Starting phenix.real_space_refine on Thu Feb 13 05:44:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ucd_42124/02_2025/8ucd_42124.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ucd_42124/02_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_42124/02_2025/8ucd_42124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ucd_42124/02_2025/8ucd_42124.map" model { file = "/net/cci-nas-00/data/ceres_data/8ucd_42124/02_2025/8ucd_42124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ucd_42124/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.90, per 1000 atoms: 0.86 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: 2.77 Conformation dependent library (CDL) restraints added in 946.2 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: 0.79 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: 2.23 Time building geometry restraints manager: 2.67 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: 6.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.850 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.350 ------------------------------------------------------------------------------- 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 : 0.839 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: 1.3327 time to fit residues: 114.6019 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 : 0.834 ------------------------------------------------------------------------------- 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 : 0.004 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 : 17.908 177.654 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 *********************** 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 : 0.859 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: 1.2548 time to fit residues: 83.2718 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 : 0.975 ------------------------------------------------------------------------------- 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 : 0.003 0.055 8324 Z= 0.223 Angle : 0.642 12.594 11395 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 *********************** 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 : 0.911 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: 1.2587 time to fit residues: 92.7427 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 : 0.870 ------------------------------------------------------------------------------- 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: 0.0010 chunk 38 optimal weight: 0.5980 overall best weight: 0.4044 ------------------------------------------------------------------------------- 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 C 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.110040 restraints weight = 9853.983| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.52 r_work: 0.3062 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1610 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= 0.178 Angle : 0.600 11.738 11395 Z= 0.274 Chirality : 0.040 0.152 1251 Planarity : 0.004 0.038 1317 Dihedral : 16.317 172.062 1260 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.57 % Allowed : 13.06 % Favored : 85.37 % 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: 1.70 (0.29), residues: 923 helix: 2.32 (0.23), residues: 582 sheet: 0.84 (0.51), residues: 112 loop : -2.06 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 274 HIS 0.006 0.001 HIS A 268 PHE 0.010 0.001 PHE B 170 TYR 0.025 0.001 TYR B 219 ARG 0.002 0.000 ARG L 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.796 Fit side-chains REVERT: A 76 LYS cc_start: 0.7763 (ttmm) cc_final: 0.7259 (mttt) REVERT: A 93 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7345 (mm-30) REVERT: B 198 GLN cc_start: 0.7775 (tt0) cc_final: 0.7094 (tt0) REVERT: C 120 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7386 (ttt) REVERT: C 243 ASP cc_start: 0.8420 (m-30) cc_final: 0.8132 (m-30) outliers start: 13 outliers final: 4 residues processed: 63 average time/residue: 1.2054 time to fit residues: 81.3449 Evaluate side-chains 61 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 120 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 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: 1.9990 chunk 37 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.131229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.103506 restraints weight = 9932.506| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.51 r_work: 0.3007 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8324 Z= 0.283 Angle : 0.681 13.942 11395 Z= 0.312 Chirality : 0.043 0.153 1251 Planarity : 0.005 0.040 1317 Dihedral : 16.201 170.081 1260 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.66 % Allowed : 12.21 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.29), residues: 923 helix: 2.11 (0.23), residues: 581 sheet: 0.69 (0.50), residues: 117 loop : -2.09 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 285 HIS 0.009 0.002 HIS A 268 PHE 0.013 0.001 PHE H 108 TYR 0.028 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 81 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.828 Fit side-chains REVERT: A 76 LYS cc_start: 0.7897 (ttmm) cc_final: 0.7467 (mttt) REVERT: A 93 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7491 (mm-30) REVERT: A 191 LYS cc_start: 0.7546 (mttt) cc_final: 0.6852 (mtpt) REVERT: B 198 GLN cc_start: 0.7929 (tt0) cc_final: 0.7305 (tt0) REVERT: B 206 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7743 (t70) REVERT: C 120 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7609 (ttt) outliers start: 22 outliers final: 7 residues processed: 72 average time/residue: 1.1972 time to fit residues: 92.2213 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 : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 284 VAL 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: 0.5980 chunk 13 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 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 B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.103674 restraints weight = 9919.785| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.44 r_work: 0.3037 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8324 Z= 0.260 Angle : 0.679 13.708 11395 Z= 0.309 Chirality : 0.042 0.151 1251 Planarity : 0.005 0.040 1317 Dihedral : 15.907 170.815 1260 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.30 % Allowed : 13.66 % Favored : 84.04 % 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: 2.07 (0.23), residues: 581 sheet: 0.69 (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 0.002 HIS A 268 PHE 0.013 0.001 PHE B 170 TYR 0.027 0.002 TYR A 219 ARG 0.002 0.000 ARG B 161 *********************** 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 77 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.877 Fit side-chains REVERT: A 76 LYS cc_start: 0.7921 (ttmm) cc_final: 0.7481 (mttt) REVERT: A 191 LYS cc_start: 0.7551 (mttt) cc_final: 0.6859 (mtpt) REVERT: B 70 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7683 (pt0) REVERT: B 198 GLN cc_start: 0.7937 (tt0) cc_final: 0.7412 (tt0) REVERT: B 206 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7736 (t70) REVERT: C 120 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7611 (ttt) outliers start: 19 outliers final: 7 residues processed: 67 average time/residue: 1.3082 time to fit residues: 93.3328 