Starting phenix.real_space_refine on Thu Nov 14 20:00:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq6_35658/11_2024/8iq6_35658.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq6_35658/11_2024/8iq6_35658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq6_35658/11_2024/8iq6_35658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq6_35658/11_2024/8iq6_35658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq6_35658/11_2024/8iq6_35658.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iq6_35658/11_2024/8iq6_35658.cif" } resolution = 3.4 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= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 4541 2.51 5 N 1203 2.21 5 O 1263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7059 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1560 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 7, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2342 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 5, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 Chain: "G" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 238 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 845 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2046 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'7WT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.65, per 1000 atoms: 0.66 Number of scatterers: 7059 At special positions: 0 Unit cell: (71.3635, 97.7131, 125.161, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1263 8.00 N 1203 7.00 C 4541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 11 sheets defined 41.3% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 17 through 38 removed outlier: 3.616A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.583A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.511A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 352 removed outlier: 3.782A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 392 Processing helix chain 'B' and resid 8 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 16 through 23 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.616A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.777A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'R' and resid 29 through 59 removed outlier: 4.367A pdb=" N SER R 33 " --> pdb=" O SER R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 62 No H-bonds generated for 'chain 'R' and resid 60 through 62' Processing helix chain 'R' and resid 64 through 94 Processing helix chain 'R' and resid 98 through 102 removed outlier: 4.320A pdb=" N PHE R 101 " --> pdb=" O TRP R 98 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP R 102 " --> pdb=" O ILE R 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 98 through 102' Processing helix chain 'R' and resid 105 through 139 Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 139 through 146 Processing helix chain 'R' and resid 147 through 173 removed outlier: 4.143A pdb=" N HIS R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL R 152 " --> pdb=" O THR R 148 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 195 through 229 removed outlier: 3.906A pdb=" N ARG R 199 " --> pdb=" O ASP R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 275 Proline residue: R 264 - end of helix Processing helix chain 'R' and resid 282 through 305 removed outlier: 4.429A pdb=" N MET R 292 " --> pdb=" O PHE R 288 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP R 295 " --> pdb=" O ARG R 291 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN R 296 " --> pdb=" O MET R 292 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.899A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.414A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.993A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.071A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.528A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.674A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.515A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.542A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 59 through 60 removed outlier: 6.637A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 178 through 179 397 hydrogen bonds defined for protein. 