Starting phenix.real_space_refine on Thu Mar 14 22:18:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlp_6731/03_2024/5xlp_6731.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlp_6731/03_2024/5xlp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlp_6731/03_2024/5xlp_6731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlp_6731/03_2024/5xlp_6731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlp_6731/03_2024/5xlp_6731.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlp_6731/03_2024/5xlp_6731.pdb" } 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 Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D ARG 218": "NH1" <-> "NH2" Residue "D PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 218": "NH1" <-> "NH2" Residue "E PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 161": "NH1" <-> "NH2" Residue "F ARG 218": "NH1" <-> "NH2" Residue "F PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 75": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.36, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 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: 4.19 Conformation dependent library (CDL) restraints added in 1.7 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: 2.67 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: 2.36 Time building geometry restraints manager: 4.48 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: 98.72 - 106.15: 372 106.15 - 113.58: 5705 113.58 - 121.02: 4542 121.02 - 128.45: 3246 128.45 - 135.88: 98 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 2.440 nonbonded pdb=" O ASN E 75 " pdb=" OG1 THR E 78 " model vdw 2.232 2.440 nonbonded pdb=" OG1 THR D 90 " pdb=" O ALA D 254 " model vdw 2.258 2.440 nonbonded pdb=" OG1 THR C 105 " pdb=" OE1 GLN C 223 " model vdw 2.278 2.440 nonbonded pdb=" OG1 THR D 105 " pdb=" OE1 GLN D 223 " model vdw 2.279 2.440 ... (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 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: 0.650 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: 2.190 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 30.960 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.430 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 5 poor density : 314 time to evaluate : 1.130 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: 0.2644 time to fit residues: 109.6537 Evaluate side-chains 184 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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: 0.7980 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 HIS C 141 ASN C 144 ASN C 151 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 GLN F 140 HIS F 151 ASN F 258 GLN F 300 GLN ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10142 Z= 0.274 Angle : 0.886 10.026 13963 Z= 0.454 Chirality : 0.046 0.269 1691 Planarity : 0.007 0.076 1783 Dihedral : 18.701 177.565 1783 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.70 % Favored : 87.00 % Rotamer: Outliers : 0.23 % Allowed : 5.61 % Favored : 94.16 % 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: -4.68 (0.19), residues: 1331 helix: -2.15 (0.27), residues: 279 sheet: -3.76 (0.30), residues: 174 loop : -3.53 (0.17), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 174 HIS 0.004 0.001 HIS E 256 PHE 0.022 0.002 PHE D 147 TYR 0.019 0.002 TYR M 20 ARG 0.008 0.001 ARG F 184 *********************** 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 242 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 1.127 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 34 ASP cc_start: 0.6433 (m-30) cc_final: 0.6040 (t0) REVERT: C 237 ASP cc_start: 0.7307 (m-30) cc_final: 0.6489 (p0) REVERT: C 274 GLU cc_start: 0.8065 (mp0) cc_final: 0.7732 (mm-30) REVERT: D 67 LEU cc_start: 0.7783 (pt) cc_final: 0.7053 (tp) REVERT: D 125 TYR cc_start: 0.5758 (t80) cc_final: 0.5547 (t80) REVERT: D 270 TRP cc_start: 0.7186 (t-100) cc_final: 0.6628 (t-100) REVERT: E 80 ASP cc_start: 0.7660 (m-30) cc_final: 0.7430 (m-30) REVERT: E 265 ARG cc_start: 0.7335 (mtp85) cc_final: 0.7026 (ttm110) REVERT: F 37 GLN cc_start: 0.5638 (mt0) cc_final: 0.5238 (mt0) REVERT: F 59 THR cc_start: 0.9057 (p) cc_final: 0.8558 (m) REVERT: F 169 GLU cc_start: 0.5897 (tt0) cc_final: 0.5554 (mt-10) REVERT: F 303 ASP cc_start: 0.5547 (m-30) cc_final: 0.5275 (t0) REVERT: F 314 ARG cc_start: 0.2265 (ttt-90) cc_final: 0.1728 (mmp80) REVERT: M 69 MET cc_start: 0.7498 (tmm) cc_final: 0.7124 (tmm) outliers start: 2 outliers final: 0 residues processed: 241 average time/residue: 0.2703 time to fit residues: 85.3588 Evaluate side-chains 172 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.0970 chunk 37 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 120 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 119 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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** D 151 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 GLN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN E 300 GLN F 140 HIS ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10142 Z= 0.178 Angle : 0.737 9.086 13963 Z= 0.385 Chirality : 0.042 0.234 1691 Planarity : 0.005 0.072 1783 Dihedral : 18.162 177.619 1783 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.87 % Favored : 87.90 % Rotamer: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % 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: -4.30 (0.20), residues: 1331 helix: -1.60 (0.29), residues: 321 sheet: -3.62 (0.32), residues: 172 loop : -3.40 (0.18), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 174 HIS 0.004 0.001 HIS D 208 PHE 0.014 0.001 PHE C 186 TYR 0.015 0.001 TYR M 20 ARG 0.007 0.001 ARG C 150 *********************** 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 234 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.042 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: C 34 ASP cc_start: 0.6264 (m-30) cc_final: 0.5855 (t0) REVERT: C 129 GLN cc_start: 0.7616 (pm20) cc_final: 0.7406 (mm-40) REVERT: C 237 ASP cc_start: 0.6765 (m-30) cc_final: 0.6338 (p0) REVERT: D 67 LEU cc_start: 0.7861 (pt) cc_final: 0.7509 (pp) REVERT: F 59 THR cc_start: 0.8853 (p) cc_final: 0.8318 (m) REVERT: M 4 ILE cc_start: 0.8150 (pt) cc_final: 0.7926 (pt) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.2659 time to fit residues: 81.7750 Evaluate side-chains 174 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 144 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10142 Z= 0.231 Angle : 0.778 9.242 13963 Z= 0.402 Chirality : 0.044 0.240 1691 Planarity : 0.005 0.060 1783 Dihedral : 18.067 176.917 1783 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.20 % Favored : 85.57 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.20), residues: 1331 helix: -1.05 (0.32), residues: 286 sheet: -3.37 (0.33), residues: 170 loop : -3.37 (0.17), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 174 HIS 0.008 0.001 HIS E 208 PHE 0.017 0.002 PHE E 95 TYR 0.015 0.001 TYR M 20 ARG 0.008 0.001 ARG C 172 *********************** 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 218 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.147 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 34 ASP cc_start: 0.6514 (m-30) cc_final: 0.6112 (t0) REVERT: C 129 GLN cc_start: 0.7426 (pm20) cc_final: 0.7173 (mm110) REVERT: D 67 LEU cc_start: 0.7810 (pt) cc_final: 0.7414 (mt) REVERT: D 210 LEU cc_start: 0.7528 (tp) cc_final: 0.7304 (tp) REVERT: E 80 ASP cc_start: 0.7789 (m-30) cc_final: 0.7572 (m-30) REVERT: F 59 THR cc_start: 0.8692 (p) cc_final: 0.8312 (m) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2679 time to fit residues: 77.5258 Evaluate side-chains 160 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 0.4980 chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 53 optimal weight: 0.0970 chunk 109 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 overall best weight: 1.4980 ------------------------------------------------------------------------------- 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 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS D 141 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.6659 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= 0.227 Angle : 0.777 11.181 13963 Z= 0.401 Chirality : 0.044 0.242 1691 Planarity : 0.005 0.054 1783 Dihedral : 17.959 174.568 1783 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.03 % Favored : 84.82 % Rotamer: Outliers : 0.23 % Allowed : 3.78 % Favored : 95.99 % 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 (0.20), residues: 1331 helix: -1.27 (0.30), residues: 320 sheet: -3.33 (0.34), residues: 182 loop : -3.37 (0.18), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 53 HIS 0.008 0.001 HIS E 208 PHE 0.029 0.002 PHE C 131 TYR 0.017 0.001 TYR E 125 ARG 0.005 0.001 ARG C 150 *********************** 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 216 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 1.016 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 34 ASP cc_start: 0.6511 (m-30) cc_final: 0.6276 (t70) REVERT: C 131 PHE cc_start: 0.7888 (m-80) cc_final: 0.7609 (m-80) REVERT: C 265 ARG cc_start: 0.5564 (mtt180) cc_final: 0.4812 (mtt180) REVERT: C 293 LYS cc_start: 0.7240 (mmtt) cc_final: 0.7013 (mmtm) REVERT: C 338 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7793 (mm-30) REVERT: D 67 LEU cc_start: 0.7909 (pt) cc_final: 0.7498 (mt) REVERT: E 80 ASP cc_start: 0.7952 (m-30) cc_final: 0.7620 (m-30) REVERT: F 37 GLN cc_start: 0.5461 (mt0) cc_final: 0.5047 (mt0) REVERT: F 59 THR cc_start: 0.8687 (p) cc_final: 0.8245 (m) REVERT: F 314 ARG cc_start: 0.1672 (mmt-90) cc_final: 0.1372 (mmt-90) REVERT: M 53 TRP cc_start: 0.7849 (p-90) cc_final: 0.7478 (p-90) outliers start: 2 outliers final: 0 residues processed: 215 average time/residue: 0.2728 time to fit residues: 76.8362 Evaluate side-chains 167 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 HIS E 141 ASN E 144 ASN E 223 GLN F 324 HIS F 329 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.8134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 