Starting phenix.real_space_refine on Mon May 12 04:39:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ucd_42124/05_2025/8ucd_42124.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ucd_42124/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ucd_42124/05_2025/8ucd_42124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ucd_42124/05_2025/8ucd_42124.map" model { file = "/net/cci-nas-00/data/ceres_data/8ucd_42124/05_2025/8ucd_42124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ucd_42124/05_2025/8ucd_42124.cif" } resolution = 3.0 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= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'ASN:plan1': 1, 'HIS:plan': 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, 'GLU:plan': 1, 'ARG: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: 6.34, per 1000 atoms: 0.79 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: 2.08 Conformation dependent library (CDL) restraints added in 810.5 milliseconds 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: 0.78 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: 2.10 Time building geometry restraints manager: 2.40 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: 5.800 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.340 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.420 ------------------------------------------------------------------------------- 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 : 4.36 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 (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: 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 TRP 0.012 0.001 TRP B 285 HIS 0.004 0.001 HIS A 268 PHE 0.011 0.001 PHE L 156 TYR 0.013 0.001 TYR A 219 ARG 0.001 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.16285 ( 451) hydrogen bonds : angle 5.28411 ( 1317) SS BOND : bond 0.00265 ( 2) SS BOND : angle 0.94542 ( 4) covalent geometry : bond 0.00662 ( 8324) covalent geometry : angle 0.86171 (11395) 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 : 0.807 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: 1.2714 time to fit residues: 109.3513 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 : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 83 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 = 0.133184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.106474 restraints weight = 9794.272| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.43 r_work: 0.3050 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1379 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 : 17.908 177.654 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 (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: 1.28 (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 TRP 0.015 0.002 TRP B 285 HIS 0.008 0.002 HIS B 268 PHE 0.013 0.001 PHE B 170 TYR 0.034 0.002 TYR B 219 ARG 0.003 0.000 ARG C 186 Details of bonding type rmsd hydrogen bonds : bond 0.07960 ( 451) hydrogen bonds : angle 3.53152 ( 1317) SS BOND : bond 0.00543 ( 2) SS BOND : angle 1.50920 ( 4) covalent geometry : bond 0.00412 ( 8324) covalent geometry : angle 0.71047 (11395) Misc. bond : bond 0.12027 ( 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 : 0.791 Fit side-chains REVERT: A 93 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7982 (mm-30) REVERT: B 198 GLN cc_start: 0.8226 (tt0) cc_final: 0.7666 (tt0) REVERT: B 206 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.7984 (t70) outliers start: 10 outliers final: 1 residues processed: 62 average time/residue: 1.1441 time to fit residues: 76.1127 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 : 0.788 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 1 optimal weight: 0.0670 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.133128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.106223 restraints weight = 10046.269| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.44 r_work: 0.3060 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 8329 Z= 0.149 Angle : 0.642 12.594 11399 Z= 0.295 Chirality : 0.041 0.145 1251 Planarity : 0.005 0.043 1317 Dihedral : 16.953 176.974 1260 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.81 % Allowed : 11.00 % Favored : 87.18 % 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: 1.40 (0.29), residues: 923 helix: 2.04 (0.23), residues: 582 sheet: 0.68 (0.50), residues: 116 loop : -2.02 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 285 HIS 0.007 0.001 HIS A 268 PHE 0.011 0.001 PHE B 170 TYR 0.028 0.002 TYR B 219 ARG 0.002 0.000 ARG C 186 Details of bonding type rmsd hydrogen bonds : bond 0.07107 ( 451) hydrogen bonds : angle 3.39797 ( 1317) SS BOND : bond 0.00383 ( 2) SS BOND : angle 1.04249 ( 4) covalent geometry : bond 0.00345 ( 8324) covalent geometry : angle 0.64214 (11395) Misc. bond : bond 0.13507 ( 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 78 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.774 Fit side-chains REVERT: A 93 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7668 (mm-30) REVERT: A 191 LYS cc_start: 0.7868 (mttt) cc_final: 0.7213 (mtpt) REVERT: B 198 GLN cc_start: 0.8205 (tt0) cc_final: 0.7643 (tt0) REVERT: B 233 