1143 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: 2.15 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1760 1.33 - 1.45: 1435 1.45 - 1.57: 3934 1.57 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 7200 Sorted by residual: bond pdb=" C02 7WT R 401 " pdb=" O01 7WT R 401 " ideal model delta sigma weight residual 1.414 1.538 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" CA ALA R 293 " pdb=" CB ALA R 293 " ideal model delta sigma weight residual 1.532 1.477 0.055 1.62e-02 3.81e+03 1.14e+01 bond pdb=" C20 7WT R 401 " pdb=" C21 7WT R 401 " ideal model delta sigma weight residual 1.497 1.556 -0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" CA ALA R 289 " pdb=" CB ALA R 289 " ideal model delta sigma weight residual 1.530 1.482 0.049 1.69e-02 3.50e+03 8.30e+00 bond pdb=" C22 7WT R 401 " pdb=" C23 7WT R 401 " ideal model delta sigma weight residual 1.496 1.550 -0.054 2.00e-02 2.50e+03 7.20e+00 ... (remaining 7195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 9729 2.74 - 5.48: 61 5.48 - 8.23: 4 8.23 - 10.97: 3 10.97 - 13.71: 1 Bond angle restraints: 9798 Sorted by residual: angle pdb=" N LEU R 290 " pdb=" CA LEU R 290 " pdb=" C LEU R 290 " ideal model delta sigma weight residual 111.36 102.64 8.72 1.09e+00 8.42e-01 6.40e+01 angle pdb=" N MET R 292 " pdb=" CA MET R 292 " pdb=" C MET R 292 " ideal model delta sigma weight residual 113.38 107.19 6.19 1.23e+00 6.61e-01 2.53e+01 angle pdb=" N ALA R 293 " pdb=" CA ALA R 293 " pdb=" C ALA R 293 " ideal model delta sigma weight residual 112.04 105.37 6.67 1.44e+00 4.82e-01 2.15e+01 angle pdb=" C20 7WT R 401 " pdb=" C21 7WT R 401 " pdb=" C22 7WT R 401 " ideal model delta sigma weight residual 128.03 114.32 13.71 3.00e+00 1.11e-01 2.09e+01 angle pdb=" N LEU R 287 " pdb=" CA LEU R 287 " pdb=" C LEU R 287 " ideal model delta sigma weight residual 111.36 107.22 4.14 1.09e+00 8.42e-01 1.45e+01 ... (remaining 9793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 3607 15.89 - 31.77: 435 31.77 - 47.66: 134 47.66 - 63.55: 21 63.55 - 79.44: 7 Dihedral angle restraints: 4204 sinusoidal: 1438 harmonic: 2766 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -142.92 56.92 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CA ARG R 100 " pdb=" C ARG R 100 " pdb=" N PHE R 101 " pdb=" CA PHE R 101 " ideal model delta harmonic sigma weight residual 180.00 155.29 24.71 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA CYS N 99 " pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " ideal model delta sinusoidal sigma weight residual 79.00 13.87 65.13 1 2.00e+01 2.50e-03 1.39e+01 ... (remaining 4201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1079 0.078 - 0.156: 86 0.156 - 0.234: 2 0.234 - 0.312: 1 0.312 - 0.391: 2 Chirality restraints: 1170 Sorted by residual: chirality pdb=" C03 7WT R 401 " pdb=" C02 7WT R 401 " pdb=" C04 7WT R 401 " pdb=" C20 7WT R 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.92 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" C04 7WT R 401 " pdb=" C03 7WT R 401 " pdb=" C05 7WT R 401 " pdb=" C08 7WT R 401 " both_signs ideal model delta sigma weight residual False 2.63 2.97 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA LEU R 290 " pdb=" N LEU R 290 " pdb=" C LEU R 290 " pdb=" CB LEU R 290 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1167 not shown) Planarity restraints: 1222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C THR B 87 " -0.033 2.00e-02 2.50e+03 pdb=" O THR B 87 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN B 88 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO G 49 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO B 236 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.022 5.00e-02 4.00e+02 ... (remaining 1219 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1627 2.78 - 3.31: 6367 3.31 - 3.84: 11555 3.84 - 4.37: 12921 4.37 - 4.90: 23796 Nonbonded interactions: 56266 Sorted by model distance: nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.259 3.040 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.261 3.120 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.267 3.040 nonbonded pdb=" OD2 ASP A 33 " pdb=" NZ LYS B 78 " model vdw 2.271 3.120 ... (remaining 56261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.210 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 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 : 0.004 0.124 7200 Z= 0.253 Angle : 0.586 13.711 9798 Z= 0.324 Chirality : 0.045 0.391 1170 Planarity : 0.004 0.064 1222 Dihedral : 15.453 79.436 2401 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.29 % Allowed : 18.83 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.28), residues: 