Starting phenix.real_space_refine on Fri Feb 14 11:37:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xlp_6731/02_2025/5xlp_6731.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xlp_6731/02_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_6731/02_2025/5xlp_6731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xlp_6731/02_2025/5xlp_6731.map" model { file = "/net/cci-nas-00/data/ceres_data/5xlp_6731/02_2025/5xlp_6731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xlp_6731/02_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.81, per 1000 atoms: 0.68 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: 2.48 Conformation dependent library (CDL) restraints added in 1.6 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: 2.90 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: 2.59 Time building geometry restraints manager: 2.89 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: 0.840 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.790 Find NCS groups from input model: 0.420 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: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.390 ------------------------------------------------------------------------------- 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= 0.586 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 *********************** 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 : 0.998 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: 0.2798 time to fit residues: 115.9042 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 : 0.989 ------------------------------------------------------------------------------- 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 = 0.4468 r_free = 0.4468 target = 0.173024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.157735 restraints weight = 24775.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.159255 restraints weight = 20543.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.160334 restraints weight = 15692.360| |-----------------------------------------------------------------------------| r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 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= 0.352 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 *********************** 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 : 1.034 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: 0.6583 (t-170) cc_final: 0.5889 (m170) REVERT: C 237 ASP cc_start: 0.6678 (m-30) cc_final: 0.6014 (p0) REVERT: C 274 GLU cc_start: 0.8104 (mp0) cc_final: 0.7740 (mm-30) REVERT: D 67 LEU cc_start: 0.7456 (pt) cc_final: 0.7158 (pp) REVERT: D 125 TYR cc_start: 0.6216 (t80) cc_final: 0.5820 (t80) REVERT: D 274 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: D 313 LEU cc_start: 0.7133 (mt) cc_final: 0.6856 (mt) REVERT: E 265 ARG cc_start: 0.7519 (mtp85) cc_final: 0.7271 (ttm110) REVERT: F 37 GLN cc_start: 0.6075 (mt0) cc_final: 0.5677 (mt0) REVERT: F 59 THR cc_start: 0.8907 (p) cc_final: 0.8638 (m) REVERT: F 169 GLU cc_start: 0.5823 (tt0) cc_final: 0.5572 (mt-10) REVERT: F 314 ARG cc_start: 0.2630 (ttt-90) cc_final: 0.1667 (mmp80) outliers start: 5 outliers final: 1 residues processed: 233 average time/residue: 0.3105 time to fit residues: 94.8133 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 : 1.146 ------------------------------------------------------------------------------- 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: 0.6980 chunk 74 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 GLN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.177297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.161462 restraints weight = 24825.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.162733 restraints weight = 20706.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.164250 restraints weight = 16247.297| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10142 Z= 0.203 Angle : 0.803 9.483 13963 Z= 0.415 Chirality : 0.044 0.266 1691 Planarity : 0.006 0.073 1783 Dihedral : 18.404 175.895 1783 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.55 % Favored : 87.38 % Rotamer: Outliers : 0.11 % Allowed : 4.81 % Favored : 95.07 % 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: -4.32 (0.20), residues: 1331 helix: -1.61 (0.29), residues: 300 sheet: -3.47 (0.30), residues: 197 loop : -3.39 (0.18), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 174 HIS 0.008 0.001 HIS E 140 PHE 0.013 0.002 PHE C 186 TYR 0.019 0.001 TYR M 20 ARG 0.007 0.001 ARG M 74 *********************** 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 238 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 1.028 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 25 MET cc_start: 0.6472 (mtt) cc_final: 