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7162 (tp) REVERT: C 120 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7802 (ttt) outliers start: 15 outliers final: 4 residues processed: 69 average time/residue: 1.1390 time to fit residues: 84.0893 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 : 0.789 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 0.0270 chunk 84 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.133750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.106294 restraints weight = 9923.694| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.51 r_work: 0.3064 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1703 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= 0.142 Angle : 0.632 12.771 11399 Z= 0.289 Chirality : 0.041 0.151 1251 Planarity : 0.004 0.041 1317 Dihedral : 16.411 171.814 1260 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.18 % Allowed : 12.33 % 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 (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: 1.55 (0.29), residues: 923 helix: 2.20 (0.23), residues: 582 sheet: 0.61 (0.50), residues: 117 loop : -2.05 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 274 HIS 0.007 0.001 HIS A 268 PHE 0.011 0.001 PHE B 170 TYR 0.026 0.002 TYR A 219 ARG 0.002 0.000 ARG C 186 Details of bonding type rmsd hydrogen bonds : bond 0.06756 ( 451) hydrogen bonds : angle 3.34007 ( 1317) SS BOND : bond 0.00390 ( 2) SS BOND : angle 0.96930 ( 4) covalent geometry : bond 0.00327 ( 8324) covalent geometry : angle 0.63172 (11395) Misc. bond : bond 0.13152 ( 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 77 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.832 Fit side-chains REVERT: A 76 LYS cc_start: 0.7903 (ttmm) cc_final: 0.7439 (mttt) REVERT: A 93 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7428 (mm-30) REVERT: A 191 LYS cc_start: 0.7496 (mttt) cc_final: 0.6803 (mtpt) REVERT: B 198 GLN cc_start: 0.7898 (tt0) cc_final: 0.7262 (tt0) REVERT: B 206 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7715 (t70) REVERT: C 120 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7556 (ttt) outliers start: 18 outliers final: 5 residues processed: 67 average time/residue: 1.2081 time to fit residues: 86.5487 Evaluate side-chains 66 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 285 TRP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 B 202 GLN C 254 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.132371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.105471 restraints weight = 9850.362| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.43 r_work: 0.3023 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 8329 Z= 0.168 Angle : 0.679 13.985 11399 Z= 0.311 Chirality : 0.042 0.152 1251 Planarity : 0.005 0.041 1317 Dihedral : 16.140 169.291 1260 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.54 % Allowed : 12.94 % 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 (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: 1.39 (0.29), residues: 923 helix: 2.06 (0.23), residues: 581 sheet: 0.65 (0.49), residues: 117 loop : -2.11 (0.35), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 285 HIS 0.008 0.002 HIS A 268 PHE 0.013 0.001 PHE B 170 TYR 0.028 0.002 TYR B 219 ARG 0.003 0.000 ARG C 186 Details of bonding type rmsd hydrogen bonds : bond 0.07942 ( 451) hydrogen bonds : angle 3.44365 ( 1317) SS BOND : bond 0.00475 ( 2) SS BOND : angle 1.18504 ( 4) covalent geometry : bond 0.00399 ( 8324) covalent geometry : angle 0.67828 (11395) Misc. bond : bond 0.13477 ( 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 81 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.885 Fit side-chains REVERT: A 76 LYS cc_start: 0.7900 (ttmm) cc_final: 0.7470 (mttt) REVERT: A 93 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7504 (mm-30) REVERT: A 191 LYS cc_start: 0.7548 (mttt) cc_final: 0.6855 (mtpt) REVERT: B 198 GLN cc_start: 0.7935 (tt0) cc_final: 0.7398 (tt0) REVERT: B 206 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7734 (t70) REVERT: C 120 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7604 (ttt) REVERT: C 243 ASP cc_start: 0.8329 (m-30) cc_final: 0.8110 (m-30) outliers start: 21 outliers final: 7 residues processed: 72 average time/residue: 1.2021 time to fit residues: 92.5061 Evaluate side-chains 69 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 138 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.131611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104344 restraints weight = 9936.876| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.46 r_work: 0.3026 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 8329 Z= 0.153 Angle : 0.656 13.198 11399 Z= 0.298 Chirality : 0.041 0.146 1251 Planarity : 0.005 0.054 1317 Dihedral : 15.835 171.306 1260 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.06 % Allowed : 14.63 % 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 (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: 1.50 (0.29), residues: 923 helix: 2.15 (0.23), residues: 581 sheet: 0.74 (0.50), residues: 117 loop : -2.12 (0.35), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 274 HIS 0.008 0.001 HIS A 268 PHE 0.011 0.001 PHE B 170 TYR 0.026 0.002 TYR