930 helix: 3.05 (0.27), residues: 354 sheet: 0.50 (0.36), residues: 202 loop : -1.01 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE R 101 TYR 0.010 0.001 TYR N 95 ARG 0.008 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: R 217 LEU cc_start: 0.8668 (tp) cc_final: 0.8225 (tp) REVERT: R 291 ARG cc_start: 0.8164 (ptp-170) cc_final: 0.6998 (ptm160) outliers start: 2 outliers final: 1 residues processed: 119 average time/residue: 0.2264 time to fit residues: 35.0509 Evaluate side-chains 115 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 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 392 ASN R 189 ASN R 243 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7200 Z= 0.220 Angle : 0.480 6.140 9798 Z= 0.264 Chirality : 0.041 0.132 1170 Planarity : 0.003 0.043 1222 Dihedral : 5.157 55.267 1048 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.77 % Allowed : 17.66 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.28), residues: 930 helix: 2.90 (0.27), residues: 364 sheet: 0.46 (0.36), residues: 203 loop : -1.06 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE B 199 TYR 0.011 0.001 TYR N 95 ARG 0.005 0.000 ARG R 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8303 (m-30) cc_final: 0.7860 (m-30) REVERT: B 237 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8544 (p0) REVERT: B 336 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8795 (tt) REVERT: R 115 MET cc_start: 0.8674 (mmm) cc_final: 0.8240 (tpt) REVERT: R 246 GLU cc_start: 0.7574 (mp0) cc_final: 0.7323 (tp30) REVERT: R 291 ARG cc_start: 0.7955 (ptp-170) cc_final: 0.6755 (ptm160) outliers start: 19 outliers final: 10 residues processed: 134 average time/residue: 0.2163 time to fit residues: 38.4133 Evaluate side-chains 127 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7200 Z= 0.209 Angle : 0.464 5.677 9798 Z= 0.257 Chirality : 0.041 0.135 1170 Planarity : 0.003 0.045 1222 Dihedral : 4.927 52.329 1048 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.55 % Favored : 96.34 % Rotamer: Outliers : 3.07 % Allowed : 17.96 % Favored : 78.98 % 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 (0.28), residues: 930 helix: 3.06 (0.27), residues: 358 sheet: 0.41 (0.36), residues: 203 loop : -0.99 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE B 199 TYR 0.011 0.001 TYR N 95 ARG 0.005 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: B 237 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8520 (p0) REVERT: B 336 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8757 (tt) REVERT: R 56 GLN cc_start: 0.7644 (mm110) cc_final: 0.7176 (mm-40) REVERT: R 59 ARG cc_start: 0.7942 (tmm-80) cc_final: 0.7430 (ttp-170) REVERT: R 115 MET cc_start: 0.8700 (mmm) cc_final: 0.8248 (tpt) REVERT: R 246 GLU cc_start: 0.7585 (mp0) cc_final: 0.7277 (tp30) outliers start: 21 outliers final: 9 residues processed: 133 average time/residue: 0.2104 time to fit residues: 36.8936 Evaluate side-chains 124 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 208 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 43 optimal weight: 0.0470 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7200 Z= 0.204 Angle : 0.457 5.493 9798 Z= 0.252 Chirality : 0.041 0.138 1170 Planarity : 0.003 0.045 1222 Dihedral : 4.492 30.027 1046 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.55 % Favored : 96.34 % Rotamer: Outliers : 3.07 % Allowed : 18.39 % Favored : 78.54 % 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: 1.44 (0.28), residues: 930 helix: 3.09 (0.26), residues: 360 sheet: 0.47 (0.36), residues: 201 loop : -1.00 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE R 101 TYR 0.011 0.001 TYR N 95 ARG 0.005 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.753 Fit side-chains REVERT: A 378 ASP cc_start: 0.8294 (m-30) cc_final: 0.7819 (m-30) REVERT: B 237 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8552 (p0) REVERT: B 336 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8690 (tt) REVERT: R 56 GLN cc_start: 0.7591 (mm110) cc_final: 0.7122 (mm-40) REVERT: R 59 ARG cc_start: 0.7960 (tmm-80) cc_final: 0.7523 (ttp-170) REVERT: R 115 MET cc_start: 0.8728 (mmm) cc_final: 0.8270 (tpt) REVERT: R 246 GLU cc_start: 0.7579 (mp0) cc_final: 0.7287 (tp30) outliers start: 21 outliers final: 13 residues processed: 131 average time/residue: 0.2230 time to fit residues: 38.1779 Evaluate side-chains 124 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 