 (m90) REVERT: A 198 MET cc_start: 0.8496 (ttm) cc_final: 0.8097 (ttm) REVERT: A 229 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7057 (t0) REVERT: A 243 MET cc_start: 0.8197 (ttm) cc_final: 0.7972 (mtp) REVERT: A 302 TYR cc_start: 0.9277 (t80) cc_final: 0.9054 (t80) REVERT: B 14 LEU cc_start: 0.9015 (mt) cc_final: 0.8781 (mt) REVERT: B 22 ARG cc_start: 0.8280 (mmp80) cc_final: 0.7832 (tpm170) REVERT: B 142 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.7902 (m-70) REVERT: B 215 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8781 (mp0) REVERT: C 22 GLU cc_start: 0.9028 (tt0) cc_final: 0.8212 (tp30) REVERT: C 36 ASP cc_start: 0.8605 (m-30) cc_final: 0.8122 (t0) REVERT: C 58 GLU cc_start: 0.8678 (mp0) cc_final: 0.8379 (pm20) REVERT: R 112 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8037 (p0) REVERT: R 322 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7712 (ttp80) REVERT: R 348 VAL cc_start: 0.8869 (t) cc_final: 0.8668 (p) outliers start: 34 outliers final: 6 residues processed: 170 average time/residue: 0.4903 time to fit residues: 87.3227 Evaluate side-chains 124 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 357 SER Chi-restraints excluded: chain R residue 360 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 2 optimal weight: 0.0060 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 30 optimal weight: 0.0370 chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 overall best weight: 0.4674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN B 225 HIS ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.128734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.081618 restraints weight = 13940.606| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.16 r_work: 0.3117 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7010 Z= 0.141 Angle : 0.738 15.174 9502 Z= 0.367 Chirality : 0.044 0.218 1111 Planarity : 0.004 0.035 1191 Dihedral : 6.144 87.220 953 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.19 % Allowed : 22.57 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.27), residues: 862 helix: 2.05 (0.25), residues: 409 sheet: 1.06 (0.42), residues: 147 loop : -1.79 (0.29), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 21 TYR 0.017 0.001 TYR R 70 PHE 0.014 0.001 PHE R 353 TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 7010) covalent geometry : angle 0.73756 / 0.37 ( 9502) hydrogen bonds : bond 0.05057 / 3.27 ( 395) hydrogen bonds : angle 4.61077 / 3.23 ( 1155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: A 195 HIS cc_start: 0.7679 (m90) cc_final: 0.7185 (m90) REVERT: A 198 MET cc_start: 0.8531 (ttm) cc_final: 0.8166 (ttm) REVERT: A 229 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7186 (t0) REVERT: B 22 ARG cc_start: 0.8401 (mmp80) cc_final: 0.7913 (tpm170) REVERT: B 142 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.8107 (m-70) REVERT: C 17 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8593 (mm-30) REVERT: C 22 GLU cc_start: 0.9029 (tt0) cc_final: 0.8217 (tp30) REVERT: C 28 ILE cc_start: 0.8410 (tp) cc_final: 0.8109 (tp) REVERT: C 36 ASP cc_start: 0.8660 (m-30) cc_final: 0.8221 (t0) REVERT: R 127 PHE cc_start: 0.7946 (m-80) cc_final: 0.7123 (m-10) REVERT: R 165 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8366 (tm-30) REVERT: R 322 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7640 (ttp80) REVERT: R 350 ASN cc_start: 0.8980 (m-40) cc_final: 0.8743 (m-40) REVERT: L 12 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6938 (pp) outliers start: 31 outliers final: 7 residues processed: 153 average time/residue: 0.4722 time to fit residues: 75.9857 Evaluate side-chains 127 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain R residue 247 PHE Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 360 ASN Chi-restraints excluded: chain L residue 12 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 80 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS A 204 GLN A 244 HIS