A 219 ARG 0.001 0.000 ARG L 145 Details of bonding type rmsd hydrogen bonds : bond 0.07255 ( 451) hydrogen bonds : angle 3.40065 ( 1317) SS BOND : bond 0.00409 ( 2) SS BOND : angle 0.95422 ( 4) covalent geometry : bond 0.00358 ( 8324) covalent geometry : angle 0.65634 (11395) Misc. bond : bond 0.13809 ( 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 75 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.812 Fit side-chains REVERT: A 76 LYS cc_start: 0.7901 (ttmm) cc_final: 0.7477 (mttt) REVERT: A 191 LYS cc_start: 0.7496 (mttt) cc_final: 0.6804 (mtpt) REVERT: B 198 GLN cc_start: 0.7921 (tt0) cc_final: 0.7273 (tt0) REVERT: C 120 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7570 (ttt) REVERT: H 113 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8114 (pt0) outliers start: 17 outliers final: 8 residues processed: 65 average time/residue: 1.2287 time to fit residues: 85.2476 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 : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN 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 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 Chi-restraints excluded: chain H residue 113 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 51 optimal weight: 0.0030 chunk 70 optimal weight: 0.0070 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.4008 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.134779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.106638 restraints weight = 9825.045| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.59 r_work: 0.3036 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1861 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= 0.127 Angle : 0.607 11.801 11399 Z= 0.275 Chirality : 0.040 0.148 1251 Planarity : 0.004 0.048 1317 Dihedral : 15.477 174.704 1260 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.81 % Allowed : 14.99 % Favored : 83.19 % 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: 1.72 (0.29), residues: 923 helix: 2.36 (0.23), residues: 581 sheet: 0.79 (0.50), residues: 118 loop : -2.12 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 274 HIS 0.006 0.001 HIS A 268 PHE 0.010 0.001 PHE B 170 TYR 0.024 0.001 TYR B 219 ARG 0.001 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.05961 ( 451) hydrogen bonds : angle 3.28179 ( 1317) SS BOND : bond 0.00340 ( 2) SS BOND : angle 0.65254 ( 4) covalent geometry : bond 0.00279 ( 8324) covalent geometry : angle 0.60718 (11395) Misc. bond : bond 0.13542 ( 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 74 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.874 Fit side-chains REVERT: A 191 LYS cc_start: 0.7202 (mttt) cc_final: 0.6513 (mtpt) REVERT: B 70 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7547 (pt0) REVERT: B 198 GLN cc_start: 0.7678 (tt0) cc_final: 0.7020 (tt0) REVERT: C 120 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7276 (ttt) REVERT: C 243 ASP cc_start: 0.8311 (m-30) cc_final: 0.8030 (m-30) outliers start: 15 outliers final: 5 residues processed: 66 average time/residue: 1.1995 time to fit residues: 84.6256 Evaluate side-chains 64 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 70 GLN 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 8 optimal weight: 0.0370 chunk 81 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.136216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.108643 restraints weight = 9953.998| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.54 r_work: 0.3048 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 8329 Z= 0.125 Angle : 0.603 11.796 11399 Z= 0.273 Chirality : 0.040 0.144 1251 Planarity : 0.004 0.044 1317 Dihedral : 15.291 178.381 1260 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.81 % Allowed : 15.36 % Favored : 82.83 % 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: 1.80 (0.29), residues: 923 helix: 2.42 (0.23), residues: 581 sheet: 0.86 (0.50), residues: 118 loop : -2.11 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 274 HIS 0.006 0.001 HIS A 268 PHE 0.010 0.001 PHE B 170 TYR 0.024 0.001 TYR A 219 ARG 0.001 0.000 ARG L 212 Details of bonding type rmsd hydrogen bonds : bond 0.05874 ( 451) hydrogen bonds : angle 3.22839 ( 1317) SS BOND : bond 0.00377 ( 2) SS BOND : angle 0.73602 ( 4) covalent geometry : bond 0.00279 ( 8324) covalent geometry : angle 0.60334 (11395) Misc. bond : bond 0.13146 ( 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 73 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.754 Fit side-chains REVERT: B 70 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7660 (pt0) REVERT: B 198 GLN cc_start: 0.7764 (tt0) cc_final: 0.7111 (tt0) REVERT: C 120 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7409 (ttt) REVERT: C 243 ASP cc_start: 0.8331 (m-30) cc_final: 0.8081 (m-30) outliers start: 15 outliers final: 5 residues processed: 66 average time/residue: 1.2259 time to fit residues: 86.4779 Evaluate side-chains 64 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 70 GLN 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 28 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.0870 chunk 5 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.136432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.109063 