Starting phenix.real_space_refine on Sat Aug 23 00:15:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ucd_42124/08_2025/8ucd_42124.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ucd_42124/08_2025/8ucd_42124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ucd_42124/08_2025/8ucd_42124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ucd_42124/08_2025/8ucd_42124.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ucd_42124/08_2025/8ucd_42124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ucd_42124/08_2025/8ucd_42124.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 3 7.16 5 P 9 5.49 5 S 22 5.16 5 C 5425 2.51 5 N 1252 2.21 5 O 1347 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8058 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1980 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1966 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 13, 'TRANS': 223} Chain breaks: 1 Chain: "C" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1969 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 12, 'TRANS': 224} Chain breaks: 1 Chain: "H" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "A" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 190 Unusual residues: {'FAD': 1, 'HEM': 1, 'LBN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FAD:plan-1': 1, 'FAD:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'FAD': 1, 'HEM': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'FAD:plan-1': 1, 'FAD:plan-3': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'FAD': 1, 'HEM': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'FAD:plan-1': 1, 'FAD:plan-3': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 1.95, per 1000 atoms: 0.24 Number of scatterers: 8058 At special positions: 0 Unit cell: (104.92, 88.58, 126.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 3 26.01 S 22 16.00 P 9 15.00 O 1347 8.00 N 1252 7.00 C 5425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 144 " - pdb=" SG CYS L 208 " 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 254.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 5 sheets defined 63.7% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 71 through 94 removed outlier: 4.005A pdb=" N ILE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.863A pdb=" N LYS A 108 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 109 " --> pdb=" O PHE A 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 105 through 109' Processing helix chain 'A' and resid 113 through 116 Processing helix chain 'A' and resid 117 through 142 removed outlier: 3.657A pdb=" N TYR A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 160 through 180 Processing helix chain 'A' and resid 185 through 202 removed outlier: 3.832A pdb=" N ARG A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 236 removed outlier: 3.924A pdb=" N VAL A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 246 through 273 removed outlier: 3.732A pdb=" N LEU A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.966A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.640A pdb=" N ILE A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 94 Processing helix chain 'B' and resid 94 through 100 Processing helix chain 'B' and resid 113 through 116 Processing helix chain 'B' and resid 117 through 141 removed outlier: 4.094A pdb=" N TYR B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Proline residue: B 132 - end of helix Processing helix chain 'B' and resid 151 through 159 Processing helix chain 'B' and resid 160 through 180 Processing helix chain 'B' and resid 185 through 202 removed outlier: 3.719A pdb=" N ARG B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 236 removed outlier: 3.980A pdb=" N VAL B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.626A pdb=" N ASP B 243 " --> pdb=" O PRO B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 273 removed outlier: 3.714A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.839A pdb=" N ILE B 278 " --> pdb=" O ASN B 275 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP B 279 " --> pdb=" O LYS B 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 275 through 279' Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.700A pdb=" N ILE B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 310 removed outlier: 3.900A pdb=" N ILE B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 71 through 94 removed outlier: 3.605A pdb=" N ILE C 75 " --> pdb=" O TRP C 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS C 76 " --> pdb=" O HIS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 100 Processing helix chain 'C' and resid 113 through 116 Processing helix chain 'C' and resid 117 through 142 removed outlier: 3.511A pdb=" N VAL C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Proline residue: C 132 - end of helix removed outlier: 3.526A pdb=" N ILE