10142 Z= 0.556 Angle : 1.146 11.702 13963 Z= 0.597 Chirality : 0.056 0.311 1691 Planarity : 0.008 0.088 1783 Dihedral : 18.879 176.393 1783 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 34.32 Ramachandran Plot: Outliers : 0.53 % Allowed : 20.89 % Favored : 78.59 % Rotamer: Outliers : 0.23 % Allowed : 5.84 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -4.66 (0.19), residues: 1331 helix: -1.87 (0.28), residues: 298 sheet: -3.20 (0.32), residues: 191 loop : -3.76 (0.17), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP C 270 HIS 0.023 0.004 HIS C 208 PHE 0.044 0.004 PHE E 95 TYR 0.032 0.004 TYR C 125 ARG 0.012 0.002 ARG D 161 *********************** 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 198 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ASP cc_start: 0.6995 (m-30) cc_final: 0.5893 (t70) REVERT: C 265 ARG cc_start: 0.5770 (mtt180) cc_final: 0.4291 (mmt-90) REVERT: D 211 LEU cc_start: 0.7655 (mt) cc_final: 0.7353 (tt) REVERT: E 58 LYS cc_start: 0.6701 (mtmt) cc_final: 0.6274 (mtmt) REVERT: E 59 THR cc_start: 0.8056 (t) cc_final: 0.7747 (p) REVERT: E 81 VAL cc_start: 0.7841 (t) cc_final: 0.7636 (t) REVERT: E 111 ASP cc_start: 0.4635 (m-30) cc_final: 0.4076 (p0) REVERT: F 25 MET cc_start: 0.4999 (mmm) cc_final: 0.4639 (tpp) REVERT: F 59 THR cc_start: 0.8833 (p) cc_final: 0.8599 (m) REVERT: F 94 ARG cc_start: 0.7661 (mtt180) cc_final: 0.7313 (mtt180) REVERT: F 99 VAL cc_start: 0.6692 (t) cc_final: 0.6325 (t) REVERT: M 17 ILE cc_start: 0.8250 (mt) cc_final: 0.7969 (mt) REVERT: M 25 LYS cc_start: 0.8363 (ptmm) cc_final: 0.7270 (mmmt) outliers start: 2 outliers final: 2 residues processed: 198 average time/residue: 0.2837 time to fit residues: 73.2206 Evaluate side-chains 159 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 8.9990 chunk 14 optimal weight: 0.0980 chunk 73 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 127 ASN C 324 HIS ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN E 144 ASN E 223 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.8345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10142 Z= 0.249 Angle : 0.852 9.469 13963 Z= 0.439 Chirality : 0.046 0.251 1691 Planarity : 0.006 0.079 1783 Dihedral : 18.292 179.110 1783 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.10 % Favored : 84.75 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -4.31 (0.20), residues: 1331 helix: -1.38 (0.30), residues: 306 sheet: -3.30 (0.34), residues: 170 loop : -3.56 (0.17), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 270 HIS 0.018 0.002 HIS D 256 PHE 0.020 0.002 PHE C 95 TYR 0.018 0.001 TYR D 125 ARG 0.011 0.001 ARG C 184 *********************** 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 207 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.016 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 301 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7510 (mttm) REVERT: E 58 LYS cc_start: 0.6491 (mtmt) cc_final: 0.6141 (mtmt) REVERT: E 80 ASP cc_start: 0.8191 (m-30) cc_final: 0.7739 (m-30) REVERT: E 270 TRP cc_start: 0.5967 (t-100) cc_final: 0.5274 (t-100) REVERT: F 59 THR cc_start: 0.8776 (p) cc_final: 0.8272 (m) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2654 time to fit residues: 72.1542 Evaluate side-chains 165 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 87 optimal weight: 0.0670 chunk 63 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 overall best weight: 2.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 HIS ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.8760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10142 Z= 0.301 Angle : 0.884 10.069 13963 Z= 0.457 Chirality : 0.047 0.261 1691 Planarity : 0.006 0.075 1783 Dihedral : 18.302 178.414 1783 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.30 % Allowed : 19.23 % Favored : 80.47 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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: -4.29 (0.20), residues: 1331 helix: -1.39 (0.29), residues: 313 sheet: -3.25 (0.33), residues: 176 loop : -3.56 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 174 HIS 0.008 0.002 HIS E 208 PHE 0.021 0.002 PHE F 226 TYR 0.025 0.002 TYR M 6 ARG 0.010 0.001 ARG F 150 *********************** 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 198 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 214 VAL cc_start: 0.7805 (t) cc_final: 0.7233 (t) REVERT: D 90 THR cc_start: 0.7402 (p) cc_final: 0.7107 (p) REVERT: E 58 LYS cc_start: 0.6446 (mtmt) cc_final: 0.6104 (mtmt) REVERT: E 81 VAL cc_start: 0.7802 (t) cc_final: 0.7600 (t) REVERT: E 211 LEU cc_start: 0.8795 (pp) cc_final: 0.8540 (mt) REVERT: E 265 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7363 (ttm-80) REVERT: E 270 TRP cc_start: 0.6069 (t-100) cc_final: 0.5445 (t-100) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2809 time to fit residues: 72.0932 Evaluate side-chains 161 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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: 8.9990 chunk 122 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 52 optimal weight: 0.0770 chunk 93 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 126 optimal weight: 0.6980 overall best weight: 1.