Starting phenix.real_space_refine on Mon Jul 28 07:40:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xlp_6731/07_2025/5xlp_6731.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xlp_6731/07_2025/5xlp_6731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5xlp_6731/07_2025/5xlp_6731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xlp_6731/07_2025/5xlp_6731.map" model { file = "/net/cci-nas-00/data/ceres_data/5xlp_6731/07_2025/5xlp_6731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xlp_6731/07_2025/5xlp_6731.cif" } resolution = 4.2 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= 0.001 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 11 5.16 5 C 6107 2.51 5 N 1737 2.21 5 O 2073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9952 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2004 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 9, 'TRANS': 277} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'TRP:plan': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 180 Chain: "D" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 195 Chain: "E" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 195 Chain: "F" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 195 Chain: "K" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 514 Classifications: {'RNA': 24} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 6, 'rna3p_pyr': 1} Link IDs: {'rna2p': 16, 'rna3p': 7} Chain: "M" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 615 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 7.20, per 1000 atoms: 0.72 Number of scatterers: 9952 At special positions: 0 Unit cell: (110.04, 111.35, 127.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 P 24 15.00 O 2073 8.00 N 1737 7.00 C 6107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.55 Conformation dependent library (CDL) restraints added in 1.4 seconds 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 29.3% alpha, 6.0% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'C' and resid 121 through 138 Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.505A pdb=" N ILE C 162 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN C 163 " --> pdb=" O VAL C 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 199 through 214 removed outlier: 4.197A pdb=" N VAL C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 293 through 297 removed outlier: 4.391A pdb=" N GLN C 297 " --> pdb=" O ALA C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 325 removed outlier: 4.900A pdb=" N GLN C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'D' and resid 74 through 83 removed outlier: 3.933A pdb=" N THR D 78 " --> pdb=" O PRO D 74 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 79 " --> pdb=" O ASN D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 138 Processing helix chain 'D' and resid 141 through 151 Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.505A pdb=" N ILE D 162 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN D 163 " --> pdb=" O VAL D 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 159 through 163' Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 199 through 214 removed outlier: 4.198A pdb=" N VAL D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 293 through 297 removed outlier: 4.390A pdb=" N GLN D 297 " --> pdb=" O ALA D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 325 removed outlier: 4.901A pdb=" N GLN D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'E' and resid 75 through 83 removed outlier: 3.520A pdb=" N VAL E 79 " --> pdb=" O ASN E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 138 Processing helix chain 'E' and resid 141 through 151 Processing helix chain 'E' and resid 159 through 163 removed outlier: 3.504A pdb=" N ILE E 162 " --> pdb=" O GLU E 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN E 163 " --> pdb=" O VAL E 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 159 through 163' Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'E' and resid 199 through 214 removed outlier: 4.198A pdb=" N VAL E 214 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 271 Processing helix chain 'E' and resid 272 through 274 No H-bonds generated for 'chain 'E' and resid 272 through 274' Processing helix chain 'E' and resid 293 through 297 removed outlier: 4.391A pdb=" N GLN E 297 " --> pdb=" O ALA E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 325 removed outlier: 4.901A pdb=" N GLN E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 336 Processing helix chain 'F' and resid 73 through 81 removed outlier: 4.084A