C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 159 Processing helix chain 'C' and resid 160 through 181 removed outlier: 3.666A pdb=" N SER C 181 " --> pdb=" O ILE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 185 through 201 removed outlier: 3.670A pdb=" N ARG C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 236 removed outlier: 3.568A pdb=" N TRP C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL C 220 " --> pdb=" O MET C 216 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER C 221 " --> pdb=" O GLU C 217 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 222 " --> pdb=" O ILE C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.689A pdb=" N ASP C 243 " --> pdb=" O PRO C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 273 removed outlier: 3.616A pdb=" N LEU C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.832A pdb=" N ILE C 293 " --> pdb=" O PRO C 289 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 295 " --> pdb=" O PHE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 310 removed outlier: 3.749A pdb=" N ILE C 299 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.654A pdb=" N ILE H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA4, first strand: chain 'L' and resid 126 through 127 removed outlier: 3.832A pdb=" N TYR L 191 " --> pdb=" O CYS L 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 131 through 133 removed outlier: 5.962A pdb=" N LEU L 132 " --> pdb=" O GLU L 225 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR L 206 " --> pdb=" O THR L 222 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP L 155 " --> pdb=" O LEU L 167 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1317 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: 1.26 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 2315 1.36 - 1.53: 5494 1.53 - 1.71: 463 1.71 - 1.88: 40 1.88 - 2.06: 12 Bond restraints: 8324 Sorted by residual: bond pdb=" C25 LBN A 403 " pdb=" O5 LBN A 403 " ideal model delta sigma weight residual 1.326 1.434 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C25 LBN B 401 " pdb=" O5 LBN B 401 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C25 LBN A 401 " pdb=" O5 LBN A 401 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C41 LBN A 403 " pdb=" C42 LBN A 403 " ideal model delta sigma weight residual 1.497 1.573 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C41 LBN B 401 " pdb=" C42 LBN B 401 " ideal model delta sigma weight residual 1.497 1.573 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 8319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 11200 3.30 - 6.60: 167 6.60 - 9.90: 22 9.90 - 13.19: 3 13.19 - 16.49: 3 Bond angle restraints: 11395 Sorted by residual: angle pdb=" O1 LBN A 401 " pdb=" P1 LBN A 401 " pdb=" O2 LBN A 401 " ideal model delta sigma weight residual 93.45 109.94 -16.49 3.00e+00 1.11e-01 3.02e+01 angle pdb=" O1 LBN B 401 " pdb=" P1 LBN B 401 " pdb=" O2 LBN B 401 " ideal model delta sigma weight residual 93.45 109.71 -16.26 3.00e+00 1.11e-01 2.94e+01 angle pdb=" O1 LBN A 403 " pdb=" P1 LBN A 403 " pdb=" O2 LBN A 403 " ideal model delta sigma weight residual 93.45 109.40 -15.95 3.00e+00 1.11e-01 2.83e+01 angle pdb=" O3 LBN A 401 " pdb=" P1 LBN A 401 " pdb=" O4 LBN A 401 " ideal model delta sigma weight residual 119.36 109.27 10.09 3.00e+00 1.11e-01 1.13e+01 angle pdb=" O3 LBN A 403 " pdb=" P1 LBN A 403 " pdb=" O4 LBN A 403 " ideal model delta sigma weight residual 119.36 109.45 9.91 3.00e+00 1.11e-01 1.09e+01 ... (remaining 11390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 4663 35.85 - 71.70: 119 71.70 - 107.55: 11 107.55 - 143.39: 7 143.39 - 179.24: 4 Dihedral angle restraints: 4804 sinusoidal: 2023 harmonic: 2781 Sorted by residual: dihedral pdb=" C40 LBN A 403 " pdb=" C41 LBN A 403 " pdb=" C42 LBN A 403 " pdb=" C5 LBN A 403 " ideal model delta sinusoidal sigma weight residual 117.80 -62.96 -179.24 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5' FAD C 401 " pdb=" O3P FAD C 401 " pdb=" P FAD C 401 " pdb=" PA FAD C 401 " ideal model delta sinusoidal sigma weight residual 298.23 131.51 166.72 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" N1 LBN A 403 " pdb=" C6 LBN A 403 " pdb=" C9 LBN A 403 " pdb=" O2 LBN A 403 " ideal model delta sinusoidal sigma weight residual 71.48 -131.23 -157.29 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 4801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 857 0.036 - 0.072: 298 0.072 - 0.108: 69 0.108 - 0.144: 24 0.144 - 0.180: 3 Chirality restraints: 1251 Sorted by residual: chirality pdb=" C2 LBN A 401 " pdb=" C1 LBN A 401 " pdb=" C3 LBN A 401 " pdb=" O7 LBN A 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.55 0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" C2 LBN B 401 " pdb=" C1 LBN B 401 " pdb=" C3 LBN B 401 " pdb=" O7 LBN B 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.52 