133 ARG Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7200 Z= 0.347 Angle : 0.526 5.530 9798 Z= 0.288 Chirality : 0.043 0.141 1170 Planarity : 0.004 0.055 1222 Dihedral : 4.717 31.602 1046 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 3.07 % Allowed : 20.29 % Favored : 76.64 % 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: 1.16 (0.28), residues: 930 helix: 2.89 (0.27), residues: 359 sheet: 0.20 (0.36), residues: 198 loop : -1.10 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS R 81 PHE 0.018 0.002 PHE B 199 TYR 0.013 0.001 TYR N 95 ARG 0.006 0.001 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.848 Fit side-chains REVERT: B 237 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8619 (p0) REVERT: B 336 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8799 (tt) REVERT: R 56 GLN cc_start: 0.7693 (mm110) cc_final: 0.7244 (mm-40) REVERT: R 59 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7464 (ttp-170) REVERT: R 115 MET cc_start: 0.8837 (mmm) cc_final: 0.8355 (tpt) REVERT: R 200 PHE cc_start: 0.8663 (t80) cc_final: 0.8414 (t80) REVERT: R 246 GLU cc_start: 0.7562 (mp0) cc_final: 0.7267 (tp30) outliers start: 21 outliers final: 12 residues processed: 128 average time/residue: 0.2007 time to fit residues: 34.1493 Evaluate side-chains 124 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 260 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7200 Z= 0.260 Angle : 0.490 5.368 9798 Z= 0.269 Chirality : 0.042 0.141 1170 Planarity : 0.003 0.053 1222 Dihedral : 4.564 28.702 1046 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 2.77 % Allowed : 21.31 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.28), residues: 930 helix: 2.90 (0.27), residues: 363 sheet: 0.21 (0.36), residues: 205 loop : -1.17 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.018 0.001 PHE B 199 TYR 0.012 0.001 TYR N 95 ARG 0.007 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.625 Fit side-chains REVERT: B 237 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8551 (p0) REVERT: B 336 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8739 (tt) REVERT: R 56 GLN cc_start: 0.7632 (mm110) cc_final: 0.7186 (mm-40) REVERT: R 59 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7510 (ttp-170) REVERT: R 200 PHE cc_start: 0.8520 (t80) cc_final: 0.8227 (t80) REVERT: R 246 GLU cc_start: 0.7633 (mp0) cc_final: 0.7192 (tp30) outliers start: 19 outliers final: 15 residues processed: 127 average time/residue: 0.1725 time to fit residues: 29.0777 Evaluate side-chains 128 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7200 Z= 0.290 Angle : 0.516 5.669 9798 Z= 0.281 Chirality : 0.042 0.148 1170 Planarity : 0.004 0.055 1222 Dihedral : 4.585 27.605 1046 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.65 % Allowed : 21.17 % Favored : 75.18 % 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: 1.14 (0.28), residues: 930 helix: 2.88 (0.26), residues: 365 sheet: 0.18 (0.36), residues: 204 loop : -1.20 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS R 81 PHE 0.018 0.001 PHE B 199 TYR 0.012 0.001 TYR N 95 ARG 0.007 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.827 Fit side-chains REVERT: A 249 ASP cc_start: 0.8486 (t70) cc_final: 0.8028 (t70) REVERT: B 237 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8578 (p0) REVERT: B 336 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8741 (tt) REVERT: R 56 GLN cc_start: 0.7616 (mm110) cc_final: 0.7165 (mm-40) REVERT: R 59 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7526 (ttp-170) REVERT: R 200 PHE cc_start: 0.8504 (t80) cc_final: 0.8211 (t80) REVERT: R 246 GLU cc_start: 0.7551 (mp0) cc_final: 0.7138 (tp30) outliers start: 25 outliers final: 16 residues processed: 131 average time/residue: 0.1846 time to fit residues: 33.1565 Evaluate side-chains 130 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 70 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7200 Z= 0.172 Angle : 0.468 6.163 9798 Z= 0.254 Chirality : 0.041 0.146 1170 Planarity : 0.003 0.049 1222 Dihedral : 4.328 25.871 1046 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 2.48 % Allowed : 21.61 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.28), residues: 930 helix: 3.11 (0.26), residues: 359 sheet: 0.34 (0.36), residues: 207 loop : -1.19 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE R 101 TYR 0.010 0.001 TYR N 95 ARG 0.007 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.899 