0.6153 (mtm) REVERT: C 161 ARG cc_start: 0.6797 (mmm160) cc_final: 0.6592 (mmm160) REVERT: D 67 LEU cc_start: 0.7693 (pt) cc_final: 0.7407 (pp) REVERT: D 322 GLN cc_start: 0.7044 (mm110) cc_final: 0.6785 (pp30) REVERT: E 34 ASP cc_start: 0.6767 (t0) cc_final: 0.6405 (t0) REVERT: E 36 SER cc_start: 0.8718 (m) cc_final: 0.8107 (t) REVERT: E 265 ARG cc_start: 0.7409 (mtp85) cc_final: 0.7137 (ttm110) REVERT: E 295 TYR cc_start: 0.7818 (m-80) cc_final: 0.7604 (m-80) REVERT: F 37 GLN cc_start: 0.5378 (mt0) cc_final: 0.4970 (mt0) REVERT: F 169 GLU cc_start: 0.6140 (tt0) cc_final: 0.5889 (mt-10) REVERT: F 314 ARG cc_start: 0.2415 (ttt-90) cc_final: 0.2046 (mmp80) REVERT: M 2 LYS cc_start: 0.6933 (mtmt) cc_final: 0.6706 (mptt) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.2908 time to fit residues: 89.1697 Evaluate side-chains 165 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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: 0.3980 chunk 56 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS C 144 ASN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS E 223 GLN E 229 GLN F 110 ASN ** F 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 = 0.4555 r_free = 0.4555 target = 0.184312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.167156 restraints weight = 24915.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.167815 restraints weight = 20157.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.169021 restraints weight = 17225.939| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10142 Z= 0.202 Angle : 0.787 9.142 13963 Z= 0.408 Chirality : 0.044 0.239 1691 Planarity : 0.005 0.059 1783 Dihedral : 18.186 175.133 1783 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.22 % Favored : 86.70 % Rotamer: Outliers : 0.11 % Allowed : 3.09 % Favored : 96.79 % 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: -4.14 (0.20), residues: 1331 helix: -1.15 (0.31), residues: 302 sheet: -3.38 (0.32), residues: 180 loop : -3.42 (0.17), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 174 HIS 0.009 0.001 HIS E 208 PHE 0.018 0.002 PHE E 186 TYR 0.022 0.001 TYR M 20 ARG 0.006 0.001 ARG F 94 *********************** 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 220 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 1.012 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: C 25 MET cc_start: 0.6646 (mtt) cc_final: 0.6072 (mtm) REVERT: D 67 LEU cc_start: 0.7607 (pt) cc_final: 0.7167 (mt) REVERT: D 211 LEU cc_start: 0.6906 (mt) cc_final: 0.6689 (tp) REVERT: E 34 ASP cc_start: 0.6747 (t0) cc_final: 0.6342 (t0) REVERT: E 36 SER cc_start: 0.8672 (m) cc_final: 0.8191 (t) REVERT: E 211 LEU cc_start: 0.8604 (pp) cc_final: 0.8383 (mt) REVERT: F 37 GLN cc_start: 0.5532 (mt0) cc_final: 0.4997 (mt0) REVERT: F 314 ARG cc_start: 0.2163 (ttt-90) cc_final: 0.1820 (mmp80) REVERT: M 1 MET cc_start: 0.6638 (tpp) cc_final: 0.6312 (mmm) outliers start: 1 outliers final: 1 residues processed: 220 average time/residue: 0.2938 time to fit residues: 85.0635 Evaluate side-chains 163 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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: 6.9990 chunk 42 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 92 optimal weight: 30.0000 chunk 79 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 85 optimal weight: 0.4980 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.162015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.147953 restraints weight = 26275.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.148069 restraints weight = 26201.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.149153 restraints weight = 23023.688| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.7597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 10142 Z= 0.473 Angle : 1.092 11.474 13963 Z= 0.568 Chirality : 0.053 0.306 1691 Planarity : 0.007 0.079 1783 Dihedral : 18.783 169.806 1783 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 27.13 Ramachandran Plot: Outliers : 0.53 % Allowed : 19.16 % Favored : 80.32 % Rotamer: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % 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: -4.60 (0.19), residues: 1331 helix: -1.77 (0.27), residues: 317 sheet: -3.41 (0.31), residues: 191 loop : -3.71 (0.18), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP M 53 HIS 0.017 0.003 HIS C 208 PHE 0.031 0.004 PHE C 131 TYR 0.027 0.003 TYR M 20 ARG 0.010 0.002 ARG D 56 *********************** 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 188 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.021 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 129 GLN cc_start: 0.7388 (mm-40) cc_final: 0.7170 (tp-100) REVERT: D 55 ASN cc_start: 0.7923 (t0) cc_final: 0.7156 (m110) REVERT: D 58 LYS cc_start: 0.7859 (mmpt) cc_final: 0.7585 (mmtt) REVERT: E 59 THR cc_start: 0.7953 (t) cc_final: 0.7686 (p) REVERT: E 211 LEU cc_start: 0.8525 (pp) cc_final: 0.8308 (mt) REVERT: E 258 GLN cc_start: 0.6667 (mt0) cc_final: 0.5917 (pm20) REVERT: E 279 PRO cc_start: 0.6349 (Cg_endo) cc_final: 0.5971 (Cg_exo) REVERT: F 25 MET cc_start: 0.5047 (mmm) cc_final: 0.4751 (tpp) REVERT: F 314 ARG cc_start: 0.2489 (ttt-90) cc_final: 0.1523 (mmp80) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2825 time to fit residues: 70.1337 Evaluate side-chains 146 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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: 0.9980 chunk 83 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 94 optimal weight: 8.9990 chunk 104 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 229 GLN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 ASN F 110 ASN F 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.172871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.158183 restraints weight = 25135.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.158011 restraints weight = 22357.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.159210 restraints weight = 20054.531| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.7792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10142 Z= 0.198 Angle : 0.824 9.756 13963 Z= 0.423 Chirality : 0.044 0.249 1691 Planarity : 0.005 0.073 1783 Dihedral : 18.285 175.710 1783 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.15 % Favored : 86.78 % Rotamer: Outliers : 0.11 % Allowed : 3.09 % Favored : 96.79 % 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: -4.16 (0.20), residues: 1331 helix: -1.33 (0.29), residues: 326 sheet: -3.40 (0.33), residues: 176 loop : -3.41 (0.18), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 174 HIS 0.009 0.002 HIS E 208 PHE 0.018 0.002 PHE F 131 TYR 0.021 0.002 TYR M 20 ARG 0.006 0.001 ARG F 150 *********************** 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 215 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.986 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: D 25 MET cc_start: 0.6202 (mpp) cc_final: 0.5990 (tpp) REVERT: D 55 ASN cc_start: 0.7249 (t0) cc_final: 0.6818 (m110) REVERT: D 56 ARG cc_start: 0.6906 (mmt180) cc_final: 0.6624 (tpt170) REVERT: D 90 THR cc_start: 0.8255 (p) cc_final: 0.7783 (p) REVERT: D 125 TYR cc_start: 0.6963 (t80) cc_final: 0.6728 (t80) REVERT: D 234 ASP cc_start: 0.6766 (m-30) cc_final: 0.6544 (m-30) REVERT: E 211 LEU cc_start: 0.8544 (pp) cc_final: 0.8302 (mt) REVERT: E 270 TRP cc_start: 0.5694 (t-100) cc_final: 0.5168 (t-100) REVERT: F 314 ARG cc_start: 0.2766 (ttt-90) cc_final: 0.2347 (mmp80) REVERT: M 53 TRP cc_start: 0.7426 (p-90) cc_final: 0.7045 (p-90) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.2749 time to fit residues: 78.4034 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 : 1.074 ------------------------------------------------------------------------------- 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: 6.9990 chunk 125 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 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 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN E 144 ASN E 322 GLN F 229 GLN F 329 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.159257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.146447 restraints weight = 27191.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.145466 restraints weight = 27192.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.146450 restraints weight = 29462.995| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.8814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 10142 Z= 0.521 Angle : 1.146 12.704 13963 Z= 0.590 Chirality : 0.054 0.311 1691 Planarity : 0.009 0.163 1783 Dihedral : 18.972 169.798 1783 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 28.77 Ramachandran Plot: Outliers : 0.68 % Allowed : 20.51 % Favored : 78.81 % Rotamer: Outliers : 0.11 % Allowed : 4.24 % Favored : 95.65 % 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: -4.69 (0.19), residues: 1331 helix: -1.66 (0.28), residues: 298 sheet: -3.61 (0.31), residues: 182 loop : -3.78 (0.18), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 270 HIS 0.013 0.003 HIS C 208 PHE 0.044 0.004 PHE E 226 TYR 0.024 0.003 TYR M 6 ARG 0.011 0.002 ARG D 314 *********************** 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 191 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 1.105 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: C 265 ARG cc_start: 0.5013 (mtt180) cc_final: 0.4497 (mtt180) REVERT: C 336 PHE cc_start: 0.7526 (m-80) cc_final: 0.7207 (m-80) REVERT: C 338 GLU cc_start: 0.9147 (mp0) cc_final: 0.8735 (mp0) REVERT: D 90 THR cc_start: 0.8561 (p) cc_final: 0.8196 (p) REVERT: D 270 TRP cc_start: 0.7205 (t-100) cc_final: 0.6857 (t-100) REVERT: E 338 GLU cc_start: 0.7744 (tp30) cc_final: 0.7407 (tp30) REVERT: F 89 ASP cc_start: 0.6295 (m-30) cc_final: 0.6059 (m-30) REVERT: F 94 ARG cc_start: 0.7649 (mtt180) cc_final: 0.7447 (mtt180) REVERT: F 314 ARG cc_start: 0.3696 (ttt-90) cc_final: 0.2109 (mmp80) REVERT: M 16 ASN cc_start: 0.6436 (t0) cc_final: 0.5053 (m-40) REVERT: M 17 ILE cc_start: 0.7760 (mm) cc_final: 0.7522 (mm) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.2962 time to fit residues: 73.3641 Evaluate side-chains 151 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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: 0.6980 chunk 101 optimal weight: 0.6980 chunk 105 optimal weight: 0.0980 chunk 27 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 3 optimal weight: 0.0670 chunk 83 optimal weight: 4.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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 141 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS C 229 GLN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN E 300 GLN F 110 ASN F 329 ASN ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.172181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.158392 restraints weight = 25691.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.158852 restraints weight = 25175.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.159942 restraints weight = 20800.059| |-----------------------------------------------------------------------------| r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.8797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10142 Z= 0.201 Angle : 0.850 11.301 13963 Z= 0.433 Chirality : 0.046 0.232 1691 Planarity : 0.005 0.074 1783 Dihedral : 18.234 177.699 1783 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.15 % Favored : 86.78 % 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: -4.10 (0.21), residues: 1331 helix: -0.99 (0.31), residues: 313 sheet: -3.47 (0.34), residues: 171 loop : -3.46 (0.18), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 270 HIS 0.009 0.001 HIS E 208 PHE 0.017 0.002 PHE D 336 TYR 0.018 0.001 TYR M 20 ARG 0.009 0.001 ARG F 94 *********************** 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 224 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.104 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 239 LYS cc_start: 0.7375 (mttp) cc_final: 0.6846 (tptm) REVERT: D 25 MET cc_start: 0.6111 (mpp) cc_final: 0.5883 (tpp) REVERT: D 55 ASN cc_start: 0.7817 (t0) cc_final: 0.7019 (m110) REVERT: D 90 THR cc_start: 0.8279 (p) cc_final: 0.7959 (p) REVERT: D 219 ILE cc_start: 0.8888 (mm) cc_final: 0.8596 (mm) REVERT: E 58 LYS cc_start: 0.6476 (ttmt) cc_final: 0.6231 (ttmt) REVERT: E 211 LEU cc_start: 0.8337 (pp) cc_final: 0.8100 (mt) REVERT: E 237 ASP cc_start: 0.5695 (m-30) cc_final: 0.5488 (m-30) REVERT: E 265 ARG cc_start: 0.7334 (ttm-80) cc_final: 0.6840 (ttm-80) REVERT: E 270 TRP cc_start: 0.5609 (t-100) cc_final: 0.4956 (t-100) REVERT: F 37 GLN cc_start: 0.5788 (mt0) cc_final: 0.4778 (mt0) REVERT: F 314 ARG cc_start: 0.2759 (ttt-90) cc_final: 0.2329 (mmp80) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3025 time to fit residues: 87.8224 Evaluate side-chains 162 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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: 9.9990 chunk 59 optimal weight: 0.0060 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- 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 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS D 324 HIS E 229 GLN E 300 GLN E 322 GLN ** M 49 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 = 0.4393 r_free = 0.4393 target = 0.167157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.153587 restraints weight = 25814.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.153466 restraints weight = 26494.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.154642 restraints weight = 23033.052| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.9028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10142 Z= 0.260 Angle : 0.882 11.134 13963 Z= 0.452 Chirality : 0.047 0.249 1691 Planarity : 0.006 0.072 1783 Dihedral : 18.174 176.251 1783 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 17.05 % Favored : 82.79 % 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: -4.10 (0.21), residues: 1331 helix: -0.94 (0.31), residues: 310 sheet: -3.44 (0.33), residues: 176 loop : -3.48 (0.18), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 270 HIS 0.012 0.002 HIS E 208 PHE 0.017 0.002 PHE D 336 TYR 0.015 0.002 TYR M 20 ARG 0.015 0.001 ARG M 74 *********************** 