0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" C2 LBN A 403 " pdb=" C1 LBN A 403 " pdb=" C3 LBN A 403 " pdb=" O7 LBN A 403 " both_signs ideal model delta sigma weight residual False -2.36 -2.52 0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 1248 not shown) Planarity restraints: 1317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP C 247 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C TRP C 247 " -0.039 2.00e-02 2.50e+03 pdb=" O TRP C 247 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG C 248 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 109 " -0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO C 110 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 135 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO L 136 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO L 136 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 136 " -0.021 5.00e-02 4.00e+02 ... (remaining 1314 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 186 2.72 - 3.26: 7528 3.26 - 3.81: 12340 3.81 - 4.35: 14906 4.35 - 4.90: 26793 Nonbonded interactions: 61753 Sorted by model distance: nonbonded pdb=" O2' FAD A 402 " pdb=" O4' FAD A 402 " model vdw 2.171 3.040 nonbonded pdb=" NE1 TRP B 71 " pdb=" O4 LBN B 401 " model vdw 2.313 3.120 nonbonded pdb=" O SER H 30 " pdb=" OG SER H 30 " model vdw 2.319 3.040 nonbonded pdb=" NE2 GLN B 70 " pdb=" O3 LBN B 401 " model vdw 2.326 3.120 nonbonded pdb=" ND2 ASN B 115 " pdb=" OH TYR B 182 " model vdw 2.346 3.120 ... (remaining 61748 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 67 through 141 or resid 150 through 310)) selection = (chain 'B' and (resid 67 through 309 or (resid 310 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'C' and (resid 67 through 141 or resid 150 through 309 or (resid 310 and \ (name N or name CA or name C or name O or name CB )))) } 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: 6.800 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.500 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.007 0.162 8329 Z= 0.330 Angle : 0.862 16.493 11399 Z= 0.356 Chirality : 0.041 0.180 1251 Planarity : 0.004 0.040 1317 Dihedral : 17.938 179.242 2998 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.12 % Allowed : 0.12 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.30), residues: 923 helix: 1.57 (0.24), residues: 578 sheet: 1.00 (0.52), residues: 111 loop : -1.95 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 TYR 0.013 0.001 TYR A 219 PHE 0.011 0.001 PHE L 156 TRP 0.012 0.001 TRP B 285 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00662 ( 8324) covalent geometry : angle 0.86171 (11395) SS BOND : bond 0.00265 ( 2) SS BOND : angle 0.94542 ( 4) hydrogen bonds : bond 0.16285 ( 451) hydrogen bonds : angle 5.28411 ( 1317) Misc. bond : bond 0.14290 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.312 Fit side-chains REVERT: B 198 GLN cc_start: 0.7657 (tt0) cc_final: 0.7306 (tt0) REVERT: L 134 LEU cc_start: 0.7762 (tp) cc_final: 0.7504 (tp) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.5968 time to fit residues: 51.2199 Evaluate side-chains 60 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 251 HIS B 202 GLN B 254 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.106378 restraints weight = 9977.397| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.44 r_work: 0.3075 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.148 8329 Z= 0.174 Angle : 0.711 14.191 11399 Z= 0.327 Chirality : 0.044 0.153 1251 Planarity : 0.005 0.047 1317 Dihedral : 17.907 177.657 1260 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.21 % Allowed : 8.22 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.29), residues: 923 helix: 1.89 (0.23), residues: 583 sheet: 0.64 (0.50), residues: 117 loop : -1.91 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 186 TYR 0.034 0.002 TYR B 219 PHE 0.013 0.001 PHE B 170 TRP 0.015 0.002 TRP B 285 HIS 0.008 0.002 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8324) covalent geometry : angle 0.71058 (11395) SS BOND : bond 0.00544 ( 2) SS BOND : angle 1.51025 ( 4) hydrogen bonds : bond 0.07960 ( 451) hydrogen bonds : angle 3.53156 ( 1317) Misc. bond : bond 0.12028 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.237 Fit side-chains REVERT: A 93 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7986 (mm-30) REVERT: B 198 GLN cc_start: 0.8231 (tt0) cc_final: 0.7672 (tt0) REVERT: B 206 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.7989 (t70) outliers start: 10 outliers final: 1 residues processed: 62 average time/residue: 0.5363 time to fit residues: 35.4829 Evaluate side-chains 59 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 278 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN C 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.106456 restraints weight = 