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 : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 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: 0.6980 chunk 70 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 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 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 = 0.132491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105400 restraints weight = 9862.954| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.45 r_work: 0.3051 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1957 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= 0.220 Angle : 0.643 12.845 11395 Z= 0.292 Chirality : 0.041 0.150 1251 Planarity : 0.004 0.037 1317 Dihedral : 15.598 174.585 1260 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.30 % Allowed : 14.27 % Favored : 83.43 % 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: 581 sheet: 0.76 (0.50), residues: 117 loop : -2.10 (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 0.025 0.002 TYR A 219 ARG 0.001 0.000 ARG B 161 *********************** 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 78 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.811 Fit side-chains REVERT: A 76 LYS cc_start: 0.7890 (ttmm) cc_final: 0.7458 (mttt) REVERT: A 191 LYS cc_start: 0.7484 (mttt) cc_final: 0.6794 (mtpt) REVERT: B 198 GLN cc_start: 0.7888 (tt0) cc_final: 0.7302 (tt0) REVERT: B 206 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7765 (t70) REVERT: C 120 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7552 (ttt) outliers start: 19 outliers final: 9 residues processed: 68 average time/residue: 1.2633 time to fit residues: 91.9794 Evaluate side-chains 71 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 206 ASP Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 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 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.130481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.103286 restraints weight = 10046.440| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.45 r_work: 0.2966 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8324 Z= 0.259 Angle : 0.676 13.826 11395 Z= 0.308 Chirality : 0.042 0.153 1251 Planarity : 0.005 0.057 1317 Dihedral : 15.589 176.569 1260 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.93 % Allowed : 15.11 % Favored : 82.95 % 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: 2.08 (0.23), residues: 581 sheet: 0.70 (0.50), residues: 117 loop : -2.15 (0.35), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 274 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 0.002 0.000 ARG L 181 *********************** 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 76 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.851 Fit side-chains REVERT: A 76 LYS cc_start: 0.7798 (ttmm) cc_final: 0.7351 (mttt) REVERT: A 191 LYS cc_start: 0.7354 (mttt) cc_final: 0.6664 (mtpt) REVERT: B 70 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7663 (pt0) REVERT: B 198 GLN cc_start: 0.7807 (tt0) cc_final: 0.7208 (tt0) REVERT: B 206 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7677 (t70) REVERT: C 120 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7466 (ttt) outliers start: 16 outliers final: 10 residues processed: 66 average time/residue: 1.2588 time to fit residues: 88.8677 Evaluate side-chains 72 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 138 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 28 optimal weight: 0.0170 chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 31 optimal weight: 0.4980 chunk 76 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.134693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107106 restraints weight = 10091.190| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.54 r_work: 0.3043 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8324 Z= 0.186 Angle : 0.612 11.990 11395 Z= 0.278 Chirality : 0.040 0.147 1251 Planarity : 0.005 0.057 1317 Dihedral : 15.295 177.823 1260 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.21 % Allowed : 16.20 % 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: 1.68 (0.29), residues: 923 helix: 2.32 (0.23), residues: 581 sheet: 0.84 (0.50), residues: 117 loop : -2.14 (0.36), residues: 225 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 0.011 0.001 PHE B 170 TYR 0.024 0.001 TYR B 219 ARG 0.001 0.000 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.817 Fit side-chains REVERT: A 191 LYS cc_start: 0.7405 (mttt) cc_final: 0.6715 (mtpt) REVERT: B 198 GLN cc_start: 0.7831 (tt0) cc_final: 0.7214 (tt0) REVERT: C 120 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7428 (ttt) outliers start: 10 outliers final: 7 residues processed: 65 average time/residue: 1.2071 time to fit residues: 84.2887 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 : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain C residue 120 MET 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: 0.5980 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 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 = 0.3455 r_free = 0.3455 target = 0.131225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.103992 restraints weight = 9886.215| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.46 r_work: 0.2993 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2082 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 : 0.666 13.677 11395 Z= 0.302 Chirality : 0.042 0.153 1251 Planarity : 0.005 0.054 1317 Dihedral : 15.327 174.543 1260 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.33 % Allowed : 16.08 % 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: 1.49 (0.29), residues: 923 helix: 2.15 (0.23), residues: 581 sheet: 0.70 (0.50), residues: 118 loop : -2.12 (0.35), 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 0.027 0.002 TYR A 219 ARG 0.002 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 70 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.930 Fit side-chains REVERT: A 76 LYS cc_start: 0.7803 (ttmm) cc_final: 0.7393 (mttt) REVERT: A 191 LYS cc_start: 0.7402 (mttt) cc_final: 0.6704 (mtpt) REVERT: B 198 GLN cc_start: 0.7856 (tt0) cc_final: 0.7265 (tt0) REVERT: C 120 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7514 (ttt) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 1.3730 time to fit residues: 92.3346 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 : 0.868 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 87 optimal weight: 0.0010 chunk 52 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.134120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106310 restraints weight = 9960.524| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.56 r_work: 0.3032 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8324 Z= 0.188 Angle : 0.614 12.097 11395 Z= 0.279 Chirality : 0.040 0.148 1251 Planarity : 0.005 0.053 1317 Dihedral : 14.988 168.094 1260 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.09 % Allowed : 16.44 % 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: 1.68 (0.29), residues: 923 helix: 2.32 (0.23), residues: 581 sheet: 0.88 (0.50), residues: 117 loop : -2.15 (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 0.024 0.001 TYR B 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: 5306.45 seconds wall clock time: 94 minutes 33.20 seconds (5673.20 seconds total)