Fit side-chains REVERT: A 22 ARG cc_start: 0.7560 (mmm-85) cc_final: 0.7133 (tpp80) REVERT: B 237 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8445 (p0) REVERT: B 336 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8794 (tt) REVERT: R 56 GLN cc_start: 0.7572 (mm110) cc_final: 0.7136 (mm-40) REVERT: R 59 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7459 (ttp-170) REVERT: R 200 PHE cc_start: 0.8400 (t80) cc_final: 0.8001 (t80) REVERT: R 217 LEU cc_start: 0.8634 (tp) cc_final: 0.8171 (tp) REVERT: R 246 GLU cc_start: 0.7453 (mp0) cc_final: 0.7105 (tp30) outliers start: 17 outliers final: 15 residues processed: 122 average time/residue: 0.1550 time to fit residues: 25.7635 Evaluate side-chains 127 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 287 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 0.0670 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7200 Z= 0.173 Angle : 0.462 6.262 9798 Z= 0.250 Chirality : 0.041 0.146 1170 Planarity : 0.003 0.046 1222 Dihedral : 4.195 24.461 1046 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.55 % Favored : 96.34 % Rotamer: Outliers : 2.63 % Allowed : 20.73 % Favored : 76.64 % 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: 1.35 (0.28), residues: 930 helix: 3.16 (0.26), residues: 358 sheet: 0.38 (0.36), residues: 207 loop : -1.19 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE R 101 TYR 0.010 0.001 TYR N 95 ARG 0.008 0.000 ARG R 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.883 Fit side-chains REVERT: A 22 ARG cc_start: 0.7430 (mmm-85) cc_final: 0.7007 (tpp80) REVERT: B 237 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8494 (p0) REVERT: B 336 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8677 (tt) REVERT: R 56 GLN cc_start: 0.7525 (mm110) cc_final: 0.7064 (mm-40) REVERT: R 59 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7438 (ttp-170) REVERT: R 217 LEU cc_start: 0.8619 (tp) cc_final: 0.8195 (tp) REVERT: R 246 GLU cc_start: 0.7368 (mp0) cc_final: 0.7135 (tp30) outliers start: 18 outliers final: 14 residues processed: 123 average time/residue: 0.2092 time to fit residues: 34.9567 Evaluate side-chains 125 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7200 Z= 0.215 Angle : 0.493 6.033 9798 Z= 0.266 Chirality : 0.041 0.148 1170 Planarity : 0.003 0.049 1222 Dihedral : 4.236 25.528 1046 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 2.77 % Allowed : 21.17 % Favored : 76.06 % 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: 1.31 (0.28), residues: 930 helix: 3.05 (0.26), residues: 364 sheet: 0.38 (0.36), residues: 203 loop : -1.20 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE R 101 TYR 0.011 0.001 TYR N 95 ARG 0.008 0.000 ARG R 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.854 Fit side-chains REVERT: A 22 ARG cc_start: 0.7597 (mmm-85) cc_final: 0.7156 (tpp80) REVERT: B 237 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8530 (p0) REVERT: B 336 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8694 (tt) REVERT: R 56 GLN cc_start: 0.7586 (mm110) cc_final: 0.7134 (mm-40) REVERT: R 59 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7456 (ttp-170) REVERT: R 200 PHE cc_start: 0.8387 (t80) cc_final: 0.7996 (t80) REVERT: R 217 LEU cc_start: 0.8645 (tp) cc_final: 0.8190 (tp) REVERT: R 246 GLU cc_start: 0.7368 (mp0) cc_final: 0.7132 (tp30) outliers start: 19 outliers final: 17 residues processed: 122 average time/residue: 0.1895 time to fit residues: 31.5546 Evaluate side-chains 130 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 64 optimal weight: 0.3980 chunk 4 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119442 restraints weight = 9587.928| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.19 r_work: 0.3276 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7200 Z= 0.174 Angle : 0.473 6.668 9798 Z= 0.254 Chirality : 0.041 0.145 1170 Planarity : 0.003 0.045 1222 Dihedral : 4.111 24.534 1046 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.44 % Favored : 96.45 % Rotamer: Outliers : 2.92 % Allowed : 20.73 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.28), residues: 930 helix: 3.21 (0.26), residues: 358 sheet: 0.45 (0.36), residues: 207 loop : -1.19 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE R 101 TYR 0.010 0.001 TYR N 95 ARG 0.008 0.000 ARG R 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1790.61 seconds wall clock time: 39 minutes 28.01 seconds (2368.01 seconds total)