Starting phenix.real_space_refine on Thu Mar 13 07:39:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ucd_42124/03_2025/8ucd_42124.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ucd_42124/03_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_42124/03_2025/8ucd_42124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ucd_42124/03_2025/8ucd_42124.map" model { file = "/net/cci-nas-00/data/ceres_data/8ucd_42124/03_2025/8ucd_42124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ucd_42124/03_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-5624/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: 6.67, per 1000 atoms: 0.83 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: 2.18 Conformation dependent library (CDL) restraints added in 929.6 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: 0.97 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: 2.21 Time building geometry restraints manager: 2.56 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: 6.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.510 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.940 ------------------------------------------------------------------------------- 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 0.108 8324 Z= 0.428 Angle : 0.862 16.493 11395 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 *********************** 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 : 0.896 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: 1.2969 time to fit residues: 111.6068 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 : 0.831 ------------------------------------------------------------------------------- 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 = 0.133189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.106484 restraints weight = 9794.599| |-----------------------------------------------------------------------------| 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: 0.2927 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.004 0.054 8324 Z= 0.266 Angle : 0.710 14.191 11395 Z= 0.326 Chirality : 0.044 0.153 1251 Planarity : 0.005 0.047 1317 Dihedral : 17.908 177.657 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 (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 *********************** 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 : 0.940 Fit side-chains REVERT: A 93 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7981 (mm-30) REVERT: B 198 GLN cc_start: 0.8227 (tt0) cc_final: 0.7667 (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: 1.2292 time to fit residues: 81.5219 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 : 0.812 ------------------------------------------------------------------------------- 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: 0.5980 chunk 63 optimal weight: 0.5980 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: 0.0980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.133280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.106402 restraints weight = 10047.468| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.44 r_work: 0.3053 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8324 Z= 0.221 Angle : 0.640 12.582 11395 Z= 0.294 Chirality : 0.041 0.147 1251 Planarity : 0.005 0.043 1317 Dihedral : 16.965 177.105 1260 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.81 % Allowed : 11.12 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.29), residues: 923 helix: 2.05 (0.23), residues: 582 sheet: 0.68 (0.50), residues: 116 loop : -2.01 (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 *********************** 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 80 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.777 Fit side-chains REVERT: A 93 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7668 (mm-30) REVERT: A 191 LYS cc_start: 0.7854 (mttt) cc_final: 0.7210 (mtpt) REVERT: B 198 GLN cc_start: 0.8206 (tt0) cc_final: 0.7610 (tt0) REVERT: B 233 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7148 (tp) REVERT: C 120 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7797 (ttt) outliers start: 15 outliers final: 4 residues processed: 71 average time/residue: 1.1719 time to fit residues: 88.9784 Evaluate side-chains 66 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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: 0.6980 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 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 B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.105659 restraints weight = 9918.189| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.51 r_work: 0.3054 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.003 0.058 8324 Z= 0.217 Angle : 0.638 12.955 11395 Z= 0.292 Chirality : 0.041 0.149 1251 Planarity : 0.004 0.041 1317 Dihedral : 16.521 170.634 1260 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.44 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: 1.52 (0.29), residues: 923 helix: 2.18 (0.23), residues: 582 sheet: 0.62 (0.50), residues: 117 loop : -2.06 (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 0.027 0.002 TYR B 219 ARG 0.002 0.000 ARG C 186 *********************** 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 76 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.882 Fit side-chains REVERT: A 76 LYS cc_start: 0.7900 (ttmm) cc_final: 0.7448 (mttt) REVERT: A 93 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7501 (mm-30) REVERT: A 191 LYS cc_start: 0.7511 (mttt) cc_final: 0.6817 (mtpt) REVERT: B 198 GLN cc_start: 0.7921 (tt0) cc_final: 0.7286 (tt0) REVERT: B 206 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7733 (t70) REVERT: C 120 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7584 (ttt) outliers start: 18 outliers final: 5 residues processed: 66 average time/residue: 1.2121 time to fit residues: 85.4127 Evaluate side-chains 65 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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: 0.8980 chunk 85 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.132403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.104972 restraints weight = 9875.128| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.49 r_work: 0.3005 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 0.059 8324 Z= 0.249 Angle : 0.667 13.639 11395 Z= 0.305 Chirality : 0.042 0.149 1251 Planarity : 0.005 0.041 1317 Dihedral : 16.166 169.011 1260 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.42 % Allowed : 12.82 % Favored : 84.76 % 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: 1.43 (0.29), residues: 923 helix: 2.10 (0.23), residues: 581 sheet: 0.69 (0.50), residues: 117 loop : -2.12 (0.36), 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 0.027 0.002 TYR A 219 ARG 0.003 0.000 ARG C 186 *********************** 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 79 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.819 Fit side-chains REVERT: A 76 LYS cc_start: 0.7885 (ttmm) cc_final: 0.7454 (mttt) REVERT: A 93 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7475 (mm-30) REVERT: A 191 LYS cc_start: 0.7522 (mttt) cc_final: 0.6830 (mtpt) REVERT: B 198 GLN cc_start: 0.7932 (tt0) cc_final: 0.7283 (tt0) REVERT: B 206 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7761 (t70) REVERT: C 120 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7603 (ttt) outliers start: 20 outliers final: 7 residues processed: 70 average time/residue: 1.2099 time to fit residues: 90.5486 Evaluate side-chains 68 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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: 0.6980 chunk 13 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 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 = 0.3483 r_free = 0.3483 target = 0.132988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.105501 restraints weight = 9859.616| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.50 r_work: 0.3037 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8324 Z= 0.231 Angle : 0.656 13.200 11395 Z= 0.297 Chirality : 0.041 0.146 1251 Planarity : 0.005 0.056 1317 Dihedral : 15.894 170.707 1260 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.06 % Allowed : 14.03 % Favored : 83.92 % 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: 1.51 (0.29), residues: 923 helix: 2.16 (0.23), residues: 581 sheet: 0.91 (0.51), residues: 112 loop : -2.13 (0.35), residues: 230 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 0.012 0.001 PHE B 170 TYR 0.026 0.002 TYR A 219 ARG 0.001 0.000 ARG L 212 *********************** 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 : 0.817 Fit side-chains REVERT: A 76 LYS cc_start: 0.7909 (ttmm) cc_final: 0.7482 (mttt) REVERT: A 191 LYS cc_start: 0.7502 (mttt) cc_final: 0.6808 (mtpt) REVERT: B 198 GLN cc_start: 0.7915 (tt0) cc_final: 0.7268 (tt0) REVERT: C 120 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7588 (ttt) outliers start: 17 outliers final: 8 residues processed: 66 average time/residue: 1.2320 time to fit residues: 86.8481 Evaluate side-chains 67 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 51 optimal weight: 0.0470 chunk 70 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.135878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.108808 restraints weight = 9759.509| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.50 r_work: 0.3030 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8324 Z= 0.194 Angle : 0.618 12.247 11395 Z= 0.280 Chirality : 0.040 0.152 1251 Planarity : 0.005 0.049 1317 Dihedral : 15.522 174.232 1260 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % 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: 1.66 (0.29), residues: 923 helix: 2.29 (0.23), residues: 582 sheet: 0.75 (0.50), residues: 118 loop : -2.10 (0.36), residues: 223 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 0.024 0.001 TYR A 219 ARG 0.001 0.000 ARG A 92 *********************** 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: 15 poor density : 58 time to evaluate : 0.871 Fit side-chains REVERT: A 191 LYS cc_start: 0.7329 (mttt) cc_final: 0.6639 (mtpt) REVERT: B 70 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7626 (pt0) REVERT: B 198 GLN cc_start: 0.7805 (tt0) cc_final: 0.7184 (tt0) REVERT: C 120 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7406 (ttt) REVERT: C 243 ASP cc_start: 0.8182 (m-30) cc_final: 0.7961 (m-30) outliers start: 15 outliers final: 6 residues processed: 65 average time/residue: 1.2346 time to fit residues: 86.4004 Evaluate side-chains 65 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.1980 chunk 81 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.134575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.106892 