B 225 HIS R 126 ASN R 296 GLN ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.126046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.077912 restraints weight = 14262.482| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.20 r_work: 0.3044 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7010 Z= 0.148 Angle : 0.740 13.106 9502 Z= 0.370 Chirality : 0.044 0.215 1111 Planarity : 0.004 0.045 1191 Dihedral : 6.150 88.564 952 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.19 % Allowed : 24.05 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.28), residues: 862 helix: 1.94 (0.25), residues: 410 sheet: 1.39 (0.43), residues: 147 loop : -1.74 (0.31), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 313 TYR 0.019 0.001 TYR A 290 PHE 0.017 0.002 PHE R 74 TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 7010) covalent geometry : angle 0.73953 / 0.37 ( 9502) hydrogen bonds : bond 0.05112 / 3.33 ( 395) hydrogen bonds : angle 4.54783 / 3.17 ( 1155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: A 198 MET cc_start: 0.8563 (ttm) cc_final: 0.8157 (ttm) REVERT: A 229 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7040 (t70) REVERT: B 68 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8758 (tpt-90) REVERT: B 142 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.8153 (m-70) REVERT: C 20 LYS cc_start: 0.9150 (pttm) cc_final: 0.8904 (pttm) REVERT: C 22 GLU cc_start: 0.9020 (tt0) cc_final: 0.8469 (tm-30) REVERT: C 24 ASN cc_start: 0.9004 (m-40) cc_final: 0.8799 (m-40) REVERT: C 36 ASP cc_start: 0.8688 (m-30) cc_final: 0.8270 (t0) REVERT: R 116 LEU cc_start: 0.9425 (tm) cc_final: 0.9174 (pp) REVERT: R 127 PHE cc_start: 0.7709 (m-10) cc_final: 0.7359 (m-80) REVERT: R 151 CYS cc_start: 0.8823 (m) cc_final: 0.8493 (p) REVERT: R 268 ARG cc_start: 0.9027 (ptp-110) cc_final: 0.8627 (ptt-90) REVERT: R 325 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6846 (mmp) REVERT: R 350 ASN cc_start: 0.8930 (m-40) cc_final: 0.8692 (m110) REVERT: R 354 TYR cc_start: 0.8481 (m-80) cc_final: 0.8244 (m-80) REVERT: L 12 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7013 (pp) outliers start: 31 outliers final: 11 residues processed: 151 average time/residue: 0.5160 time to fit residues: 81.5458 Evaluate side-chains 126 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 247 PHE Chi-restraints excluded: chain R residue 315 CYS Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 360 ASN Chi-restraints excluded: chain L residue 12 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 11 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 225 HIS R 320 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.124471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.076486 restraints weight = 14305.035| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.17 r_work: 0.3019 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7010 Z= 0.154 Angle : 0.751 12.843 9502 Z= 0.375 Chirality : 0.044 0.212 1111 Planarity : 0.004 0.044 1191 Dihedral : 6.117 84.035 952 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.86 % Allowed : 24.73 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.28), residues: 862 helix: 1.79 (0.25), residues: 410 sheet: 1.42 (0.44), residues: 145 loop : -1.71 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 42 TYR 0.032 0.001 TYR A 290 PHE 0.017 0.001 PHE R 146 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 7010) covalent geometry : angle 0.75101 / 0.38 ( 9502) hydrogen bonds : bond 0.05047 / 3.30 ( 395) hydrogen bonds : angle 4.55172 / 3.17 ( 1155) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: A 198 MET cc_start: 0.8613 (ttm) cc_final: 0.8201 (ttm) REVERT: A 229 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7149 (t70) REVERT: A 302 TYR cc_start: 0.9279 (t80) cc_final: 0.8482 (t80) REVERT: A 306 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8683 (mm110) REVERT: A 313 ARG cc_start: 0.7612 (ptp-170) cc_final: 0.7259 (ptp-170) REVERT: B 68 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8705 (tpt-90) REVERT: B 96 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8240 (ttp-110) REVERT: B 137 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7601 (tpp-160) REVERT: B 142 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.8169 (m-70) REVERT: B 172 GLU cc_start: 0.8458 (tp30) cc_final: 0.8143 (tp30) REVERT: C 13 ARG cc_start: 0.9517 (ptp-170) cc_final: 0.9277 (mpt-90) REVERT: C 22 GLU cc_start: 0.8978 (tt0) cc_final: 0.8552 (tm-30) REVERT: C 24 ASN cc_start: 0.9013 (m-40) cc_final: 0.8812 (m-40) REVERT: C 36 ASP cc_start: 0.8697 (m-30) cc_final: 0.8314 (t0) REVERT: R 151 CYS cc_start: 0.8908 (m) cc_final: 0.8555 (p) REVERT: R 196 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.8016 (t) REVERT: R 268 ARG cc_start: 0.9088 (ptp-110) cc_final: 0.8773 (ptt-90) REVERT: R 350 ASN cc_start: 0.8978 (m-40) cc_final: 0.8735 (m110) outliers start: 36 outliers final: 12 residues processed: 144 average time/residue: 0.5151 time to fit residues: 77.8172 Evaluate side-chains 123 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 247 PHE Chi-restraints excluded: chain R residue 315 CYS Chi-restraints excluded: chain R residue 339 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 39 optimal weight: 0.0970 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.125754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.077971 restraints weight = 14224.408| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.17 r_work: 0.3048 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7010 Z= 0.136 Angle : 0.762 13.935 9502 Z= 0.374 Chirality : 0.045 0.290 1111 Planarity : 0.004 0.044 1191 Dihedral : 5.890 74.844 952 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.78 % Allowed : 26.22 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.29), residues: 862 helix: 1.70 (0.26), residues: 409 sheet: 1.31 (0.44), residues: 147 loop : -1.57 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 21 TYR 0.023 0.001 TYR A 296 PHE 0.023 0.001 PHE R 127 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 7010) covalent geometry : angle 0.76204 / 0.37 ( 9502) hydrogen bonds : bond 0.04596 / 2.99 ( 395) hydrogen bonds : angle 4.52961 / 3.17 ( 1155) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: A 198 MET cc_start: 0.8501 (ttm) cc_final: 0.8048 (ttm) REVERT: A 229 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7180 (t70) REVERT: A 302 TYR cc_start: 0.9319 (t80) cc_final: 0.8906 (t80) REVERT: A 305 CYS cc_start: 0.9133 (p) cc_final: 0.8717 (p) REVERT: A 313 ARG cc_start: 0.7673 (ptp-170) cc_final: 0.7165 (ptp-170) REVERT: B 10 GLU cc_start: 0.9397 (tp30) cc_final: 0.9090 (tp30) REVERT: B 68 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8553 (tpt-90) REVERT: B 96 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8239 (ttp-110) REVERT: B 142 HIS cc_start: 0.8782 (OUTLIER) cc_final: 0.8169 (m-70) REVERT: C 22 GLU cc_start: 0.8976 (tt0) cc_final: 0.8542 (tm-30) REVERT: C 36 ASP cc_start: 0.8690 (m-30) cc_final: 0.8257 (t0) REVERT: R 116 LEU cc_start: 0.9414 (tm) cc_final: 0.9185 (pp) REVERT: R 151 CYS cc_start: 0.8912 (m) cc_final: 0.8565 (p) REVERT: R 325 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6720 (mmp) REVERT: R 345 PHE cc_start: 0.9034 (t80) cc_final: 0.8302 (t80) REVERT: R 350 ASN cc_start: 0.9053 (m-40) cc_final: 0.8605 (m110) outliers start: 28 outliers final: 13 residues processed: 135 average time/residue: 0.5173 time to fit residues: 73.1428 Evaluate side-chains 124 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 247 PHE Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 339 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 0.0050 chunk 40 optimal weight: 0.0030 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 25 optimal weight: 0.0050 overall best weight: 0.2218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 225 HIS R 126 