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 195 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.040 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: 0.7647 (t) cc_final: 0.7393 (t) REVERT: D 25 MET cc_start: 0.6672 (mpp) cc_final: 0.6062 (mmt) REVERT: D 210 LEU cc_start: 0.7449 (mt) cc_final: 0.7178 (tp) REVERT: D 214 VAL cc_start: 0.8097 (t) cc_final: 0.6573 (p) REVERT: D 239 LYS cc_start: 0.8158 (tmmt) cc_final: 0.7817 (tttt) REVERT: E 36 SER cc_start: 0.8799 (m) cc_final: 0.8529 (t) REVERT: E 211 LEU cc_start: 0.8618 (pp) cc_final: 0.8274 (mt) REVERT: E 265 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.6834 (ttm-80) REVERT: E 270 TRP cc_start: 0.5765 (t-100) cc_final: 0.5132 (t-100) REVERT: F 314 ARG cc_start: 0.3086 (ttt-90) cc_final: 0.2296 (mmp80) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2907 time to fit residues: 74.4389 Evaluate side-chains 160 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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: 8.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS E 223 GLN E 322 GLN F 329 ASN ** M 49 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 = 0.4365 r_free = 0.4365 target = 0.164634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.151753 restraints weight = 25854.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.152121 restraints weight = 23064.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.152945 restraints weight = 20554.056| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.9389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10142 Z= 0.303 Angle : 0.932 10.322 13963 Z= 0.477 Chirality : 0.048 0.259 1691 Planarity : 0.006 0.074 1783 Dihedral : 18.071 165.773 1783 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 18.48 % Favored : 81.37 % Rotamer: Outliers : 0.11 % Allowed : 0.69 % Favored : 99.20 % 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: -4.19 (0.21), residues: 1331 helix: -1.18 (0.30), residues: 316 sheet: -3.39 (0.33), residues: 173 loop : -3.50 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 270 HIS 0.012 0.002 HIS E 208 PHE 0.025 0.003 PHE D 336 TYR 0.019 0.002 TYR M 20 ARG 0.015 0.002 ARG M 74 ********************** 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 191 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 1.266 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 214 VAL cc_start: 0.7757 (t) cc_final: 0.6542 (t) REVERT: D 25 MET cc_start: 0.6665 (mpp) cc_final: 0.6216 (mpp) REVERT: D 214 VAL cc_start: 0.7688 (t) cc_final: 0.6678 (p) REVERT: E 36 SER cc_start: 0.9077 (m) cc_final: 0.8672 (t) REVERT: E 59 THR cc_start: 0.7696 (t) cc_final: 0.7410 (p) REVERT: E 111 ASP cc_start: 0.3980 (m-30) cc_final: 0.3477 (p0) REVERT: E 211 LEU cc_start: 0.8477 (pp) cc_final: 0.8191 (mt) REVERT: E 265 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.7056 (ttm-80) REVERT: E 270 TRP cc_start: 0.5836 (t-100) cc_final: 0.5217 (t-100) REVERT: E 300 GLN cc_start: 0.8232 (mp10) cc_final: 0.8017 (pm20) REVERT: E 338 GLU cc_start: 0.7421 (tp30) cc_final: 0.7078 (tp30) REVERT: F 314 ARG cc_start: 0.3496 (ttt-90) cc_final: 0.2234 (mmt180) outliers start: 1 outliers final: 1 residues processed: 191 average time/residue: 0.3110 time to fit residues: 77.3369 Evaluate side-chains 164 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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: 4.9990 chunk 8 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 117 optimal weight: 0.0670 chunk 10 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 229 GLN E 223 GLN E 322 GLN ** M 49 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 = 0.4440 r_free = 0.4440 target = 0.170812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.156340 restraints weight = 24775.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.156084 restraints weight = 24041.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.157810 restraints weight = 21593.189| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.9535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10142 Z= 0.211 Angle : 0.851 13.679 13963 Z= 0.430 Chirality : 0.044 0.237 1691 Planarity : 0.005 0.068 1783 Dihedral : 17.768 167.210 1783 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.88 % Favored : 84.97 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -3.93 (0.21), residues: 1331 helix: -0.83 (0.31), residues: 310 sheet: -3.24 (0.35), residues: 167 loop : -3.39 (0.18), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP C 270 HIS 0.011 0.001 HIS E 208 PHE 0.018 0.002 PHE M 54 TYR 0.015 0.001 TYR M 20 ARG 0.009 0.001 ARG D 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2838.87 seconds wall clock time: 52 minutes 1.55 seconds (3121.55 seconds total)