Starting phenix.real_space_refine on Fri Mar 15 07:51:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0m_32244/03_2024/7w0m_32244_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0m_32244/03_2024/7w0m_32244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0m_32244/03_2024/7w0m_32244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0m_32244/03_2024/7w0m_32244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0m_32244/03_2024/7w0m_32244_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w0m_32244/03_2024/7w0m_32244_updated.pdb" } resolution = 3.71 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2101 atoms to isotropic. 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 67 5.16 5 C 5690 2.51 5 N 1509 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8929 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 418 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "R" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2321 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain: "S" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1794 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'8EH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.61, per 1000 atoms: 0.63 Number of scatterers: 8929 At special positions: 0 Unit cell: (92.65, 119.85, 131.75, 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 67 16.00 O 1663 8.00 N 1509 7.00 C 5690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.63 Conformation dependent library (CDL) restraints added in 1.8 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 14 sheets defined 32.6% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.409A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.695A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.558A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.503A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 297 through 310 removed outlier: 3.883A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.878A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 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 'C' and resid 39 through 54 removed outlier: 3.562A pdb=" N GLN C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 75 removed outlier: 3.561A pdb=" N LEU C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS C 75 " --> pdb=" O TYR C 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 54 Processing helix chain 'R' and resid 65 through 80 Processing helix chain 'R' and resid 82 through 90 removed outlier: 3.958A pdb=" N THR R 89 " --> pdb=" O TRP R 85 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR R 90 " --> pdb=" O ALA R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 131 Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 149 through 161 removed outlier: 4.604A pdb=" N TRP R 154 " --> pdb=" O THR R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 166 No H-bonds generated for 'chain 'R' and resid 163 through 166' Processing helix chain 'R' and resid 191 through 230 removed outlier: 4.600A pdb=" N TRP R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA R 196 " --> pdb=" O SER R 192 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR R 207 " --> pdb=" O VAL R 203 " (cutoff:3.500A) Proline residue: R 213 - end of helix Processing helix chain 'R' and resid 239 through 275 removed outlier: 4.333A pdb=" N VAL R 254 " --> pdb=" O ILE R 250 " (cutoff:3.500A) Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 281 through 291 removed outlier: 3.888A pdb=" N LEU R 285 " --> pdb=" O ASP R 282 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE R 291 " --> pdb=" O MET R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 303 removed outlier: 3.716A pdb=" N SER R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 310 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing sheet with id= A, first strand: chain 'A' and resid 185 through 187 Processing sheet with id= B, first strand: chain 'A' and resid 220 through 225 removed outlier: 7.199A pdb=" N SER A 263 