pdb=" N GLN F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL F 79 " --> pdb=" O ASN F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 138 Processing helix chain 'F' and resid 141 through 151 Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.505A pdb=" N ILE F 162 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN F 163 " --> pdb=" O VAL F 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 163' Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 199 through 214 removed outlier: 4.198A pdb=" N VAL F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 271 Processing helix chain 'F' and resid 272 through 274 No H-bonds generated for 'chain 'F' and resid 272 through 274' Processing helix chain 'F' and resid 293 through 297 removed outlier: 4.391A pdb=" N GLN F 297 " --> pdb=" O ALA F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 325 removed outlier: 4.902A pdb=" N GLN F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 336 Processing helix chain 'M' and resid 46 through 56 removed outlier: 4.256A pdb=" N SER M 52 " --> pdb=" O GLU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 74 removed outlier: 3.596A pdb=" N ILE M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG M 74 " --> pdb=" O ASN M 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 36 through 37 removed outlier: 3.745A pdb=" N ARG C 50 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.659A pdb=" N SER C 107 " --> pdb=" O ASP C 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 168 through 172 Processing sheet with id=AA4, first strand: chain 'C' and resid 174 through 175 Processing sheet with id=AA5, first strand: chain 'D' and resid 36 through 37 removed outlier: 3.745A pdb=" N ARG D 50 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 56 through 59 Processing sheet with id=AA7, first strand: chain 'D' and resid 107 through 108 removed outlier: 3.658A pdb=" N SER D 107 " --> pdb=" O ASP D 221 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 168 through 172 Processing sheet with id=AA9, first strand: chain 'D' and resid 174 through 175 Processing sheet with id=AB1, first strand: chain 'E' and resid 36 through 37 removed outlier: 3.746A pdb=" N ARG E 50 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 57 through 59 Processing sheet with id=AB3, first strand: chain 'E' and resid 107 through 108 removed outlier: 3.658A pdb=" N SER E 107 " --> pdb=" O ASP E 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 168 through 172 Processing sheet with id=AB5, first strand: chain 'E' and resid 174 through 175 Processing sheet with id=AB6, first strand: chain 'F' and resid 36 through 37 removed outlier: 3.744A pdb=" N ARG F 50 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 55 through 58 removed outlier: 3.626A pdb=" N ASN F 55 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 107 through 108 removed outlier: 3.658A pdb=" N SER F 107 " --> pdb=" O ASP F 221 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 168 through 172 Processing sheet with id=AC1, first strand: chain 'F' and resid 174 through 175 Processing sheet with id=AC2, first strand: chain 'M' and resid 19 through 21 248 hydrogen bonds defined for protein. 684 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 3.01 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: 2658 1.33 - 1.45: 1827 1.45 - 1.57: 5592 1.57 - 1.69: 47 1.69 - 1.80: 18 Bond restraints: 10142 Sorted by residual: bond pdb=" C HIS E 164 " pdb=" N ILE E 165 " ideal model delta sigma weight residual 1.334 1.306 0.028 1.24e-02 6.50e+03 5.00e+00 bond pdb=" C HIS C 164 " pdb=" N ILE C 165 " ideal model delta sigma weight residual 1.334 1.306 0.028 1.24e-02 6.50e+03 4.94e+00 bond pdb=" C LEU M 12 " pdb=" N ASN M 13 " ideal model delta sigma weight residual 1.331 1.282 0.049 2.22e-02 2.03e+03 4.85e+00 bond pdb=" C HIS F 164 " pdb=" N ILE F 165 " ideal model delta sigma weight residual 1.334 1.307 0.027 1.24e-02 6.50e+03 4.77e+00 bond pdb=" C HIS D 164 " pdb=" N ILE D 165 " ideal model delta sigma weight residual 1.334 1.307 0.027 1.24e-02 6.50e+03 4.72e+00 ... (remaining 10137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 13457 3.05 - 6.10: 402 6.10 - 9.16: 80 9.16 - 12.21: 22 12.21 - 15.26: 2 Bond angle restraints: 13963 Sorted by residual: angle pdb=" N VAL E 42 " pdb=" CA VAL E 42 " pdb=" C VAL E 42 " ideal model delta sigma weight residual 111.88 101.65 10.23 1.06e+00 8.90e-01 9.32e+01 angle pdb=" N VAL D 42 " pdb=" CA VAL D 42 " pdb=" C VAL D 42 " ideal model delta sigma weight residual 111.88 101.66 10.22 1.06e+00 8.90e-01 9.29e+01 angle