Starting phenix.real_space_refine on Tue Jan 14 17:49:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iq4_35657/01_2025/8iq4_35657.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iq4_35657/01_2025/8iq4_35657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iq4_35657/01_2025/8iq4_35657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iq4_35657/01_2025/8iq4_35657.map" model { file = "/net/cci-nas-00/data/ceres_data/8iq4_35657/01_2025/8iq4_35657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iq4_35657/01_2025/8iq4_35657.cif" } resolution = 2.7 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= 0.101 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 52 5.16 5 C 4555 2.51 5 N 1208 2.21 5 O 1265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7080 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2065 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1564 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 7, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2342 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 5, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 Chain: "G" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 238 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 845 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'87Q': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.03, per 1000 atoms: 0.71 Number of scatterers: 7080 At special positions: 0 Unit cell: (70.2656, 96.6152, 124.063, 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 52 16.00 O 1265 8.00 N 1208 7.00 C 4555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 11 sheets defined 40.9% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'R' and resid 29 through 60 removed outlier: 4.471A pdb=" N SER R 33 " --> pdb=" O SER R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 94 Processing helix chain 'R' and resid 105 through 139 Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 139 through 146 Processing helix chain 'R' and resid 147 through 173 removed outlier: 4.164A pdb=" N HIS R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL R 152 " --> pdb=" O THR R 148 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 195 through 229 removed outlier: 4.018A pdb=" N ARG R 199 " --> pdb=" O ASP R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 275 Proline residue: R 264 - end of helix Processing helix chain 'R' and resid 282 through 305 removed outlier: 3.826A pdb=" N PHE R 288 " --> pdb=" O GLU R 284 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 313 Processing helix chain 'A' and resid 18 through 39 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.532A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 337 through 352 removed outlier: 3.759A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 392 Processing helix chain 'B' and resid 8 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 16 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'R' and resid 178 through 179 Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.721A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.472A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.746A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, 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: 4.409A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.153A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.450A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.550A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.575A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.529A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1173 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: 2.13 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2261 1.34 - 1.46: 1812 1.46 - 1.58: 3078 1.58 - 1.70: 0 1.70 - 1.82: 71 Bond restraints: 7222 Sorted by residual: bond pdb=" C13 87Q R 401 " pdb=" C14 87Q R 401 " ideal model delta sigma weight residual 1.499 1.563 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C10 87Q R 401 " pdb=" C11 87Q R 401 " ideal model delta sigma weight residual 1.490 1.540 -0.050 2.00e-02 2.50e+03 6.19e+00 bond pdb=" C15 87Q R 401 " pdb=" C16 87Q R 401 " ideal model delta sigma weight residual 1.500 1.546 -0.046 2.00e-02 2.50e+03 5.23e+00 bond pdb=" C06 87Q R 401 " pdb=" C09 87Q R 401 " ideal model delta sigma weight residual 1.505 1.542 -0.037 2.00e-02 2.50e+03 3.34e+00 bond pdb=" C06 87Q R 401 " pdb=" O08 87Q R 401 " ideal model delta sigma weight residual 1.426 1.391 0.035 2.00e-02 2.50e+03 3.08e+00 ... (remaining 7217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.18: 9818 5.18 - 10.36: 6 10.36 - 15.55: 2 15.55 - 20.73: 0 20.73 - 25.91: 1 Bond angle restraints: 9827 Sorted by residual: angle pdb=" C09 87Q R 401 " pdb=" C10 87Q R 401 " pdb=" C11 87Q R 401 " ideal model delta sigma weight residual 124.44 150.35 -25.91 3.00e+00 1.11e-01 7.46e+01 angle pdb=" C13 87Q R 401 " pdb=" C14 87Q R 401 " pdb=" C15 87Q R 401 " ideal model delta sigma weight residual 126.67 114.18 12.49 3.00e+00 1.11e-01 1.73e+01 angle pdb=" C06 87Q R 401 " pdb=" C09 87Q R 401 " pdb=" C10 87Q R 401 " ideal model delta sigma weight residual 127.22 114.91 12.31 3.00e+00 1.11e-01 1.68e+01 angle pdb=" C ARG R 59 " pdb=" N GLN R 60 " pdb=" CA GLN R 60 " ideal model delta sigma weight residual 122.31 115.55 6.76 1.81e+00 3.05e-01 1.40e+01 angle pdb=" C14 87Q R 401 " pdb=" C15 87Q R 401 " pdb=" C16 