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.128112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.080591 restraints weight = 14228.669| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.20 r_work: 0.3096 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.6542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7010 Z= 0.134 Angle : 0.759 14.637 9502 Z= 0.371 Chirality : 0.045 0.256 1111 Planarity : 0.004 0.043 1191 Dihedral : 5.617 63.041 952 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.67 % Favored : 97.22 % Rotamer: Outliers : 3.78 % Allowed : 27.43 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.29), residues: 862 helix: 1.70 (0.26), residues: 408 sheet: 1.28 (0.44), residues: 147 loop : -1.51 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 21 TYR 0.026 0.001 TYR A 290 PHE 0.023 0.001 PHE R 127 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 7010) covalent geometry : angle 0.75900 / 0.37 ( 9502) hydrogen bonds : bond 0.04150 / 2.69 ( 395) hydrogen bonds : angle 4.43909 / 3.11 ( 1155) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: A 229 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7348 (t70) REVERT: A 269 ASN cc_start: 0.8724 (m-40) cc_final: 0.8380 (m110) REVERT: A 313 ARG cc_start: 0.7613 (ptp-170) cc_final: 0.7134 (ptp-170) REVERT: B 14 LEU cc_start: 0.9133 (mt) cc_final: 0.8815 (mt) REVERT: B 17 GLN cc_start: 0.9093 (pp30) cc_final: 0.8803 (pp30) REVERT: B 96 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8145 (ttp-110) REVERT: B 142 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8255 (m-70) REVERT: C 22 GLU cc_start: 0.8951 (tt0) cc_final: 0.8482 (tm-30) REVERT: C 36 ASP cc_start: 0.8667 (m-30) cc_final: 0.8272 (t0) REVERT: R 261 ASN cc_start: 0.9393 (t0) cc_final: 0.9170 (t0) REVERT: R 345 PHE cc_start: 0.8976 (t80) cc_final: 0.8229 (t80) REVERT: R 346 TYR cc_start: 0.6894 (t80) cc_final: 0.6551 (t80) REVERT: R 350 ASN cc_start: 0.9014 (m-40) cc_final: 0.8625 (m110) outliers start: 28 outliers final: 9 residues processed: 146 average time/residue: 0.4670 time to fit residues: 71.5690 Evaluate side-chains 118 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 341 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.6502 > 50: distance: 16 - 31: 6.749 distance: 20 - 36: 23.818 distance: 28 - 31: 5.104 distance: 31 - 32: 9.116 distance: 32 - 33: 12.099 distance: 32 - 35: 14.703 distance: 33 - 34: 20.956 distance: 33 - 36: 15.956 distance: 36 - 37: 10.263 distance: 37 - 38: 6.230 distance: 37 - 40: 20.286 distance: 38 - 39: 11.184 distance: 38 - 43: 15.296 distance: 40 - 41: 11.439 distance: 40 - 42: 14.078 distance: 43 - 44: 11.897 distance: 44 - 45: 15.901 distance: 44 - 47: 20.354 distance: 45 - 46: 15.735 distance: 45 - 51: 10.644 distance: 47 - 48: 6.176 distance: 48 - 49: 11.557 distance: 48 - 50: 21.240 distance: 51 - 52: 20.559 distance: 52 - 53: 14.103 distance: 52 - 55: 30.741 distance: 53 - 54: 12.632 distance: 53 - 56: 31.956 distance: 56 - 57: 11.579 distance: 57 - 58: 17.706 distance: 57 - 60: 34.207 distance: 58 - 59: 26.051 distance: 58 - 62: 18.612 distance: 59 - 78: 30.136 distance: 60 - 61: 11.369 distance: 62 - 63: 19.735 distance: 63 - 64: 13.409 distance: 63 - 66: 12.642 distance: 64 - 65: 8.368 distance: 64 - 67: 14.524 distance: 65 - 85: 20.839 distance: 67 - 68: 12.059 distance: 68 - 69: 17.565 distance: 68 - 71: 7.211 distance: 69 - 70: 16.455 distance: 69 - 73: 9.551 distance: 70 - 94: 16.426 distance: 71 - 72: 26.126 distance: 73 - 74: 11.925 distance: 74 - 75: 10.611 distance: 74 - 77: 11.038 distance: 75 - 76: 8.906 distance: 75 - 78: 11.438 distance: 76 - 102: 14.039 distance: 78 - 79: 8.503 distance: 79 - 80: 8.466 distance: 79 - 82: 16.170 distance: 80 - 81: 5.218 distance: 80 - 85: 16.945 distance: 82 - 83: 8.819 distance: 82 - 84: 10.711 distance: 85 - 86: 5.284 distance: 86 - 87: 9.570 distance: 87 - 88: 20.361 distance: 87 - 94: 14.313 distance: 89 - 90: 7.173 distance: 90 - 91: 4.684 distance: 91 - 92: 5.185 distance: 92 - 93: 7.314