pdb=" N VAL C 42 " pdb=" CA VAL C 42 " pdb=" C VAL C 42 " ideal model delta sigma weight residual 111.88 101.67 10.21 1.06e+00 8.90e-01 9.28e+01 angle pdb=" N VAL F 42 " pdb=" CA VAL F 42 " pdb=" C VAL F 42 " ideal model delta sigma weight residual 111.88 101.67 10.21 1.06e+00 8.90e-01 9.27e+01 angle pdb=" N ILE D 280 " pdb=" CA ILE D 280 " pdb=" C ILE D 280 " ideal model delta sigma weight residual 111.88 102.37 9.51 1.06e+00 8.90e-01 8.06e+01 ... (remaining 13958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 5961 35.85 - 71.71: 106 71.71 - 107.56: 17 107.56 - 143.41: 1 143.41 - 179.27: 6 Dihedral angle restraints: 6091 sinusoidal: 2250 harmonic: 3841 Sorted by residual: dihedral pdb=" CA HIS M 11 " pdb=" C HIS M 11 " pdb=" N LEU M 12 " pdb=" CA LEU M 12 " ideal model delta harmonic sigma weight residual -180.00 -118.49 -61.51 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" C5' C K 12 " pdb=" C4' C K 12 " pdb=" C3' C K 12 " pdb=" O3' C K 12 " ideal model delta sinusoidal sigma weight residual 147.00 84.74 62.26 1 8.00e+00 1.56e-02 8.02e+01 dihedral pdb=" O4' C K 5 " pdb=" C1' C K 5 " pdb=" N1 C K 5 " pdb=" C2 C K 5 " ideal model delta sinusoidal sigma weight residual 200.00 48.73 151.27 1 1.50e+01 4.44e-03 8.01e+01 ... (remaining 6088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1424 0.083 - 0.165: 241 0.165 - 0.248: 21 0.248 - 0.330: 2 0.330 - 0.413: 3 Chirality restraints: 1691 Sorted by residual: chirality pdb=" C3' G K 18 " pdb=" C4' G K 18 " pdb=" O3' G K 18 " pdb=" C2' G K 18 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" C3' A K 16 " pdb=" C4' A K 16 " pdb=" O3' A K 16 " pdb=" C2' A K 16 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C3' G K 9 " pdb=" C4' G K 9 " pdb=" O3' G K 9 " pdb=" C2' G K 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 1688 not shown) Planarity restraints: 1783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS M 11 " 0.023 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C HIS M 11 " -0.080 2.00e-02 2.50e+03 pdb=" O HIS M 11 " 0.029 2.00e-02 2.50e+03 pdb=" N LEU M 12 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR F 271 " -0.051 5.00e-02 4.00e+02 7.60e-02 9.24e+00 pdb=" N PRO F 272 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO F 272 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 272 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 271 " -0.051 5.00e-02 4.00e+02 7.60e-02 9.24e+00 pdb=" N PRO E 272 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO E 272 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 272 " -0.042 5.00e-02 4.00e+02 ... (remaining 1780 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1094 2.74 - 3.28: 9866 3.28 - 3.82: 15966 3.82 - 4.36: 18829 4.36 - 4.90: 30316 Nonbonded interactions: 76071 Sorted by model distance: nonbonded pdb=" OD1 ASP F 80 " pdb=" OH TYR M 6 " model vdw 2.194 3.040 nonbonded pdb=" O ASN E 75 " pdb=" OG1 THR E 78 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR D 90 " pdb=" O ALA D 254 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR C 105 " pdb=" OE1 GLN C 223 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR D 105 " pdb=" OE1 GLN D 223 " model vdw 2.279 3.040 ... (remaining 76066 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 'C' selection = (chain 'D' and (resid 15 through 53 or resid 93 through 340)) selection = (chain 'E' and (resid 15 through 53 or resid 93 through 340)) selection = (chain 'F' and (resid 15 through 53 or resid 93 through 340)) } 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 group one per residue 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: 0.770 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.500 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 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 : 0.009 0.095 10142 Z= 0.419 Angle : 1.358 15.262 13963 Z= 0.748 Chirality : 0.064 0.413 1691 Planarity : 0.009 0.076 1783 Dihedral : 16.051 179.265 3611 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.45 % Allowed : 18.18 % Favored : 81.37 % Rotamer: Outliers : 0.57 % Allowed : 1.95 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -5.53 (0.17), residues: 1331 helix: -3.73 (0.19), residues: 253 sheet: -3.98 (0.28), residues: 206 loop : -3.80 (0.16), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.008 TRP C 174 HIS 0.007 0.003 HIS F 140 PHE 0.035 0.004 PHE C 147 TYR 0.026 0.002 TYR M 20 ARG 0.008 0.002 ARG M 42 Details of bonding type rmsd hydrogen bonds : bond 0.16158 ( 248) hydrogen bonds : angle 13.70777 ( 684) covalent geometry : bond 0.00873 (10142) covalent geometry : angle 1.35814 (13963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 314 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ASP cc_start: 0.6378 (m-30) cc_final: 0.5951 (t0) REVERT: C 237 ASP cc_start: 0.7657 (m-30) cc_final: 0.7368 (m-30) REVERT: C 284 PRO cc_start: 0.6843 (Cg_endo) cc_final: 0.6427 (Cg_exo) REVERT: C 321 GLU cc_start: 0.8239 (tt0) cc_final: 0.7844 (tm-30) REVERT: D 153 VAL cc_start: 0.7714 (t) cc_final: 0.7320 (p) REVERT: D 219 ILE cc_start: 0.7611 (mt) cc_final: 0.7284 (mt) REVERT: E 256 HIS cc_start: 0.7428 (m90) cc_final: 0.7188 (m90) REVERT: F 58 LYS cc_start: 0.6354 (mttt) cc_final: 0.5186 (mttt) REVERT: F 59 THR cc_start: 0.8927 (p) cc_final: 0.8650 (m) REVERT: F 314 ARG cc_start: 0.2850 (ttt-90) cc_final: 0.1939 (mmp80) REVERT: M 72 ILE cc_start: 0.8433 (mm) cc_final: 0.8070 (mm) outliers start: 5 outliers final: 1 residues processed: 318 average time/residue: 0.2774 time to fit residues: 115.6375 Evaluate side-chains 184 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN E 223 GLN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS F 151 ASN ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 GLN M 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.172877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.157101 restraints weight = 24624.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.158804 restraints weight = 20160.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.159795 restraints weight = 15140.059| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10142 Z= 0.248 Angle : 0.997 10.448 13963 Z= 0.511 Chirality : 0.049 0.287 1691 Planarity : 0.008 0.080 1783 Dihedral : 18.844 171.470 1783 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.67 % Favored : 85.95 % Rotamer: Outliers : 0.57 % Allowed : 6.19 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.79 (0.18), residues: 1331 helix: -2.14 (0.27), residues: 276 sheet: -3.83 (0.29), residues: 180 loop : -3.63 (0.17), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP C 174 HIS 0.008 0.002 HIS D 208 PHE 0.030 0.003 PHE D 147 TYR 0.020 0.002 TYR M 20 ARG 0.006 0.001 ARG E 161 Details of bonding type rmsd hydrogen bonds : bond 0.04576 ( 248) hydrogen bonds : angle 8.38448 ( 684) covalent geometry : bond 0.00522 (10142) covalent geometry : angle 0.99651 (13963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 229 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 HIS cc_start: 0.6613 (t-170) cc_final: 0.5906 (m170) REVERT: C 237 ASP cc_start: 0.6705 (m-30) cc_final: 0.6027 (p0) REVERT: C 274 GLU cc_start: 0.8111 (mp0) cc_final: 0.7740 (mm-30) REVERT: D 67 LEU cc_start: 0.7463 (pt) cc_final: 0.7164 (pp) REVERT: D 125 TYR cc_start: 0.6225 (t80) cc_final: 0.5829 (t80) REVERT: D 274 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: D 313 LEU cc_start: 0.7137 (mt) cc_final: 0.6859 (mt) REVERT: E 265 ARG cc_start: 0.7527 (mtp85) cc_final: 0.7273 (ttm110) REVERT: F 37 GLN cc_start: 0.6091 (mt0) cc_final: 0.5683 (mt0) REVERT: F 59 THR cc_start: 0.8906 (p) cc_final: 0.8639 (m) REVERT: F 169 GLU cc_start: 0.5852 (tt0) cc_final: 0.5583 (mt-10) REVERT: F 314 ARG cc_start: 0.2625 (ttt-90) cc_final: 0.1656 (mmp80) outliers start: 5 outliers final: 1 residues processed: 233 average time/residue: 0.3268 time to fit residues: 99.0812 Evaluate side-chains 172 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 71 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN D 208 HIS ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 GLN E 300 GLN F 140 HIS F 208 HIS ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.172650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.157284 restraints weight = 24942.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.157216 restraints weight = 24235.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.158645 restraints weight = 19886.070| |-----------------------------------------------------------------------------| r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10142 Z= 0.193 Angle : 0.868 9.975 13963 Z= 0.451 Chirality : 0.046 0.287 1691 Planarity : 0.007 0.075 1783 Dihedral : 18.510 175.346 1783 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.97 % Favored : 85.88 % Rotamer: Outliers : 0.23 % Allowed : 5.38 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.45 (0.20), residues: 1331 helix: -1.91 (0.27), residues: 317 sheet: -3.60 (0.33), residues: 174 loop : -3.43 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 174 HIS 0.009 0.002 HIS E 140 PHE 0.020 0.002 PHE E 95 TYR 0.018 0.002 TYR D 125 ARG 0.009 0.001 ARG C 184 