restraints weight = 9967.595| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.54 r_work: 0.3017 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8324 Z= 0.191 Angle : 0.616 12.309 11395 Z= 0.279 Chirality : 0.040 0.147 1251 Planarity : 0.004 0.045 1317 Dihedral : 15.347 178.166 1260 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.45 % Allowed : 15.72 % 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: 1.71 (0.29), residues: 923 helix: 2.34 (0.23), residues: 582 sheet: 0.80 (0.50), residues: 118 loop : -2.10 (0.36), residues: 223 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 0.011 0.001 PHE B 170 TYR 0.025 0.001 TYR A 219 ARG 0.001 0.000 ARG C 215 *********************** 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 71 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.928 Fit side-chains REVERT: B 70 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7623 (pt0) REVERT: B 198 GLN cc_start: 0.7771 (tt0) cc_final: 0.7156 (tt0) REVERT: C 120 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7406 (ttt) outliers start: 12 outliers final: 7 residues processed: 64 average time/residue: 1.8451 time to fit residues: 126.6798 Evaluate side-chains 67 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 2.108 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.131459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.104146 restraints weight = 10108.190| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.47 r_work: 0.2973 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8324 Z= 0.254 Angle : 0.670 13.742 11395 Z= 0.304 Chirality : 0.042 0.153 1251 Planarity : 0.005 0.048 1317 Dihedral : 15.458 178.971 1260 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.81 % Allowed : 15.72 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.29), residues: 923 helix: 2.15 (0.23), residues: 581 sheet: 0.72 (0.50), residues: 118 loop : -2.09 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 274 HIS 0.008 0.002 HIS A 268 PHE 0.012 0.001 PHE B 170 TYR 0.028 0.002 TYR A 219 ARG 0.001 0.000 ARG C 186 *********************** 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 74 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.870 Fit side-chains REVERT: A 76 LYS cc_start: 0.7769 (ttmm) cc_final: 0.7354 (mttt) REVERT: A 191 LYS cc_start: 0.7378 (mttt) cc_final: 0.6693 (mtpt) REVERT: B 70 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: B 198 GLN cc_start: 0.7829 (tt0) cc_final: 0.7229 (tt0) REVERT: C 120 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7489 (ttt) outliers start: 15 outliers final: 9 residues processed: 64 average time/residue: 1.1989 time to fit residues: 82.0836 Evaluate side-chains 70 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 47 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 53 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 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 = 0.3473 r_free = 0.3473 target = 0.132767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.105546 restraints weight = 9865.595| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.47 r_work: 0.3015 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8324 Z= 0.213 Angle : 0.638 12.817 11395 Z= 0.290 Chirality : 0.041 0.151 1251 Planarity : 0.005 0.045 1317 Dihedral : 15.241 173.789 1260 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.45 % Allowed : 16.08 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.29), residues: 923 helix: 2.23 (0.23), residues: 581 sheet: 0.85 (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 0.007 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 C 186 ********************** 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 69 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.869 Fit side-chains REVERT: B 70 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7674 (pt0) REVERT: B 198 GLN cc_start: 0.7834 (tt0) cc_final: 0.7242 (tt0) REVERT: C 120 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7470 (ttt) outliers start: 12 outliers final: 10 residues processed: 63 average time/residue: 1.2004 time to fit residues: 80.9110 Evaluate side-chains 69 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 280 ILE 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 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: 0.4980 chunk 52 optimal weight: 0.0870 chunk 4 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.134904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.107179 restraints weight = 9954.065| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.56 r_work: 0.3039 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8324 Z= 0.180 Angle : 0.605 11.849 11395 Z= 0.275 Chirality : 0.040 0.149 1251 Planarity : 0.004 0.046 1317 Dihedral : 14.903 166.450 1260 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.33 % Allowed : 16.44 % Favored : 82.22 % 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: 1.74 (0.29), residues: 923 helix: 2.37 (0.23), residues: 581 sheet: 0.84 (0.50), residues: 118 loop : -2.12 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 274 HIS 0.006 0.001 HIS A 268 PHE 0.011 0.001 PHE B 170 TYR 0.024 0.001 TYR A 219 ARG 0.001 0.000 ARG C 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5903.09 seconds wall clock time: 104 minutes 56.51 seconds (6296.51 seconds total)