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE A 223 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 265 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL A 225 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE A 267 " --> pdb=" O VAL A 225 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.837A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.039A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.820A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP B 169 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE B 180 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.663A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.539A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 294 through 298 removed outlier: 4.163A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.628A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'R' and resid 168 through 171 removed outlier: 3.736A pdb=" N GLN R 180 " --> pdb=" O GLY R 171 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 5 through 7 removed outlier: 3.818A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU S 81 " --> pdb=" O LEU S 20 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP S 73 " --> pdb=" O THR S 78 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR S 69 " --> pdb=" O GLN S 82 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 96 through 99 removed outlier: 3.849A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 156 through 160 Processing sheet with id= N, first strand: chain 'S' and resid 174 through 179 318 hydrogen bonds defined for protein. 903 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: 2.34 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2854 1.35 - 1.47: 2370 1.47 - 1.60: 3801 1.60 - 1.72: 1 1.72 - 1.85: 98 Bond restraints: 9124 Sorted by residual: bond pdb=" C30 8EH R 401 " pdb=" C31 8EH R 401 " ideal model delta sigma weight residual 1.472 1.569 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C30 8EH R 401 " pdb=" N29 8EH R 401 " ideal model delta sigma weight residual 1.313 1.399 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C10 8EH R 401 " pdb=" N11 8EH R 401 " ideal model delta sigma weight residual 1.421 1.500 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C12 8EH R 401 " pdb=" N28 8EH R 401 " ideal model delta sigma weight residual 1.307 1.386 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C30 8EH R 401 " pdb=" N11 8EH R 401 " ideal model delta sigma weight residual 1.375 1.446 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 9119 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.10: 150 106.10 - 113.09: 4900 113.09 - 120.07: 3241 120.07 - 127.05: 3975 127.05 - 134.04: 99 Bond angle restraints: 12365 Sorted by residual: angle pdb=" C LEU R 167 " pdb=" N ARG R 168 " pdb=" CA ARG R 168 " ideal model delta sigma weight residual 120.75 128.01 -7.26 1.51e+00 4.39e-01 2.31e+01 angle pdb=" CA VAL R 166 " pdb=" CB VAL R 166 " pdb=" CG2 VAL R 166 " ideal model delta sigma weight residual 110.40 117.90 -7.50 1.70e+00 3.46e-01 1.94e+01 angle pdb=" O15 8EH R 401 " pdb=" S14 8EH R 401 " pdb=" O16 8EH R 401 " ideal model delta sigma weight residual 119.97 107.69 12.28 3.00e+00 1.11e-01 1.68e+01 angle pdb=" N VAL R 148 " pdb=" CA VAL R 148 " pdb=" C VAL R 148 " ideal model delta sigma weight residual 112.96 108.95 4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" CA GLU S 234 " pdb=" C GLU S 234 " pdb=" O GLU S 234 " ideal model delta sigma weight residual 121.16 116.83 4.33 1.12e+00 7.97e-01 1.50e+01 ... (remaining 12360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4863 17.87 - 35.74: 444 35.74 - 53.61: 62 53.61 - 71.48: 15 71.48 - 89.35: 12 Dihedral angle restraints: 5396 sinusoidal: 2108 harmonic: 3288 Sorted by residual: dihedral pdb=" CB CYS R 102 " pdb=" SG CYS R 102 " pdb=" SG CYS R 181 " pdb=" CB CYS R 181 " ideal model delta sinusoidal sigma weight residual 93.00 171.61 -78.61 1 1.00e+01 1.00e-02 7.70e+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 