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 248) hydrogen bonds : angle 7.46774 ( 684) covalent geometry : bond 0.00416 (10142) covalent geometry : angle 0.86804 (13963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 224 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 HIS cc_start: 0.6625 (t-170) cc_final: 0.6245 (m170) REVERT: C 237 ASP cc_start: 0.6326 (m-30) cc_final: 0.6010 (p0) REVERT: D 67 LEU cc_start: 0.7724 (pt) cc_final: 0.7430 (pp) REVERT: E 43 THR cc_start: 0.6995 (OUTLIER) cc_final: 0.6486 (t) REVERT: E 265 ARG cc_start: 0.7416 (mtp85) cc_final: 0.7181 (ttm110) REVERT: F 37 GLN cc_start: 0.5604 (mt0) cc_final: 0.5022 (mt0) REVERT: F 169 GLU cc_start: 0.6198 (tt0) cc_final: 0.5708 (mt-10) REVERT: F 314 ARG cc_start: 0.2346 (ttt-90) cc_final: 0.1843 (mmp80) outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.2909 time to fit residues: 85.6233 Evaluate side-chains 161 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 46 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 31 optimal weight: 0.0370 chunk 104 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 HIS ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 GLN ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.162671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.148032 restraints weight = 25917.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.148385 restraints weight = 24755.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.149615 restraints weight = 21027.600| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.7378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 10142 Z= 0.321 Angle : 1.082 11.450 13963 Z= 0.562 Chirality : 0.052 0.294 1691 Planarity : 0.008 0.080 1783 Dihedral : 18.940 171.410 1783 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 25.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 19.23 % Favored : 80.39 % Rotamer: Outliers : 0.23 % Allowed : 6.99 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -4.70 (0.19), residues: 1331 helix: -1.77 (0.28), residues: 294 sheet: -3.63 (0.32), residues: 176 loop : -3.75 (0.17), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP C 174 HIS 0.019 0.003 HIS C 208 PHE 0.033 0.004 PHE D 336 TYR 0.027 0.003 TYR M 20 ARG 0.009 0.001 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.05039 ( 248) hydrogen bonds : angle 8.22168 ( 684) covalent geometry : bond 0.00685 (10142) covalent geometry : angle 1.08221 (13963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 237 ASP cc_start: 0.6945 (m-30) cc_final: 0.6372 (t0) REVERT: C 265 ARG cc_start: 0.5244 (mtt180) cc_final: 0.4571 (mtt180) REVERT: C 275 ASP cc_start: 0.7583 (t70) cc_final: 0.7077 (t0) REVERT: C 324 HIS cc_start: 0.6088 (m-70) cc_final: 0.5747 (m170) REVERT: C 338 GLU cc_start: 0.9044 (mp0) cc_final: 0.8688 (mp0) REVERT: D 67 LEU cc_start: 0.7803 (pt) cc_final: 0.7535 (mt) REVERT: D 219 ILE cc_start: 0.8985 (mm) cc_final: 0.8646 (mm) REVERT: E 59 THR cc_start: 0.8118 (t) cc_final: 0.7904 (p) REVERT: E 279 PRO cc_start: 0.6347 (Cg_endo) cc_final: 0.5970 (Cg_exo) REVERT: F 37 GLN cc_start: 0.6361 (mt0) cc_final: 0.5194 (mt0) REVERT: F 56 ARG cc_start: 0.6001 (tmm-80) cc_final: 0.5437 (ttp80) REVERT: F 89 ASP cc_start: 0.6699 (m-30) cc_final: 0.6441 (m-30) REVERT: F 161 ARG cc_start: 0.5820 (ttt180) cc_final: 0.5439 (ttt180) REVERT: F 301 LYS cc_start: 0.6371 (pttm) cc_final: 0.6148 (pttm) REVERT: F 314 ARG cc_start: 0.2784 (ttt-90) cc_final: 0.1839 (mmp80) outliers start: 2 outliers final: 2 residues processed: 198 average time/residue: 0.3151 time to fit residues: 82.0196 Evaluate side-chains 159 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 157 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 110 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 98 optimal weight: 0.0020 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 92 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 88 optimal weight: 0.0000 chunk 132 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.174152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.160313 restraints weight = 24657.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.160222 restraints weight = 25093.