9879.556| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.51 r_work: 0.3075 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 8329 Z= 0.142 Angle : 0.630 12.309 11399 Z= 0.289 Chirality : 0.041 0.147 1251 Planarity : 0.004 0.041 1317 Dihedral : 16.952 177.622 1260 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.69 % Allowed : 10.88 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.29), residues: 923 helix: 2.09 (0.23), residues: 582 sheet: 0.71 (0.50), residues: 116 loop : -2.00 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 186 TYR 0.028 0.002 TYR B 219 PHE 0.011 0.001 PHE B 170 TRP 0.012 0.001 TRP B 285 HIS 0.006 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8324) covalent geometry : angle 0.62987 (11395) SS BOND : bond 0.00392 ( 2) SS BOND : angle 0.96981 ( 4) hydrogen bonds : bond 0.06803 ( 451) hydrogen bonds : angle 3.37099 ( 1317) Misc. bond : bond 0.13472 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.302 Fit side-chains REVERT: A 93 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7625 (mm-30) REVERT: A 191 LYS cc_start: 0.7745 (mttt) cc_final: 0.7085 (mtpt) REVERT: B 198 GLN cc_start: 0.8142 (tt0) cc_final: 0.7533 (tt0) REVERT: B 233 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.7024 (tp) REVERT: C 120 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7732 (ttt) outliers start: 14 outliers final: 3 residues processed: 70 average time/residue: 0.5401 time to fit residues: 40.2823 Evaluate side-chains 65 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 120 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 81 optimal weight: 2.9990 chunk 44 optimal weight: 0.0570 chunk 66 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 0.0570 chunk 13 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109956 restraints weight = 9990.928| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.52 r_work: 0.3052 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 8329 Z= 0.127 Angle : 0.601 11.839 11399 Z= 0.275 Chirality : 0.040 0.154 1251 Planarity : 0.004 0.038 1317 Dihedral : 16.297 170.298 1260 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.69 % Allowed : 12.70 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.29), residues: 923 helix: 2.32 (0.23), residues: 582 sheet: 0.84 (0.51), residues: 112 loop : -2.03 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 186 TYR 0.025 0.001 TYR B 219 PHE 0.010 0.001 PHE B 170 TRP 0.010 0.001 TRP C 274 HIS 0.006 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8324) covalent geometry : angle 0.60138 (11395) SS BOND : bond 0.00350 ( 2) SS BOND : angle 0.83044 ( 4) hydrogen bonds : bond 0.05964 ( 451) hydrogen bonds : angle 3.25710 ( 1317) Misc. bond : bond 0.12850 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.182 Fit side-chains REVERT: A 76 LYS cc_start: 0.7770 (ttmm) cc_final: 0.7264 (mttt) REVERT: B 198 GLN cc_start: 0.7792 (tt0) cc_final: 0.7111 (tt0) REVERT: C 120 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7372 (ttt) REVERT: C 243 ASP cc_start: 0.8417 (m-30) cc_final: 0.8129 (m-30) outliers start: 14 outliers final: 4 residues processed: 63 average time/residue: 0.5491 time to fit residues: 36.8970 Evaluate side-chains 62 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 120 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.133083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.105951 restraints weight = 9935.641| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.45 r_work: 0.3039 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 8329 Z= 0.163 Angle : 0.664 13.634 11399 Z= 0.303 Chirality : 0.042 0.150 1251 Planarity : 0.005 0.039 1317 Dihedral : 16.102 169.700 1260 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.93 % Allowed : 12.58 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.29), residues: 923 helix: 2.18 (0.23), residues: 582 sheet: 0.89 (0.51), residues: 112 loop : -2.12 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 186 TYR 0.028 0.002 TYR A 219 PHE 0.013 0.001 PHE B 170 TRP 0.012 0.001 TRP B 285 HIS 0.008 0.002 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8324) covalent geometry : angle 0.66353 (11395) SS BOND : bond 0.00481 ( 2) SS BOND : angle 1.16148 ( 4) hydrogen bonds : bond 0.07549 ( 451) hydrogen bonds : angle 3.37999 ( 1317) Misc. bond : bond 0.13301 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.306 Fit side-chains REVERT: A 76 LYS cc_start: 0.7905 (ttmm) cc_final: 0.7462 (mttt) REVERT: A 191 LYS cc_start: 0.7508 (mttt) cc_final: 0.6811 (mtpt) REVERT: B 198 GLN cc_start: 0.7914 (tt0) cc_final: 0.7252 (tt0) REVERT: B 206 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7734 (t70) REVERT: C 120 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7598 (ttt) outliers start: 16 outliers final: 4 residues processed: 66 average time/residue: 0.5906 time to fit residues: 41.5538 Evaluate