87Q R 401 " ideal model delta sigma weight residual 126.41 117.48 8.93 3.00e+00 1.11e-01 8.86e+00 ... (remaining 9822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3777 17.81 - 35.62: 337 35.62 - 53.44: 83 53.44 - 71.25: 17 71.25 - 89.06: 5 Dihedral angle restraints: 4219 sinusoidal: 1453 harmonic: 2766 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -121.49 35.49 1 1.00e+01 1.00e-02 1.78e+01 dihedral pdb=" CA ARG R 100 " pdb=" C ARG R 100 " pdb=" N PHE R 101 " pdb=" CA PHE R 101 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" SG CYS N 99 " pdb=" CB CYS N 107 " pdb=" SG CYS N 107 " pdb=" CA CYS N 107 " ideal model delta sinusoidal sigma weight residual -73.00 -1.88 -71.12 1 2.00e+01 2.50e-03 1.62e+01 ... (remaining 4216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1098 0.082 - 0.163: 68 0.163 - 0.244: 2 0.244 - 0.326: 1 0.326 - 0.407: 1 Chirality restraints: 1170 Sorted by residual: chirality pdb=" C12 87Q R 401 " pdb=" C11 87Q R 401 " pdb=" C13 87Q R 401 " pdb=" C22 87Q R 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.94 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" C11 87Q R 401 " pdb=" C10 87Q R 401 " pdb=" C12 87Q R 401 " pdb=" C25 87Q R 401 " both_signs ideal model delta sigma weight residual False 2.63 2.92 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C06 87Q R 401 " pdb=" C05 87Q R 401 " pdb=" C07 87Q R 401 " pdb=" C09 87Q R 401 " both_signs ideal model delta sigma weight residual False -2.54 -2.75 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1167 not shown) Planarity restraints: 1225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER R 263 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO R 264 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO R 264 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 264 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO B 236 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C THR B 87 " 0.028 2.00e-02 2.50e+03 pdb=" O THR B 87 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN B 88 " -0.010 2.00e-02 2.50e+03 ... (remaining 1222 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 945 2.75 - 3.29: 6525 3.29 - 3.83: 11972 3.83 - 4.36: 14102 4.36 - 4.90: 25373 Nonbonded interactions: 58917 Sorted by model distance: nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.218 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.263 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.266 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD2 ASP B 163 " model vdw 2.269 3.040 ... (remaining 58912 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.200 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 : 0.003 0.064 7222 Z= 0.202 Angle : 0.603 25.912 9827 Z= 0.294 Chirality : 0.043 0.407 1170 Planarity : 0.003 0.047 1225 Dihedral : 14.910 89.058 2416 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.58 % Allowed : 12.77 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.27), residues: 930 helix: 3.05 (0.26), residues: 340 sheet: 1.05 (0.35), residues: 206 loop : -1.16 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.019 0.001 PHE R 165 TYR 0.012 0.001 TYR A 37 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.803 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 99 average time/residue: 1.1724 time to fit residues: 123.0155 Evaluate side-chains 98 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 365 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 ASN B 175 GLN ** B 237 ASN ** 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 = 0.3559 r_free = 0.3559 target = 0.135743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.111760 restraints weight = 7702.889| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.42 r_work: 0.3167 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7222 Z= 0.290 Angle : 0.551 6.745 9827 Z= 0.303 Chirality : 0.043 0.153 1170 Planarity : 0.004 0.051 1225 Dihedral : 6.156 83.602 1052 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.47 % Allowed : 12.63 % Favored : 84.91 % 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: 1.36 (0.27), residues: 930 helix: 2.96 (0.26), residues: 343 sheet: 0.92 (0.34), residues: 213 loop : -1.17 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 63 HIS 0.009 0.001 HIS A 357 PHE 0.018 0.002 PHE R 101 TYR 0.015 0.002 TYR B 105 ARG 0.004 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.805 Fit side-chains REVERT: B 219 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7649 (mtp180) REVERT: B 234 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8446 (t80) REVERT: N 95 TYR cc_start: 0.8756 (m-80) cc_final: 0.8511 (m-80) outliers start: 17 outliers final: 9 residues processed: 110 average time/residue: 1.1161 time to fit residues: 130.5953 Evaluate side-chains 109 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 56 optimal weight: 0.0270 chunk 6 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.138486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.114401 restraints weight = 7782.798| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.45 r_work: 0.3202 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7222 Z= 0.174 Angle : 0.478 6.382 9827 Z= 0.267 Chirality : 0.040 0.147 1170 Planarity : 0.003 0.050 1225 Dihedral : 5.730 88.973 1050 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.18 % Allowed : 14.22 % Favored : 83.60 % 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: 