Starting phenix.real_space_refine on Wed Mar 12 02:10:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iq4_35657/03_2025/8iq4_35657.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iq4_35657/03_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_35657/03_2025/8iq4_35657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iq4_35657/03_2025/8iq4_35657.map" model { file = "/net/cci-nas-00/data/ceres_data/8iq4_35657/03_2025/8iq4_35657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iq4_35657/03_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-5624/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: 4.82, per 1000 atoms: 0.68 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: 1.78 Conformation dependent library (CDL) restraints added in 1.0 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: 0.82 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: 1.99 Time building geometry restraints manager: 2.09 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.320 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.880 ------------------------------------------------------------------------------- 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 : 0.756 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 99 average time/residue: 1.1528 time to fit residues: 120.8946 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 : 0.747 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.111761 restraints weight = 7702.888| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.42 r_work: 0.3167 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 : 0.760 Fit side-chains REVERT: B 219 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7650 (mtp180) REVERT: B 234 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8448 (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: 1.0200 time to fit residues: 119.5925 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 : 0.828 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.8980 chunk 56 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.137187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.113009 restraints weight = 7794.992| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.46 r_work: 0.3186 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7222 Z= 0.207 Angle : 0.499 6.531 9827 Z= 0.277 Chirality : 0.041 0.150 1170 Planarity : 0.004 0.051 1225 Dihedral : 5.835 88.373 1050 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.32 % Allowed : 14.08 % 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: 1.41 (0.27), residues: 930 helix: 3.05 (0.26), residues: 344 sheet: 1.00 (0.33), residues: 212 loop : -1.24 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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: 16 poor density : 99 time to evaluate : 0.839 Fit side-chains REVERT: B 219 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7683 (mtp180) REVERT: B 234 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8417 (t80) REVERT: N 95 TYR cc_start: 0.8700 (m-80) cc_final: 0.8479 (m-80) outliers start: 16 outliers final: 8 residues processed: 111 average time/residue: 1.0960 time to fit residues: 129.3389 Evaluate side-chains 110 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 179 THR 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: 0.9990 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: 0.8980 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.136109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.112059 restraints weight = 7861.829| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.43 r_work: 0.3180 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7222 Z= 0.227 Angle : 0.518 8.308 9827 Z= 0.284 Chirality : 0.041 0.153 1170 Planarity : 0.004 0.051 1225 Dihedral : 5.829 89.177 1050 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.18 % Allowed : 14.80 % Favored : 83.02 % 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: 0.91 (0.33), residues: 214 loop : -1.25 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 63 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.002 PHE R 101 TYR 0.014 0.001 TYR A 37 ARG 0.003 0.000 ARG A 231 *********************** 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 113 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.769 Fit side-chains REVERT: B 219 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7547 (mmp-170) REVERT: B 234 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8453 (t80) REVERT: N 95 TYR cc_start: 0.8693 (m-80) cc_final: 0.8468 (m-80) outliers start: 15 outliers final: 11 residues processed: 109 average time/residue: 1.0249 time to fit residues: 119.1256 Evaluate side-chains 111 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.135632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.111701 restraints weight = 7706.976| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.41 r_work: 0.3168 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7222 Z= 0.254 Angle : 0.527 6.770 9827 Z= 0.291 Chirality : 0.042 0.159 1170 Planarity : 0.004 0.054 1225 Dihedral : 5.857 86.832 1050 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.34 % Allowed : 13.93 % 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: 1.31 (0.27), residues: 930 helix: 2.97 (0.26), residues: 344 sheet: 0.96 (0.33), residues: 212 loop : -1.30 (0.30), residues: 374 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 121 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.811 Fit side-chains REVERT: B 219 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7533 (mmp-170) REVERT: B 234 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8485 (t80) REVERT: N 95 TYR cc_start: 0.8746 (m-80) cc_final: 0.8465 (m-80) outliers start: 23 outliers final: 13 residues processed: 113 average time/residue: 1.0281 time to fit residues: 123.7787 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 : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 SER 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 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 ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 49 optimal weight: 0.0020 chunk 72 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 0.0000 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 0.0170 chunk 51 optimal weight: 2.9990 overall best weight: 0.3830 ------------------------------------------------------------------------------- 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 N 35 ASN N 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116251 restraints weight = 7760.148| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.43 r_work: 0.3235 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7222 Z= 0.137 Angle : 0.461 9.408 9827 Z= 0.254 Chirality : 0.040 0.152 1170 Planarity : 0.003 0.050 1225 Dihedral : 5.371 83.713 1050 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.74 % Allowed : 16.11 % Favored : 82.15 % 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: 1.56 (0.27), residues: 930 helix: 3.24 (0.26), residues: 343 sheet: 1.08 (0.35), residues: 195 loop : -1.12 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE R 165 TYR 0.011 0.001 TYR A 37 ARG 0.002 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 6 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 118 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.796 Fit side-chains REVERT: B 219 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7639 (mtp180) REVERT: B 234 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8291 (t80) REVERT: N 38 ARG cc_start: 0.8972 (ptt180) cc_final: 0.8603 (ptt180) REVERT: N 95 TYR cc_start: 0.8653 (m-80) cc_final: 0.8390 (m-80) outliers start: 12 outliers final: 9 residues processed: 116 average time/residue: 0.9776 time to fit residues: 121.0166 Evaluate side-chains 113 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 