side-chains 65 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 120 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 46 optimal weight: 0.0670 chunk 81 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 91 optimal weight: 0.0970 chunk 68 optimal weight: 0.4980 chunk 45 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.136984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108885 restraints weight = 9882.705| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.59 r_work: 0.3068 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 8329 Z= 0.119 Angle : 0.590 11.000 11399 Z= 0.267 Chirality : 0.040 0.144 1251 Planarity : 0.004 0.036 1317 Dihedral : 15.500 171.309 1260 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.57 % Allowed : 13.91 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.29), residues: 923 helix: 2.44 (0.23), residues: 583 sheet: 0.93 (0.51), residues: 112 loop : -2.02 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 212 TYR 0.022 0.001 TYR B 219 PHE 0.008 0.001 PHE B 170 TRP 0.010 0.001 TRP C 274 HIS 0.005 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8324) covalent geometry : angle 0.59028 (11395) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.51957 ( 4) hydrogen bonds : bond 0.05365 ( 451) hydrogen bonds : angle 3.21314 ( 1317) Misc. bond : bond 0.13932 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.392 Fit side-chains REVERT: B 198 GLN cc_start: 0.7677 (tt0) cc_final: 0.6976 (tt0) REVERT: C 120 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7189 (ttt) outliers start: 13 outliers final: 5 residues processed: 63 average time/residue: 0.5833 time to fit residues: 39.3118 Evaluate side-chains 61 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 120 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 70 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.137017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110207 restraints weight = 9807.884| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.47 r_work: 0.3031 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 8329 Z= 0.144 Angle : 0.640 12.930 11399 Z= 0.289 Chirality : 0.041 0.151 1251 Planarity : 0.004 0.036 1317 Dihedral : 15.483 173.263 1260 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.93 % Allowed : 13.78 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.29), residues: 923 helix: 2.34 (0.23), residues: 582 sheet: 0.78 (0.50), residues: 118 loop : -2.05 (0.36), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 181 TYR 0.026 0.002 TYR A 219 PHE 0.011 0.001 PHE B 170 TRP 0.010 0.001 TRP C 274 HIS 0.007 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8324) covalent geometry : angle 0.63958 (11395) SS BOND : bond 0.00457 ( 2) SS BOND : angle 1.01513 ( 4) hydrogen bonds : bond 0.06859 ( 451) hydrogen bonds : angle 3.29414 ( 1317) Misc. bond : bond 0.13184 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.308 Fit side-chains REVERT: B 70 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7623 (pt0) REVERT: B 198 GLN cc_start: 0.7760 (tt0) cc_final: 0.7107 (tt0) REVERT: B 206 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7651 (t70) REVERT: C 120 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7438 (ttt) outliers start: 16 outliers final: 7 residues processed: 63 average time/residue: 0.6146 time to fit residues: 41.2483 Evaluate side-chains 68 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 55 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 1 optimal weight: 0.0770 chunk 78 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 69 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.135091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.107649 restraints weight = 9882.823| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.51 r_work: 0.3029 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 8329 Z= 0.138 Angle : 0.624 12.435 11399 Z= 0.283 Chirality : 0.041 0.149 1251 Planarity : 0.005 0.055 1317 Dihedral : 15.370 176.103 1260 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.69 % Allowed : 14.51 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.29), residues: 923 helix: 2.35 (0.23), residues: 582 sheet: 0.81 (0.51), residues: 118 loop : -2.07 (0.36), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 139 TYR 0.026 0.001 TYR A 219 PHE 0.012 0.001 PHE B 170 TRP 0.011 0.001 TRP C 274 HIS 0.007 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8324) covalent geometry : angle 0.62415 (11395) SS BOND : bond 0.00386 ( 2) SS BOND : angle 0.86564 ( 4) hydrogen bonds : bond 0.06523 ( 451) hydrogen bonds : angle 3.28648 ( 1317) Misc. bond : bond 0.13758 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.312 Fit side-chains REVERT: A 191 LYS cc_start: 0.7309 (mttt) cc_final: 0.6624 (mtpt) REVERT: B 70 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7639 (pt0) REVERT: B 198 GLN cc_start: 0.7785 (tt0) cc_final: 0.7175 (tt0) REVERT: B 206 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7653 (t70) REVERT: C 120 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7426 (ttt) outliers start: 14 outliers final: 8 residues processed: 64 average time/residue: 0.5957 time to fit residues: 40.7173 Evaluate side-chains 68 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 85 optimal weight: 0.5980 chunk 22 optimal weight: 0.0570 chunk 42 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.106203 restraints weight = 9954.188| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.46 r_work: 0.3040 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 8329 Z= 0.141 Angle : 0.630 12.700 11399 Z= 0.286 Chirality : 0.041 0.148 1251 Planarity : 0.005 0.056 1317 Dihedral : 15.358 179.542 1260 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.57 % Allowed : 14.87 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.29), residues: 923 helix: 2.33 (0.23), residues: 582 sheet: 0.82 (0.51), residues: 118 loop : -2.06 (0.36), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 186 TYR 0.026 0.001 TYR A 219 PHE 0.011 0.001 PHE B 170 TRP 0.011 0.001 TRP C 274 HIS 0.007 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8324) covalent geometry : angle 0.63030 (11395) SS BOND : bond 0.00409 ( 2) SS BOND : angle 0.88336 ( 4) hydrogen bonds : bond 0.06687 ( 451) hydrogen bonds : angle 3.29421 ( 1317) Misc. bond : bond 0.13481 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.311 Fit side-chains REVERT: A 191 LYS cc_start: 0.7351 (mttt) cc_final: 0.6659 (mtpt) REVERT: B 70 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7643 (pt0) REVERT: B 198 GLN cc_start: 0.7787 (tt0) cc_final: 0.7191 (tt0) REVERT: B 206 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7658 (t70) REVERT: C 120 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7466 (ttt) outliers start: 13 outliers final: 7 residues processed: 61 average time/residue: 0.5944 time to fit residues: 38.7115 Evaluate side-chains 66 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 0.0770 chunk 21 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 chunk 27 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.109686 restraints weight = 9800.618| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.52 r_work: 0.3073 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 8329 Z= 0.121 Angle : 0.592 11.245 11399 Z= 0.269 Chirality : 0.040 0.148 1251 Planarity : 0.004 0.049 1317 Dihedral : 15.102 173.139 1260 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.97 % Allowed : 15.72 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.29), residues: 923 helix: 2.49 (0.23), residues: 581 sheet: 0.89 (0.51), residues: 118 loop : -2.05 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 161 TYR 0.023 0.001 TYR A 219 PHE 0.010 0.001 PHE B 170 TRP 0.012 0.001 TRP C 274 HIS 0.006 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8324) covalent geometry : angle 0.59184 (11395) SS BOND : bond 0.00340 ( 2) SS BOND : angle 0.65431 ( 4) hydrogen bonds : bond 0.05603 ( 451) hydrogen bonds : angle 3.20960 ( 1317) Misc. bond : bond 0.13594 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.219 Fit side-chains REVERT: B 198 GLN cc_start: 0.7864 (tt0) cc_final: 0.7242 (tt0) REVERT: B 206 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7678 (t70) REVERT: C 120 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7476 (ttt) outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 0.5009 time to fit residues: 32.5446 Evaluate side-chains 63 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 7 optimal weight: 0.0980 chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.134290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.106744 restraints weight = 9933.211| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.53 r_work: 0.3032 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 8329 Z= 0.140 Angle : 0.627 12.699 11399 Z= 0.284 Chirality : 0.041 0.151 1251 Planarity : 0.005 0.053 1317 Dihedral : 15.062 169.207 1260 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.09 % Allowed : 15.60 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.29), residues: 923 helix: 2.38 (0.23), residues: 582 sheet: 0.84 (0.50), residues: 118 loop : -2.03 (0.36), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 186 TYR 0.026 0.001 TYR A 219 PHE 0.011 0.001 PHE B 170 TRP 0.011 0.001 TRP C 274 HIS 0.007 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8324) covalent geometry : angle 0.62730 (11395) SS BOND : bond 0.00411 ( 2) SS BOND : angle 0.91815 ( 4) hydrogen bonds : bond 0.06594 ( 451) hydrogen bonds : angle 3.27123 ( 1317) Misc. bond : bond 0.13377 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2649.99 seconds wall clock time: 45 minutes 50.52 seconds (2750.52 seconds total)