1.49 (0.27), residues: 930 helix: 3.16 (0.26), residues: 343 sheet: 1.02 (0.33), residues: 212 loop : -1.21 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.001 PHE R 165 TYR 0.013 0.001 TYR A 37 ARG 0.003 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.790 Fit side-chains REVERT: B 219 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7685 (mtp180) REVERT: B 234 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8342 (t80) REVERT: N 95 TYR cc_start: 0.8684 (m-80) cc_final: 0.8470 (m-80) outliers start: 15 outliers final: 7 residues processed: 111 average time/residue: 1.0478 time to fit residues: 123.8191 Evaluate side-chains 108 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 2 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.137423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.113255 restraints weight = 7820.469| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.46 r_work: 0.3185 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7222 Z= 0.206 Angle : 0.505 8.378 9827 Z= 0.277 Chirality : 0.041 0.151 1170 Planarity : 0.004 0.050 1225 Dihedral : 5.736 88.908 1050 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.47 % Allowed : 14.66 % Favored : 82.87 % 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: 1.45 (0.27), residues: 930 helix: 3.10 (0.26), residues: 344 sheet: 0.94 (0.33), residues: 214 loop : -1.20 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 63 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.001 PHE R 165 TYR 0.013 0.001 TYR A 37 ARG 0.003 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.811 Fit side-chains REVERT: B 219 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7682 (mtp180) REVERT: B 234 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8393 (t80) REVERT: N 95 TYR cc_start: 0.8694 (m-80) cc_final: 0.8471 (m-80) outliers start: 17 outliers final: 12 residues processed: 109 average time/residue: 1.0889 time to fit residues: 126.3144 Evaluate side-chains 112 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.136016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.111848 restraints weight = 7712.084| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.44 r_work: 0.3168 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7222 Z= 0.247 Angle : 0.523 6.724 9827 Z= 0.289 Chirality : 0.042 0.159 1170 Planarity : 0.004 0.052 1225 Dihedral : 5.840 88.721 1050 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.90 % Allowed : 14.37 % Favored : 82.73 % 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: 1.36 (0.27), residues: 930 helix: 3.02 (0.26), residues: 344 sheet: 0.90 (0.33), residues: 214 loop : -1.25 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 63 HIS 0.007 0.001 HIS A 357 PHE 0.018 0.002 PHE R 165 TYR 0.015 0.001 TYR A 358 ARG 0.003 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.740 Fit side-chains REVERT: B 219 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7644 (mtp180) REVERT: B 234 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8481 (t80) REVERT: N 95 TYR cc_start: 0.8748 (m-80) cc_final: 0.8466 (m-80) outliers start: 20 outliers final: 13 residues processed: 111 average time/residue: 1.0486 time to fit residues: 123.9896 Evaluate side-chains 112 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 196 TRP Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.9249 > 50: distance: 33 - 49: 5.136 distance: 37 - 53: 15.487 distance: 41 - 59: 10.850 distance: 45 - 49: 3.134 distance: 46 - 66: 12.179 distance: 49 - 50: 8.769 distance: 50 - 51: 6.326 distance: 51 - 52: 4.409 distance: 51 - 53: 5.777 distance: 52 - 74: 12.926 distance: 54 - 55: 8.161 distance: 54 - 57: 10.031 distance: 55 - 56: 3.533 distance: 56 - 79: 15.901 distance: 57 - 58: 11.048 distance: 59 - 60: 4.877 distance: 60 - 61: 5.212 distance: 60 - 63: 5.115 distance: 61 - 66: 5.476 distance: 62 - 87: 11.556 distance: 63 - 65: 5.358 distance: 66 - 67: 4.427 distance: 67 - 68: 3.095 distance: 67 - 70: 3.453 distance: 69 - 96: 22.250 distance: 71 - 72: 10.737 distance: 72 - 73: 4.344 distance: 74 - 75: 4.429 distance: 75 - 76: 13.283 distance: 75 - 78: 17.079 distance: 76 - 77: 6.989 distance: 77 - 107: 14.659 distance: 79 - 80: 3.104 distance: 80 - 81: 6.382 distance: 81 - 82: 5.291 distance: 81 - 87: 6.099 distance: 82 - 113: 37.422 distance: 83 - 84: 13.445 distance: 83 - 85: 9.185 distance: 84 - 86: 17.159 distance: 87 - 88: 8.250 distance: 88 - 89: 7.552 distance: 88 - 91: 8.368 distance: 89 - 90: 10.295 distance: 89 - 96: 3.522 distance: 90 - 121: 22.888 distance: 91 - 92: 5.347 distance: 92 - 93: 5.994 distance: 93 - 94: 10.447 distance: 93 - 95: 6.462 distance: 96 - 97: 3.718 distance: 97 - 98: 6.928 distance: 97 - 100: 6.544 distance: 98 - 99: 14.894 distance: 98 - 107: 6.948 distance: 99 - 125: 19.817 distance: 100 - 101: 3.674 distance: 101 - 102: 12.713 distance: 102 - 103: 9.783 distance: 103 - 104: 5.337 distance: 104 - 105: 13.501 distance: 104 - 106: 13.570 distance: 107 - 108: 3.573 distance: 108 - 109: 12.381 distance: 108 - 111: 15.321 distance: 109 - 110: 15.726 distance: 109 - 113: 34.955 distance: 110 - 132: 6.868 distance: 111 - 112: 13.223 distance: 113 - 114: 38.957 distance: 114 - 115: 7.503 distance: 114 - 117: 17.026 distance: 115 - 116: 21.290 distance: 115 - 121: 10.367 distance: 116 - 138: 27.927 distance: 117 - 118: 25.098 distance: 117 - 119: 14.618 distance: 118 - 120: 25.390