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.161417 restraints weight = 22562.487| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.7499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10142 Z= 0.138 Angle : 0.818 9.000 13963 Z= 0.421 Chirality : 0.044 0.242 1691 Planarity : 0.005 0.068 1783 Dihedral : 18.245 175.983 1783 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.40 % Favored : 87.60 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.22 (0.20), residues: 1331 helix: -1.25 (0.30), residues: 314 sheet: -3.53 (0.33), residues: 176 loop : -3.47 (0.18), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 174 HIS 0.010 0.002 HIS C 140 PHE 0.018 0.002 PHE F 131 TYR 0.022 0.001 TYR M 20 ARG 0.015 0.001 ARG F 150 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 248) hydrogen bonds : angle 6.81126 ( 684) covalent geometry : bond 0.00285 (10142) covalent geometry : angle 0.81824 (13963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 ARG cc_start: 0.6905 (mtp-110) cc_final: 0.6619 (mtp85) REVERT: D 67 LEU cc_start: 0.7626 (pt) cc_final: 0.7291 (mt) REVERT: D 219 ILE cc_start: 0.8581 (mm) cc_final: 0.8332 (mm) REVERT: E 34 ASP cc_start: 0.6973 (t0) cc_final: 0.6613 (t0) REVERT: E 36 SER cc_start: 0.8761 (m) cc_final: 0.8420 (t) REVERT: F 37 GLN cc_start: 0.5222 (mt0) cc_final: 0.4244 (mt0) REVERT: F 314 ARG cc_start: 0.2831 (ttt-90) cc_final: 0.2418 (mmp80) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.3546 time to fit residues: 108.8034 Evaluate side-chains 171 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 0.0980 chunk 104 optimal weight: 20.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS D 140 HIS E 144 ASN E 223 GLN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.167710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.154131 restraints weight = 25610.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.153384 restraints weight = 24512.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.154744 restraints weight = 22670.949| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.8029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10142 Z= 0.203 Angle : 0.896 9.505 13963 Z= 0.461 Chirality : 0.046 0.258 1691 Planarity : 0.006 0.058 1783 Dihedral : 18.292 172.782 1783 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 17.05 % Favored : 82.72 % Rotamer: Outliers : 0.11 % Allowed : 4.12 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.23 (0.20), residues: 1331 helix: -1.26 (0.29), residues: 317 sheet: -3.34 (0.36), residues: 170 loop : -3.53 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 53 HIS 0.007 0.002 HIS E 208 PHE 0.024 0.002 PHE D 336 TYR 0.021 0.002 TYR M 20 ARG 0.008 0.001 ARG F 265 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 248) hydrogen bonds : angle 7.10718 ( 684) covalent geometry : bond 0.00440 (10142) covalent geometry : angle 0.89632 (13963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 ARG cc_start: 0.7109 (mtp-110) cc_final: 0.6843 (mtp85) REVERT: C 239 LYS cc_start: 0.7513 (mttp) cc_final: 0.6857 (tptm) REVERT: C 284 PRO cc_start: 0.6283 (Cg_endo) cc_final: 0.6067 (Cg_exo) REVERT: D 67 LEU cc_start: 0.7770 (pt) cc_final: 0.7445 (mt) REVERT: D 210 LEU cc_start: 0.7557 (mt) cc_final: 0.7211 (tp) REVERT: E 211 LEU cc_start: 0.8619 (pp) cc_final: 0.8355 (mt) REVERT: F 37 GLN cc_start: 0.5924 (mt0) cc_final: 0.4860 (mt0) REVERT: F 94 ARG cc_start: 0.7566 (mtt180) cc_final: 0.7034 (mtt180) REVERT: F 301 LYS cc_start: 0.5999 (pttm) cc_final: 0.5632 (pttm) REVERT: F 314 ARG cc_start: 0.3030 (ttt-90) cc_final: 0.1922 (mmt180) outliers start: 1 outliers final: 1 residues processed: 202 average time/residue: 0.2890 time to fit residues: 76.9752 Evaluate side-chains 159 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 75 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 51 optimal weight: 0.0370 overall best weight: 2.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS D 140 HIS E 144 ASN E 223 GLN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.167201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.152404 restraints weight = 26653.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.152583 restraints weight = 25779.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.153532 restraints weight = 26443.951| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.8397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10142 Z= 0.194 Angle : 0.888 13.101 13963 Z= 0.454 Chirality : 0.047 0.257 1691 Planarity : 0.005 0.058 1783 Dihedral : 18.291 172.734 1783 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 16.08 % Favored : 83.70 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.14 (0.20), residues: 1331 helix: -1.16 (0.29), residues: 317 sheet: -3.26 (0.36), residues: 170 loop : -3.50 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 174 HIS 0.017 0.003 HIS C 208 PHE 0.023 0.002 PHE F 131 TYR 0.021 0.002 TYR M 20 ARG 0.008 0.001 ARG D 314 