180.00 154.31 25.69 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA THR B 164 " pdb=" C THR B 164 " pdb=" N THR B 165 " pdb=" CA THR B 165 " ideal model delta harmonic sigma weight residual 180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 5393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1257 0.072 - 0.144: 128 0.144 - 0.217: 4 0.217 - 0.289: 2 0.289 - 0.361: 3 Chirality restraints: 1394 Sorted by residual: chirality pdb=" C19 8EH R 401 " pdb=" C17 8EH R 401 " pdb=" C21 8EH R 401 " pdb=" O20 8EH R 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.79 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA LEU S 233 " pdb=" N LEU S 233 " pdb=" C LEU S 233 " pdb=" CB LEU S 233 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB VAL R 166 " pdb=" CA VAL R 166 " pdb=" CG1 VAL R 166 " pdb=" CG2 VAL R 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 1391 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL S 147 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO S 148 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO S 148 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO S 148 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 313 " -0.040 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO R 314 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO R 314 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 314 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP R 95 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO R 96 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 96 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 96 " 0.027 5.00e-02 4.00e+02 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1560 2.76 - 3.30: 8573 3.30 - 3.83: 14016 3.83 - 4.37: 15776 4.37 - 4.90: 27309 Nonbonded interactions: 67234 Sorted by model distance: nonbonded pdb=" OG SER B 97 " pdb=" OD2 ASP B 118 " model vdw 2.230 2.440 nonbonded pdb=" NE ARG R 91 " pdb=" O ASP R 94 " model vdw 2.269 2.520 nonbonded pdb=" OE1 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.270 2.440 nonbonded pdb=" O THR A 327 " pdb=" N LYS A 330 " model vdw 2.272 2.520 nonbonded pdb=" ND2 ASN R 46 " pdb=" O ALA R 72 " model vdw 2.277 2.520 ... (remaining 67229 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 6.950 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.890 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 : 0.004 0.100 9124 Z= 0.291 Angle : 0.761 12.279 12365 Z= 0.405 Chirality : 0.047 0.361 1394 Planarity : 0.005 0.076 1555 Dihedral : 14.112 89.348 3275 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -1.90 (0.25), residues: 1118 helix: 0.51 (0.29), residues: 352 sheet: -1.72 (0.32), residues: 256 loop : -2.30 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.027 0.001 PHE S 27 TYR 0.022 0.002 TYR S 235 ARG 0.005 0.000 ARG R 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7512 (tm-30) REVERT: A 191 PHE cc_start: 0.8395 (t80) cc_final: 0.8183 (t80) REVERT: A 193 ASP cc_start: 0.7955 (m-30) cc_final: 0.7741 (m-30) REVERT: A 245 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 271 LYS cc_start: 0.8171 (tptp) cc_final: 0.7911 (tptt) REVERT: A 344 ILE cc_start: 0.7883 (tt) cc_final: 0.7677 (tt) REVERT: A 348 LEU cc_start: 0.7514 (tp) cc_final: 0.7254 (tt) REVERT: B 25 CYS cc_start: 0.8399 (m) cc_final: 0.7912 (t) REVERT: B 61 MET cc_start: 0.6892 (tmm) cc_final: 0.6578 (tmm) REVERT: B 124 TYR cc_start: 0.8294 (m-80) cc_final: 0.7711 (m-80) REVERT: B 197 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7578 (mtp85) REVERT: B 199 PHE cc_start: 0.8189 (p90) cc_final: 0.7933 (p90) REVERT: B 212 ASP cc_start: 0.7593 (t0) cc_final: 0.7318 (t70) REVERT: B 220 GLN cc_start: 0.7811 (mt0) cc_final: 0.7520 (mt0) REVERT: B 233 CYS cc_start: 0.7497 (t) cc_final: 0.7115 (t) REVERT: B 247 ASP cc_start: 0.7413 (t0) cc_final: 0.7060 (t0) REVERT: B 314 ARG cc_start: 0.7502 (ptp-170) cc_final: 0.7216 (ptm160) REVERT: R 97 PHE cc_start: 0.7240 (m-10) cc_final: 0.7018 (m-10) REVERT: R 162 MET cc_start: 0.5536 (mmp) cc_final: 0.5175 (mmp) REVERT: R 165 MET cc_start: 0.7280 (tpt) cc_final: 0.6920 (tpt) REVERT: R 166 VAL cc_start: 0.7767 (t) cc_final: 0.7111 (t) REVERT: R 183 MET cc_start: 0.4866 (tmm) cc_final: 0.4437 (tmm) REVERT: R 268 LYS cc_start: 0.8837 (mttt) cc_final: 0.8499 (mttt) REVERT: R 284 ASP cc_start: 0.8074 (t0) cc_final: 0.7810 (t0) REVERT: R 301 ASN cc_start: 0.7790 (t0) cc_final: 0.7429 (t0) REVERT: S 34 MET cc_start: 0.7776 (mmm) cc_final: 0.7165 (mmm) REVERT: S 85 SER cc_start: 0.7950 (p) cc_final: 0.7679 (m) REVERT: S 89 GLU cc_start: 0.7756 (tp30) cc_final: 0.7500 (tp30) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.2170 time to fit residues: 90.1492 Evaluate side-chains 279 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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** A 255 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9124 Z= 0.190 Angle : 0.616 8.058 12365 Z= 0.311 Chirality : 0.042 0.222 1394 Planarity : 0.004 0.049 1555 Dihedral : 8.635 73.803 1261 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.55 % Allowed : 12.89 % Favored : 85.57 % 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: -1.71 (0.25), residues: 1118 helix: 0.58 (0.29), residues: 351 sheet: -1.35 (0.32), residues: 247 loop : -2.27 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 261 HIS 0.004 0.001 HIS A 213 PHE 0.016 0.001 PHE R 291 TYR 0.030 0.001 TYR S 235 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 281 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7538 (tm-30) REVERT: A 193 ASP cc_start: 0.7953 (m-30) cc_final: 0.7732 (m-30) REVERT: A 197 LYS cc_start: 0.7955 (tttp) cc_final: 0.7469 (tptt) REVERT: A 205 ARG cc_start: 0.7088 (mmp80) cc_final: 0.6738 (mmp80) REVERT: A 216 GLU cc_start: 0.7668 (tp30) cc_final: 0.7464 (tp30) REVERT: A 245 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 271 LYS cc_start: 0.8250 (tptp) cc_final: 0.7899 (tptt) REVERT: A 304 GLN cc_start: 0.8415 (tt0) cc_final: 0.8164 (tt0) REVERT: A 344 ILE cc_start: 0.7907 (tt) cc_final: 0.7688 (tt) REVERT: A 348 LEU cc_start: 0.7533 (tp) cc_final: 0.7324 (tp) REVERT: B 25 CYS cc_start: 0.8456 (m) cc_final: 0.7912 (t) REVERT: B 59 TYR cc_start: 0.8436 (m-80) cc_final: 0.8031 (m-80) REVERT: B 61 MET cc_start: 0.7015 (tmm) cc_final: 0.6547 (tmm) REVERT: B 102 THR cc_start: 0.8441 (t) cc_final: 0.8091 (m) REVERT: B 212 ASP cc_start: 0.7644 (t0) cc_final: 0.7338 (t70) REVERT: B 233 CYS cc_start: 0.7640 (t) cc_final: 0.7181 (t) REVERT: R 36 MET cc_start: 0.6729 (mmp) cc_final: 0.6453 (mmp) REVERT: R 71 LEU cc_start: 0.7451 (tp) cc_final: 0.6863 (mm) REVERT: R 97 PHE cc_start: 0.7259 (m-10) cc_final: 0.6991 (m-10) REVERT: R 162 MET cc_start: 0.4916 (mmp) cc_final: 0.4602 (mmp) REVERT: R 183 MET cc_start: 0.5023 (tmm) cc_final: 0.4375 (tmm) REVERT: R 268 LYS cc_start: 0.8927 (mttt) cc_final: 0.8514 (mttt) REVERT: R 284 ASP cc_start: 0.8247 (t0) cc_final: 0.8011 (t0) REVERT: S 34 MET cc_start: 0.7723 (mmm) cc_final: 0.6892 (mmm) REVERT: S 89 GLU cc_start: 0.7755 (tp30) cc_final: 0.7537 (tp30) REVERT: S 230 MET cc_start: 0.7881 (ttp) cc_final: 0.7606 (ttt) outliers start: 15 outliers final: 10 residues processed: 283 average time/residue: 0.2148 time to fit residues: 82.5503 Evaluate side-chains 282 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 272 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 89 optimal weight: 0.0570 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9124 Z= 0.184 Angle : 0.590 7.416 12365 Z= 0.300 Chirality : 0.041 0.229 1394 Planarity : 0.004 0.041 1555 Dihedral : 8.372 71.279 1261 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.55 % Allowed : 15.98 % Favored : 82.47 % 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: -1.64 (0.25), residues: 1118 helix: 0.62 (0.28), residues: 352 sheet: -1.27 (0.31), residues: 257 loop : -2.26 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 261 HIS 0.005 0.001 HIS A 213 PHE 0.022 0.001 PHE S 27 TYR 0.028 0.001 TYR