Starting phenix.real_space_refine on Sat Dec 9 03:26:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlp_6731/12_2023/5xlp_6731.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlp_6731/12_2023/5xlp_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_6731/12_2023/5xlp_6731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlp_6731/12_2023/5xlp_6731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlp_6731/12_2023/5xlp_6731.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlp_6731/12_2023/5xlp_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-1.21rc1-5172/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: 5.98, per 1000 atoms: 0.60 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 1.8 seconds 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 29.3% alpha, 6.0% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 3.12 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: 2.40 Time building geometry restraints manager: 4.43 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: 5948 35.85 - 71.71: 95 71.71 - 107.56: 17 107.56 - 143.41: 1 143.41 - 179.27: 6 Dihedral angle restraints: 6067 sinusoidal: 2226 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 6064 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: 0.440 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: 0.000 Extract box with map and model: 2.070 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.150 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- 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 : 15.793 179.265 3587 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 : 1.085 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 outliers start: 5 outliers final: 1 residues processed: 318 average time/residue: 0.2783 time to fit residues: 115.5956 Evaluate side-chains 181 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0912 time to fit residues: 1.6610 ------------------------------------------------------------------------------- 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: 3.9990 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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: 0.6200 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10142 Z= 0.297 Angle : 0.907 12.290 13963 Z= 0.466 Chirality : 0.046 0.279 1691 Planarity : 0.007 0.076 1783 Dihedral : 18.385 177.927 1759 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.67 % Favored : 85.95 % Rotamer: Outliers : 0.23 % Allowed : 5.96 % Favored : 93.81 % 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: -4.81 (0.19), residues: 1331 helix: -2.32 (0.26), residues: 293 sheet: -3.83 (0.29), residues: 180 loop : -3.59 (0.17), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 174 HIS 0.006 0.001 HIS D 208 PHE 0.023 0.002 PHE D 147 TYR 0.020 0.002 TYR M 20 ARG 0.006 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 238 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 236 time to evaluate : 1.091 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 outliers start: 2 outliers final: 0 residues processed: 237 average time/residue: 0.2883 time to fit residues: 89.4554 Evaluate side-chains 168 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4645 ------------------------------------------------------------------------------- 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: 8.9990 chunk 37 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS D 208 HIS ** 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 256 HIS E 300 GLN F 127 ASN F 208 HIS ** M 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.6893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 10142 Z= 0.519 Angle : 1.145 11.276 13963 Z= 0.600 Chirality : 0.054 0.325 1691 Planarity : 0.009 0.091 1783 Dihedral : 18.922 177.670 1759 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 33.16 Ramachandran Plot: Outliers : 0.45 % Allowed : 20.14 % Favored : 79.41 % Rotamer: Outliers : 1.15 % Allowed : 7.33 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.78 % 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: -4.93 (0.19), residues: 1331 helix: -2.23 (0.26), residues: 291 sheet: -3.60 (0.30), residues: 183 loop : -3.82 (0.18), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP D 174 HIS 0.012 0.003 HIS D 208 PHE 0.031 0.004 PHE C 226 TYR 0.033 0.003 TYR C 125 ARG 0.015 0.002 ARG E 161 *********************** 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 207 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 197 time to evaluate : 1.098 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 outliers start: 10 outliers final: 6 residues processed: 205 average time/residue: 0.2769 time to fit residues: 74.9300 Evaluate side-chains 155 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1021 time to fit residues: 2.5606 ------------------------------------------------------------------------------- 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: 0.0970 chunk 90 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 115 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** 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 127 ASN F 140 HIS ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.7134 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= 0.197 Angle : 0.809 9.544 13963 Z= 0.419 Chirality : 0.043 0.244 1691 Planarity : 0.006 0.092 1783 Dihedral : 18.104 177.588 1759 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.77 % Favored : 87.00 % Rotamer: Outliers : 0.23 % Allowed : 4.35 % Favored : 95.42 % 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: -4.39 (0.20), residues: 1331 helix: -1.43 (0.30), residues: 310 sheet: -3.85 (0.32), residues: 161 loop : -3.52 (0.18), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 270 HIS 0.012 0.002 HIS E 140 PHE 0.013 0.002 PHE F 95 TYR 0.018 0.001 TYR M 20 ARG 0.005 0.001 ARG D 161 *********************** 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 231 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 229 time to evaluate : 0.960 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 outliers start: 2 outliers final: 0 residues processed: 230 average time/residue: 0.2906 time to fit residues: 86.6391 Evaluate side-chains 161 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5248 ------------------------------------------------------------------------------- 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: 9.9990 chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN E 127 ASN E 223 GLN E 256 HIS E 300 GLN F 329 ASN ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.7853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10142 Z= 0.337 Angle : 0.930 11.734 13963 Z= 0.481 Chirality : 0.047 0.265 1691 Planarity : 0.007 0.086 1783 Dihedral : 18.194 179.301 1759 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 25.81 Ramachandran Plot: Outliers : 0.38 % Allowed : 19.53 % Favored : 80.09 % Rotamer: Outliers : 0.11 % Allowed : 6.07 % Favored : 93.81 % 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: -4.37 (0.20), residues: 1331 helix: -1.27 (0.30), residues: 299 sheet: -3.45 (0.32), residues: 192 loop : -3.61 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 270 HIS 0.007 0.002 HIS E 208 PHE 0.024 0.003 PHE F 95 TYR 0.020 0.002 TYR M 20 ARG 0.009 0.001 ARG F 265 *********************** 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 192 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 1.152 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 outliers start: 1 outliers final: 1 residues processed: 192 average time/residue: 0.3116 time to fit residues: 77.4243 Evaluate side-chains 151 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0893 time to fit residues: 1.5926 ------------------------------------------------------------------------------- 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: 0.9980 chunk 115 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 GLN C 241 GLN C 324 HIS D 83 ASN ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS E 127 ASN E 241 GLN E 300 GLN ** F 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN M 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.8059 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= 0.194 Angle : 0.794 9.262 13963 Z= 0.408 Chirality : 0.043 0.234 1691 Planarity : 0.005 0.070 1783 Dihedral : 17.765 177.673 1759 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.00 % Favored : 86.78 % Rotamer: Outliers : 0.11 % Allowed : 3.67 % 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: -4.08 (0.21), residues: 1331 helix: -0.90 (0.31), residues: 311 sheet: -3.49 (0.34), residues: 171 loop : -3.47 (0.18), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP M 53 HIS 0.008 0.002 HIS E 208 PHE 0.012 0.001 PHE E 186 TYR 0.021 0.001 TYR D 125 ARG 0.013 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 213 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 1.126 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 outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.2719 time to fit residues: 76.6868 Evaluate side-chains 165 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5023 ------------------------------------------------------------------------------- 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: 10.0000 chunk 14 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 128 optimal weight: 0.1980 chunk 80 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS E 127 ASN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS E 300 GLN E 322 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.8702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 10142 Z= 0.390 Angle : 0.995 12.116 13963 Z= 0.511 Chirality : 0.049 0.273 1691 Planarity : 0.007 0.078 1783 Dihedral : 18.231 178.290 1759 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 28.24 Ramachandran Plot: Outliers : 0.45 % Allowed : 20.74 % Favored : 78.81 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -4.35 (0.20), residues: 1331 helix: -1.25 (0.29), residues: 322 sheet: -3.30 (0.35), residues: 176 loop : -3.71 (0.18), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP M 53 HIS 0.008 0.002 HIS E 208 PHE 0.028 0.003 PHE D 336 TYR 0.031 0.003 TYR D 125 ARG 0.012 0.001 ARG E 172 *********************** 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 fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.171 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 outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2966 time to fit residues: 73.7224 Evaluate side-chains 149 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4261 ------------------------------------------------------------------------------- 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: 7.9990 chunk 51 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 140 HIS E 127 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN E 310 ASN E 322 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.8930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10142 