restraints weight = 10056.718| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.53 r_work: 0.3059 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 8329 Z= 0.127 Angle : 0.602 11.918 11399 Z= 0.273 Chirality : 0.040 0.150 1251 Planarity : 0.004 0.047 1317 Dihedral : 15.142 177.210 1260 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.69 % Allowed : 15.48 % Favored : 82.83 % 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: 1.80 (0.29), residues: 923 helix: 2.42 (0.23), residues: 581 sheet: 0.89 (0.50), residues: 118 loop : -2.11 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 274 HIS 0.006 0.001 HIS A 268 PHE 0.010 0.001 PHE B 170 TYR 0.024 0.001 TYR A 219 ARG 0.001 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.05954 ( 451) hydrogen bonds : angle 3.22704 ( 1317) SS BOND : bond 0.00387 ( 2) SS BOND : angle 0.78835 ( 4) covalent geometry : bond 0.00284 ( 8324) covalent geometry : angle 0.60163 (11395) Misc. bond : bond 0.13343 ( 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 71 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.793 Fit side-chains REVERT: B 70 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7733 (pt0) REVERT: B 198 GLN cc_start: 0.7896 (tt0) cc_final: 0.7255 (tt0) REVERT: C 120 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7505 (ttt) REVERT: C 243 ASP cc_start: 0.8472 (m-30) cc_final: 0.8222 (m-30) outliers start: 14 outliers final: 6 residues processed: 63 average time/residue: 1.2635 time to fit residues: 85.2802 Evaluate side-chains 64 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain B residue 70 GLN 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 2 VAL 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 49 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 chunk 83 optimal weight: 0.0870 chunk 81 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.134955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.107443 restraints weight = 9842.713| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.52 r_work: 0.3018 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 8329 Z= 0.134 Angle : 0.623 12.427 11399 Z= 0.281 Chirality : 0.040 0.151 1251 Planarity : 0.004 0.045 1317 Dihedral : 15.054 172.145 1260 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.09 % Allowed : 16.32 % Favored : 82.59 % 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: 1.77 (0.29), residues: 923 helix: 2.39 (0.23), residues: 581 sheet: 0.85 (0.50), residues: 118 loop : -2.11 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 274 HIS 0.007 0.001 HIS A 268 PHE 0.010 0.001 PHE B 170 TYR 0.026 0.001 TYR A 219 ARG 0.001 0.000 ARG L 212 Details of bonding type rmsd hydrogen bonds : bond 0.06360 ( 451) hydrogen bonds : angle 3.26138 ( 1317) SS BOND : bond 0.00401 ( 2) SS BOND : angle 0.86440 ( 4) covalent geometry : bond 0.00307 ( 8324) covalent geometry : angle 0.62274 (11395) Misc. bond : bond 0.13513 ( 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: 9 poor density : 57 time to evaluate : 0.766 Fit side-chains REVERT: B 70 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7625 (pt0) REVERT: B 198 GLN cc_start: 0.7740 (tt0) cc_final: 0.7131 (tt0) REVERT: C 120 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7400 (ttt) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 1.2587 time to fit residues: 81.9225 Evaluate side-chains 66 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 70 GLN 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 2 VAL 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 72 optimal weight: 4.9990 chunk 87 optimal weight: 0.0170 chunk 52 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 3 optimal weight: 0.1980 chunk 27 optimal weight: 0.0980 chunk 55 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 67 optimal weight: 0.0020 overall best weight: 0.1026 ------------------------------------------------------------------------------- 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 A 211 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.144638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117951 restraints weight = 9847.814| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.54 r_work: 0.3153 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 8329 Z= 0.104 Angle : 0.550 8.810 11399 Z= 0.251 Chirality : 0.039 0.149 1251 Planarity : 0.004 0.045 1317 Dihedral : 14.536 160.346 1260 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.97 % Allowed : 16.69 % Favored : 82.35 % 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: 2.02 (0.30), residues: 923 helix: 2.59 (0.23), residues: 582 sheet: 0.94 (0.51), residues: 118 loop : -2.04 (0.37), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 274 HIS 0.004 0.001 HIS A 268 PHE 0.009 0.001 PHE A 169 TYR 0.022 0.001 TYR B 219 ARG 0.001 0.000 ARG C 185 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 451) hydrogen bonds : angle 3.07154 ( 1317) SS BOND : bond 0.00259 ( 2) SS BOND : angle 0.41167 ( 4) covalent geometry : bond 0.00223 ( 8324) covalent geometry : angle 0.55032 (11395) Misc. bond : bond 0.11787 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5402.90 seconds wall clock time: 93 minutes 55.93 seconds (5635.93 seconds total)