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 ASN E 322 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.8965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10142 Z= 0.253 Angle : 0.860 12.941 13963 Z= 0.441 Chirality : 0.046 0.250 1691 Planarity : 0.005 0.073 1783 Dihedral : 18.155 177.489 1783 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 16.00 % Favored : 83.77 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % 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: -4.13 (0.20), residues: 1331 helix: -1.24 (0.30), residues: 313 sheet: -3.15 (0.35), residues: 167 loop : -3.48 (0.18), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 174 HIS 0.009 0.002 HIS C 324 PHE 0.023 0.002 PHE F 131 TYR 0.019 0.002 TYR E 125 ARG 0.009 0.001 ARG C 94 *********************** 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 203 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.130 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: D 90 THR cc_start: 0.7203 (p) cc_final: 0.6923 (p) REVERT: D 210 LEU cc_start: 0.7735 (mt) cc_final: 0.7415 (tp) REVERT: E 58 LYS cc_start: 0.6390 (mtmt) cc_final: 0.6087 (mtmt) REVERT: E 218 ARG cc_start: 0.3819 (mpt180) cc_final: 0.3533 (mpt180) REVERT: E 270 TRP cc_start: 0.5852 (t-100) cc_final: 0.5144 (t-100) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2749 time to fit residues: 73.3652 Evaluate side-chains 160 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 87 optimal weight: 0.0050 chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 overall best weight: 3.3800 ------------------------------------------------------------------------------- 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 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN C 324 HIS D 140 HIS ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN E 322 GLN F 329 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.9473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 10142 Z= 0.397 Angle : 0.995 12.674 13963 Z= 0.515 Chirality : 0.050 0.275 1691 Planarity : 0.007 0.073 1783 Dihedral : 18.513 179.189 1783 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 28.61 Ramachandran Plot: Outliers : 0.30 % Allowed : 21.34 % Favored : 78.36 % Rotamer: Outliers : 0.11 % Allowed : 0.46 % Favored : 99.43 % 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: -4.24 (0.20), residues: 1331 helix: -1.41 (0.29), residues: 319 sheet: -3.25 (0.34), residues: 177 loop : -3.50 (0.18), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP D 174 HIS 0.007 0.002 HIS E 208 PHE 0.029 0.003 PHE E 226 TYR 0.024 0.003 TYR E 125 ARG 0.014 0.001 ARG C 172 ********************** 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 178 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 214 VAL cc_start: 0.8151 (t) cc_final: 0.7518 (t) REVERT: C 265 ARG cc_start: 0.6296 (mtt180) cc_final: 0.4982 (mmt-90) REVERT: D 301 LYS cc_start: 0.8192 (mptt) cc_final: 0.7744 (tmtt) REVERT: E 58 LYS cc_start: 0.6993 (mtmt) cc_final: 0.6458 (mtmt) REVERT: E 270 TRP cc_start: 0.6213 (t-100) cc_final: 0.5495 (t-100) REVERT: M 1 MET cc_start: 0.7071 (tpp) cc_final: 0.6755 (tpp) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.2626 time to fit residues: 62.0261 Evaluate side-chains 154 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 0.0020 chunk 44 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 6 optimal weight: 0.0020 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS D 151 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 HIS E 322 GLN F 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.168550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.155513 restraints weight = 25590.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.155206 restraints weight = 30195.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.156367 restraints weight = 26542.573| |-----------------------------------------------------------------------------| r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.9550 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 : 0.833 12.706 13963 Z= 0.425 Chirality : 0.045 0.238 1691 Planarity : 0.005 0.069 1783 Dihedral : 18.141 176.739 1783 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.30 % Allowed : 15.63 % Favored : 84.07 % Rotamer: Outliers : 0.11 % Allowed : 0.46 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.20), residues: 1331 helix: -1.15 (0.30), residues: 312 sheet: -3.10 (0.35), residues: 167 loop : -3.41 (0.18), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 174 HIS 0.009 0.001 HIS E 208 PHE 0.015 0.002 PHE C 95 TYR 0.017 0.001 TYR E 125 ARG 0.007 0.001 ARG E 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2212.09 seconds wall clock time: 40 minutes 24.45 seconds (2424.45 seconds total)