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 R residue 260 ILE 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 Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 0.0670 chunk 81 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN 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 = 0.3578 r_free = 0.3578 target = 0.137424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.113588 restraints weight = 7726.634| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.41 r_work: 0.3194 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7222 Z= 0.214 Angle : 0.501 6.678 9827 Z= 0.277 Chirality : 0.041 0.158 1170 Planarity : 0.004 0.052 1225 Dihedral : 5.638 88.431 1050 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.03 % Allowed : 15.97 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.27), residues: 930 helix: 3.11 (0.26), residues: 346 sheet: 0.99 (0.34), residues: 213 loop : -1.25 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 63 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.001 PHE R 165 TYR 0.014 0.001 TYR A 37 ARG 0.002 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 7 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 114 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.744 Fit side-chains REVERT: B 219 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7612 (mmp-170) REVERT: B 234 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8324 (t80) REVERT: N 38 ARG cc_start: 0.8999 (ptt180) cc_final: 0.8615 (ptt180) REVERT: N 95 TYR cc_start: 0.8699 (m-80) cc_final: 0.8457 (m-80) outliers start: 14 outliers final: 11 residues processed: 109 average time/residue: 1.0701 time to fit residues: 123.9997 Evaluate side-chains 113 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 0.0030 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.0070 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.2906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN N 31 ASN N 35 ASN N 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.141763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117837 restraints weight = 7720.400| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.46 r_work: 0.3247 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7222 Z= 0.124 Angle : 0.455 9.258 9827 Z= 0.250 Chirality : 0.039 0.154 1170 Planarity : 0.003 0.049 1225 Dihedral : 5.264 82.677 1050 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.89 % Allowed : 17.13 % Favored : 80.99 % 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: 1.59 (0.27), residues: 930 helix: 3.23 (0.26), residues: 347 sheet: 1.02 (0.34), residues: 209 loop : -1.14 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE R 165 TYR 0.011 0.001 TYR A 37 ARG 0.002 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 8 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 119 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.828 Fit side-chains REVERT: R 161 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7911 (mm) REVERT: B 219 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7651 (mtp180) REVERT: B 234 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8222 (t80) REVERT: N 95 TYR cc_start: 0.8608 (m-80) cc_final: 0.8393 (m-80) outliers start: 13 outliers final: 8 residues processed: 117 average time/residue: 0.9888 time to fit residues: 123.4485 Evaluate side-chains 113 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 SER 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 R residue 260 ILE Chi-restraints excluded: chain A residue 55 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 81 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3595 r_free = 0.3595 target = 0.138900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114974 restraints weight = 7807.840| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.42 r_work: 0.3213 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7222 Z= 0.186 Angle : 0.482 6.452 9827 Z= 0.266 Chirality : 0.041 0.162 1170 Planarity : 0.003 0.050 1225 Dihedral : 5.486 87.275 1050 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.03 % Allowed : 16.84 % Favored : 81.13 % 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: 1.56 (0.27), residues: 930 helix: 3.20 (0.25), residues: 346 sheet: 1.13 (0.34), residues: 211 loop : -1.24 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE R 165 TYR 0.014 0.001 TYR A 37 ARG 0.002 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 9 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 118 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.777 Fit side-chains REVERT: B 219 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7658 (mtp180) REVERT: B 234 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8262 (t80) REVERT: N 95 TYR cc_start: 0.8665 (m-80) cc_final: 0.8424 (m-80) outliers start: 14 outliers final: 10 residues processed: 115 average time/residue: 1.0640 time to fit residues: 130.4709 Evaluate side-chains 116 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 SER 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 R residue 260 ILE Chi-restraints excluded: chain A residue 55 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 25 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 0.0040 chunk 90 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3593 r_free = 0.3593 target = 0.138677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.114761 restraints weight = 7873.488| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.42 r_work: 0.3201 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7222 Z= 0.189 Angle : 0.502 10.126 9827 Z= 0.273 Chirality : 0.041 0.162 1170 Planarity : 0.003 0.050 1225 Dihedral : 5.567 89.232 1050 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.89 % Allowed : 17.13 % Favored : 80.99 % 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: 1.48 (0.27), residues: 930 helix: 3.05 (0.25), residues: 350 sheet: 1.12 (0.34), residues: 211 loop : -1.26 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE R 165 TYR 0.014 0.001 TYR A 37 ARG 0.002 0.000 ARG A 231 ********************** REFINEMENT MACRO_CYCLE 10 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 116 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.774 Fit side-chains REVERT: B 219 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7653 (mtp180) REVERT: B 234 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8283 (t80) REVERT: N 95 TYR cc_start: 0.8680 (m-80) cc_final: 0.8440 (m-80) outliers start: 13 outliers final: 10 residues processed: 112 average time/residue: 1.0234 time to fit residues: 122.4861 Evaluate side-chains 115 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 SER 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 R residue 260 ILE Chi-restraints excluded: chain A residue 55 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN 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 = 0.3588 r_free = 0.3588 target = 0.138252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114247 restraints weight = 7729.054| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.42 r_work: 0.3200 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7222 Z= 0.200 Angle : 0.498 6.507 9827 Z= 0.275 Chirality : 0.041 0.164 1170 Planarity : 0.003 0.050 1225 Dihedral : 5.579 87.793 1050 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.18 % Allowed : 16.40 % Favored : 81.42 % 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: 1.46 (0.27), residues: 930 helix: 3.10 (0.25), residues: 346 sheet: 1.07 (0.34), residues: 212 loop : -1.29 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.001 PHE R 165 TYR 0.013 0.001 TYR A 37 ARG 0.002 0.000 ARG N 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5115.29 seconds wall clock time: 87 minutes 49.18 seconds (5269.18 seconds total)