S 235 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 274 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7545 (tm-30) REVERT: A 193 ASP cc_start: 0.7965 (m-30) cc_final: 0.7730 (m-30) REVERT: A 197 LYS cc_start: 0.7970 (tttp) cc_final: 0.7483 (tptt) REVERT: A 205 ARG cc_start: 0.7120 (mmp80) cc_final: 0.6752 (mmp80) REVERT: A 216 GLU cc_start: 0.7685 (tp30) cc_final: 0.7454 (tp30) REVERT: A 245 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7729 (mm-30) REVERT: A 304 GLN cc_start: 0.8422 (tt0) cc_final: 0.8215 (tt0) REVERT: A 344 ILE cc_start: 0.7948 (tt) cc_final: 0.7732 (tt) REVERT: B 25 CYS cc_start: 0.8473 (m) cc_final: 0.7900 (t) REVERT: B 59 TYR cc_start: 0.8407 (m-80) cc_final: 0.7995 (m-80) REVERT: B 61 MET cc_start: 0.7017 (tmm) cc_final: 0.6548 (tmm) REVERT: B 212 ASP cc_start: 0.7654 (t0) cc_final: 0.7352 (t70) REVERT: B 233 CYS cc_start: 0.7558 (t) cc_final: 0.7217 (t) REVERT: R 36 MET cc_start: 0.6815 (mmp) cc_final: 0.6518 (mmp) REVERT: R 97 PHE cc_start: 0.7256 (m-10) cc_final: 0.7004 (m-10) REVERT: R 162 MET cc_start: 0.4943 (mmp) cc_final: 0.4600 (mmp) REVERT: R 166 VAL cc_start: 0.7250 (OUTLIER) cc_final: 0.6938 (t) REVERT: R 183 MET cc_start: 0.5019 (tmm) cc_final: 0.4303 (tmm) REVERT: R 268 LYS cc_start: 0.8909 (mttt) cc_final: 0.8528 (mttt) REVERT: S 18 ARG cc_start: 0.8250 (ttm-80) cc_final: 0.8028 (ttm170) REVERT: S 89 GLU cc_start: 0.7769 (tp30) cc_final: 0.7530 (tp30) REVERT: S 230 MET cc_start: 0.7934 (ttp) cc_final: 0.7588 (ttt) outliers start: 15 outliers final: 11 residues processed: 280 average time/residue: 0.2078 time to fit residues: 79.2737 Evaluate side-chains 283 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 271 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 175 TYR Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.8322 > 50: distance: 2 - 21: 18.127 distance: 8 - 33: 26.054 distance: 12 - 41: 29.205 distance: 15 - 21: 14.520 distance: 16 - 49: 35.910 distance: 21 - 22: 33.450 distance: 22 - 23: 19.413 distance: 22 - 25: 23.333 distance: 23 - 24: 24.849 distance: 23 - 33: 13.098 distance: 24 - 56: 17.811 distance: 25 - 26: 19.096 distance: 26 - 27: 7.530 distance: 26 - 28: 25.403 distance: 27 - 29: 24.926 distance: 28 - 30: 14.674 distance: 29 - 31: 14.782 distance: 30 - 31: 6.767 distance: 31 - 32: 16.101 distance: 33 - 34: 10.549 distance: 34 - 35: 15.577 distance: 34 - 37: 26.218 distance: 35 - 36: 31.437 distance: 35 - 41: 17.062 distance: 36 - 67: 11.231 distance: 41 - 42: 18.834 distance: 42 - 43: 12.332 distance: 42 - 45: 15.850 distance: 43 - 44: 11.271 distance: 43 - 49: 14.137 distance: 44 - 75: 26.991 distance: 45 - 46: 16.663 distance: 46 - 47: 22.152 distance: 46 - 48: 4.963 distance: 49 - 50: 19.562 distance: 50 - 51: 19.981 distance: 50 - 53: 29.335 distance: 51 - 52: 15.483 distance: 51 - 56: 18.704 distance: 52 - 83: 11.819 distance: 53 - 54: 16.964 distance: 53 - 55: 25.569 distance: 56 - 57: 34.095 distance: 57 - 58: 34.335 distance: 58 - 67: 24.168 distance: 59 - 87: 50.710 distance: 62 - 64: 31.155 distance: 63 - 65: 7.292 distance: 64 - 66: 18.391 distance: 65 - 66: 29.368 distance: 67 - 68: 23.469 distance: 68 - 69: 18.402 distance: 68 - 71: 11.286 distance: 69 - 70: 12.758 distance: 69 - 75: 22.335 distance: 70 - 94: 18.084 distance: 71 - 72: 22.253 distance: 72 - 73: 17.118 distance: 72 - 74: 22.578 distance: 75 - 76: 8.706 distance: 76 - 77: 50.359 distance: 77 - 78: 40.392 distance: 77 - 83: 11.443 distance: 78 - 101: 36.699 distance: 83 - 84: 21.442 distance: 84 - 85: 36.694 distance: 85 - 86: 18.179 distance: 85 - 87: 26.853 distance: 86 - 105: 31.222 distance: 87 - 88: 8.043 distance: 88 - 89: 39.800 distance: 88 - 91: 13.661 distance: 89 - 94: 25.444 distance: 90 - 111: 37.229 distance: 91 - 92: 16.972 distance: 91 - 93: 27.096 distance: 94 - 95: 17.395 distance: 95 - 96: 29.603 distance: 95 - 98: 25.755 distance: 96 - 97: 38.288 distance: 96 - 101: 7.853 distance: 97 - 114: 32.502 distance: 98 - 99: 13.561 distance: 98 - 100: 9.237