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 248) hydrogen bonds : angle 7.08978 ( 684) covalent geometry : bond 0.00417 (10142) covalent geometry : angle 0.88750 (13963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 284 PRO cc_start: 0.6161 (Cg_endo) cc_final: 0.5945 (Cg_exo) REVERT: D 67 LEU cc_start: 0.7842 (pt) cc_final: 0.7602 (mt) REVERT: D 90 THR cc_start: 0.8460 (p) cc_final: 0.8183 (p) REVERT: D 210 LEU cc_start: 0.7667 (mt) cc_final: 0.7279 (tp) REVERT: D 270 TRP cc_start: 0.6808 (t-100) cc_final: 0.6343 (t-100) REVERT: D 274 GLU cc_start: 0.8256 (mp0) cc_final: 0.7929 (mp0) REVERT: E 36 SER cc_start: 0.8746 (m) cc_final: 0.8367 (t) REVERT: E 300 GLN cc_start: 0.8252 (mp10) cc_final: 0.7993 (mp10) REVERT: F 37 GLN cc_start: 0.5980 (mt0) cc_final: 0.4741 (mt0) REVERT: F 301 LYS cc_start: 0.5826 (pttm) cc_final: 0.5571 (pttm) REVERT: F 314 ARG cc_start: 0.3048 (ttt-90) cc_final: 0.1813 (mmt180) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.3293 time to fit residues: 90.0001 Evaluate side-chains 170 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 76 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 131 optimal weight: 0.0470 chunk 3 optimal weight: 6.9990 chunk 83 optimal weight: 0.0980 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 ASN C 223 GLN C 256 HIS C 324 HIS D 140 HIS D 324 HIS E 144 ASN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.169420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.156170 restraints weight = 26280.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.155636 restraints weight = 31267.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.156794 restraints weight = 28382.522| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.8744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10142 Z= 0.170 Angle : 0.861 11.959 13963 Z= 0.440 Chirality : 0.045 0.245 1691 Planarity : 0.005 0.054 1783 Dihedral : 18.181 176.863 1783 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.30 % Favored : 83.62 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.04 (0.20), residues: 1331 helix: -0.94 (0.30), residues: 316 sheet: -3.35 (0.34), residues: 176 loop : -3.45 (0.18), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP M 53 HIS 0.014 0.002 HIS C 208 PHE 0.015 0.002 PHE D 336 TYR 0.020 0.001 TYR M 20 ARG 0.007 0.001 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 248) hydrogen bonds : angle 6.84901 ( 684) covalent geometry : bond 0.00369 (10142) covalent geometry : angle 0.86061 (13963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 ARG cc_start: 0.7171 (mtp85) cc_final: 0.6835 (mmm160) REVERT: C 284 PRO cc_start: 0.6321 (Cg_endo) cc_final: 0.6093 (Cg_exo) REVERT: D 90 THR cc_start: 0.8201 (p) cc_final: 0.7937 (p) REVERT: D 210 LEU cc_start: 0.7430 (mt) cc_final: 0.7064 (tp) REVERT: E 34 ASP cc_start: 0.6858 (t0) cc_final: 0.6607 (t0) REVERT: E 36 SER cc_start: 0.8735 (m) cc_final: 0.8458 (t) REVERT: E 300 GLN cc_start: 0.8049 (mp10) cc_final: 0.7758 (mp10) REVERT: F 37 GLN cc_start: 0.5561 (mt0) cc_final: 0.4616 (mt0) REVERT: F 94 ARG cc_start: 0.7261 (mtt180) cc_final: 0.6664 (mtt180) REVERT: F 301 LYS cc_start: 0.5926 (pttm) cc_final: 0.5607 (pttm) REVERT: F 314 ARG cc_start: 0.3232 (ttt-90) cc_final: 0.2181 (mmt180) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.4615 time to fit residues: 138.7406 Evaluate side-chains 177 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 10.0000 chunk 59 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN C 324 HIS D 140 HIS ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 HIS ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.170380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.156501 restraints weight = 25133.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.156877 restraints weight = 28486.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.158061 restraints weight = 24159.467| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.8927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10142 Z= 0.146 Angle : 0.834 11.408 13963 Z= 0.424 Chirality : 0.045 0.231 1691 Planarity : 0.005 0.052 1783 Dihedral : 18.066 177.541 1783 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.03 % Favored : 84.90 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -3.92 (0.21), residues: 1331 helix: -0.82 (0.30), residues: 318 sheet: -3.32 (0.35), residues: 170 loop : -3.38 (0.18), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 174 HIS 0.013 0.002 HIS C 208 PHE 0.024 0.002 PHE F 131 TYR 0.018 0.001 TYR M 20 ARG 0.011 0.001 ARG C 94 Details of bonding type rmsd hydrogen