Z= 0.246 Angle : 0.867 9.792 13963 Z= 0.443 Chirality : 0.045 0.248 1691 Planarity : 0.006 0.072 1783 Dihedral : 17.963 177.347 1759 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 16.15 % Favored : 83.62 % Rotamer: Outliers : 0.11 % Allowed : 1.49 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.15 (0.21), residues: 1331 helix: -1.11 (0.29), residues: 325 sheet: -3.20 (0.35), residues: 182 loop : -3.56 (0.18), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 270 HIS 0.007 0.001 HIS E 208 PHE 0.028 0.002 PHE C 95 TYR 0.021 0.002 TYR M 20 ARG 0.017 0.001 ARG E 161 *********************** 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 202 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 1.173 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 outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.2990 time to fit residues: 78.4618 Evaluate side-chains 162 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4604 ------------------------------------------------------------------------------- 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: 5.9990 chunk 122 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 119 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 324 HIS D 129 GLN D 141 ASN E 258 GLN E 322 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.9357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10142 Z= 0.335 Angle : 0.940 10.420 13963 Z= 0.482 Chirality : 0.047 0.260 1691 Planarity : 0.006 0.069 1783 Dihedral : 18.140 177.121 1759 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 27.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 20.81 % Favored : 78.96 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -4.26 (0.21), residues: 1331 helix: -1.14 (0.30), residues: 318 sheet: -3.27 (0.35), residues: 176 loop : -3.65 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP M 53 HIS 0.010 0.002 HIS C 324 PHE 0.026 0.003 PHE D 336 TYR 0.024 0.002 TYR M 20 ARG 0.011 0.001 ARG D 56 *********************** 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 186 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.050 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 outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2957 time to fit residues: 72.5759 Evaluate side-chains 150 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4103 ------------------------------------------------------------------------------- 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: 0.9980 chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 0.0050 chunk 132 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 overall best weight: 1.7398 ------------------------------------------------------------------------------- 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 324 HIS D 140 HIS ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN E 300 GLN E 322 GLN F 329 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.9513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10142 Z= 0.253 Angle : 0.864 9.968 13963 Z= 0.441 Chirality : 0.046 0.245 1691 Planarity : 0.006 0.071 1783 Dihedral : 17.884 176.082 1759 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 16.68 % Favored : 83.10 % Rotamer: Outliers : 0.23 % Allowed : 0.80 % Favored : 98.97 % 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: -4.11 (0.21), residues: 1331 helix: -1.11 (0.30), residues: 327 sheet: -3.30 (0.35), residues: 170 loop : -3.50 (0.18), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP M 53 HIS 0.008 0.002 HIS C 324 PHE 0.026 0.002 PHE C 216 TYR 0.022 0.002 TYR M 20 ARG 0.004 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 197 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 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 outliers start: 2 outliers final: 1 residues processed: 197 average time/residue: 0.3146 time to fit residues: 80.1113 Evaluate side-chains 156 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0897 time to fit residues: 1.5543 ------------------------------------------------------------------------------- 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: 4.9990 chunk 97 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 324 HIS ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN E 322 GLN ** M 13 ASN ** 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 = 0.4353 r_free = 0.4353 target = 0.163664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.150695 restraints weight = 26190.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.149512 restraints weight = 28833.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.150663 restraints weight = 28589.354| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.9766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10142 Z= 0.305 Angle : 0.908 9.845 13963 Z= 0.465 Chirality : 0.047 0.252 1691 Planarity : 0.006 0.070 1783 Dihedral : 17.961 175.892 1759 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 25.70 Ramachandran Plot: Outliers : 0.30 % Allowed : 20.21 % Favored : 79.49 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -0.94 (0.31), residues: 306 sheet: -3.39 (0.32), residues: 194 loop : -3.57 (0.18), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP M 53 HIS 0.008 0.002 HIS E 208 PHE 0.025 0.003 PHE F 131 TYR 0.022 0.002 TYR M 20 ARG 0.007 0.001 ARG D 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2272.16 seconds wall clock time: 41 minutes 51.62 seconds (2511.62 seconds total)