bonds : bond 0.03116 ( 248) hydrogen bonds : angle 6.61293 ( 684) covalent geometry : bond 0.00314 (10142) covalent geometry : angle 0.83355 (13963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 284 PRO cc_start: 0.6247 (Cg_endo) cc_final: 0.6044 (Cg_exo) REVERT: E 34 ASP cc_start: 0.6752 (t0) cc_final: 0.6460 (t0) REVERT: E 211 LEU cc_start: 0.8396 (pp) cc_final: 0.8075 (mt) REVERT: F 37 GLN cc_start: 0.5377 (mt0) cc_final: 0.4542 (mt0) REVERT: F 94 ARG cc_start: 0.7131 (mtt180) cc_final: 0.6790 (mtm180) REVERT: F 293 LYS cc_start: 0.7146 (pptt) cc_final: 0.6748 (mtpp) REVERT: F 301 LYS cc_start: 0.5942 (pttm) cc_final: 0.5670 (pttm) REVERT: F 314 ARG cc_start: 0.2895 (ttt-90) cc_final: 0.2396 (mmp80) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.5250 time to fit residues: 141.4935 Evaluate side-chains 173 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 123 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS D 262 ASN E 223 GLN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN F 229 GLN F 324 HIS F 329 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.158605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.145070 restraints weight = 26841.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.144900 restraints weight = 29320.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.145634 restraints weight = 24817.965| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.9596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 10142 Z= 0.360 Angle : 1.158 13.023 13963 Z= 0.597 Chirality : 0.055 0.301 1691 Planarity : 0.008 0.099 1783 Dihedral : 18.899 167.322 1783 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 29.40 Ramachandran Plot: Outliers : 0.53 % Allowed : 21.49 % Favored : 77.99 % Rotamer: Outliers : 0.11 % Allowed : 1.49 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -4.54 (0.20), residues: 1331 helix: -1.48 (0.28), residues: 317 sheet: -3.80 (0.30), residues: 189 loop : -3.66 (0.18), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.005 TRP M 53 HIS 0.022 0.003 HIS C 208 PHE 0.040 0.004 PHE E 226 TYR 0.023 0.003 TYR M 20 ARG 0.022 0.002 ARG E 172 Details of bonding type rmsd hydrogen bonds : bond 0.05143 ( 248) hydrogen bonds : angle 8.04725 ( 684) covalent geometry : bond 0.00764 (10142) covalent geometry : angle 1.15757 (13963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 214 VAL cc_start: 0.7826 (t) cc_final: 0.7435 (t) REVERT: C 284 PRO cc_start: 0.6487 (Cg_endo) cc_final: 0.6243 (Cg_exo) REVERT: C 338 GLU cc_start: 0.9067 (mp0) cc_final: 0.8849 (mp0) REVERT: D 25 MET cc_start: 0.6487 (mpp) cc_final: 0.6141 (mmp) REVERT: D 270 TRP cc_start: 0.7495 (t-100) cc_final: 0.7068 (t-100) REVERT: F 56 ARG cc_start: 0.6450 (tmm-80) cc_final: 0.6183 (ttp-170) REVERT: F 89 ASP cc_start: 0.6605 (m-30) cc_final: 0.6336 (m-30) REVERT: M 16 ASN cc_start: 0.6711 (t0) cc_final: 0.6433 (t0) outliers start: 1 outliers final: 1 residues processed: 192 average time/residue: 0.3643 time to fit residues: 92.8360 Evaluate side-chains 148 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 90 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 2 optimal weight: 0.0170 chunk 36 optimal weight: 0.6980 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN C 262 ASN C 324 HIS D 140 HIS ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.168726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.155170 restraints weight = 25674.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.154380 restraints weight = 28707.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.155608 restraints weight = 26946.997| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.9648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10142 Z= 0.153 Angle : 0.876 10.639 13963 Z= 0.447 Chirality : 0.046 0.248 1691 Planarity : 0.006 0.080 1783 Dihedral : 18.356 178.502 1783 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.43 % Favored : 85.35 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.10 (0.21), residues: 1331 helix: -0.89 (0.30), residues: 308 sheet: -3.57 (0.32), residues: 191 loop : -3.44 (0.18), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP M 53 HIS 0.013 0.002 HIS C 208 PHE 0.024 0.002 PHE D 336 TYR 0.019 0.001 TYR M 20 ARG 0.010 0.002 ARG C 172 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 248) hydrogen bonds : angle 6.86072 ( 684) covalent geometry : bond 0.00330 (10142) covalent geometry : angle 0.87649 (13963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3744.45 seconds wall clock time: 71 minutes 16.44 seconds (4276.44 seconds total)