Starting phenix.real_space_refine on Mon Aug 5 22:14:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt7_37828/08_2024/8wt7_37828.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt7_37828/08_2024/8wt7_37828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt7_37828/08_2024/8wt7_37828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt7_37828/08_2024/8wt7_37828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt7_37828/08_2024/8wt7_37828.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt7_37828/08_2024/8wt7_37828.cif" } resolution = 2.7 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= -0.002 sd= 0.082 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: 6 Type Number sf(0) Gaussians P 239 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 8481 2.51 5 N 2743 2.21 5 O 3333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 143": "OD1" <-> "OD2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 18": "OD1" <-> "OD2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "C ASP 18": "OD1" <-> "OD2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ASP 143": "OD1" <-> "OD2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 320": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14846 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2420 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 306, 2420 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain breaks: 1 bond proxies already assigned to first conformer: 2457 Chain: "B" Number of atoms: 2512 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 318, 2503 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 305} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 318, 2503 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 305} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2542 Chain: "C" Number of atoms: 2420 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 305, 2411 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 12, 'TRANS': 292} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 305, 2411 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 12, 'TRANS': 292} Chain breaks: 1 bond proxies already assigned to first conformer: 2448 Chain: "D" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2494 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 304} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1250 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 11, 'rna3p_pur': 22, 'rna3p_pyr': 22} Link IDs: {'rna2p': 15, 'rna3p': 43} Chain: "F" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1441 Classifications: {'RNA': 68} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 27, 'rna3p_pyr': 28} Link IDs: {'rna2p': 13, 'rna3p': 54} Chain: "G" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 548 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "H" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 557 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "I" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 587 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain breaks: 1 Chain: "J" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 602 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AGLN A 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 139 " occ=0.50 residue: pdb=" N AGLN B 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 139 " occ=0.50 residue: pdb=" N AGLN C 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 139 " occ=0.50 Time building chain proxies: 12.21, per 1000 atoms: 0.82 Number of scatterers: 14846 At special positions: 0 Unit cell: (118.413, 125.053, 117.307, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 239 15.00 Mg 2 11.99 O 3333 8.00 N 2743 7.00 C 8481 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: 7.10 Conformation dependent library (CDL) restraints added in 3.4 seconds 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 68.7% alpha, 9.3% beta 91 base pairs and 140 stacking pairs defined. Time for finding SS restraints: 6.45 Creating SS restraints... Processing helix chain 'A' and resid 36 through 49 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 84 through 95 removed outlier: 3.574A pdb=" N GLY A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 117 Processing helix chain 'A' and resid 125 through 155 removed outlier: 3.550A pdb=" N THR A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 159 through 188 removed outlier: 3.839A pdb=" N ASP A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 200 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.531A pdb=" N ALA A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.768A pdb=" N PHE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.642A pdb=" N ALA A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 290 through 313 Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.665A pdb=" N ARG A 320 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 66 through 77 Processing helix chain 'B' and resid 84 through 96 removed outlier: 3.613A pdb=" N GLY B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 125 through 155 removed outlier: 3.736A pdb=" N GLU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 188 removed outlier: 3.613A pdb=" N ASP B 188 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 200 Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.750A pdb=" N PHE B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 263 Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 274 through 287 removed outlier: 3.565A pdb=" N ASN B 287 " --> pdb=" O ARG B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 313 Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 84 through 95 removed outlier: 3.643A pdb=" N GLY C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 117 Processing helix chain 'C' and resid 125 through 155 removed outlier: 3.527A pdb=" N THR C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 188 removed outlier: 3.633A pdb=" N ASP C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 200 Processing helix chain 'C' and resid 205 through 217 Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.677A pdb=" N PHE C 228 " --> pdb=" O HIS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.566A pdb=" N ALA C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 290 through 313 Processing helix chain 'C' and resid 317 through 321 removed outlier: 3.613A pdb=" N ARG C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 50 Processing helix chain 'D' and resid 66 through 77 Processing helix chain 'D' and resid 84 through 95 removed outlier: 3.794A pdb=" N GLY D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 Processing helix chain 'D' and resid 125 through 155 removed outlier: 4.086A pdb=" N GLU D 153 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 188 removed outlier: 3.649A pdb=" N ASP D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 199 Processing helix chain 'D' and resid 205 through 217 Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.610A pdb=" N PHE D 228 " --> pdb=" O HIS D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.558A pdb=" N LEU D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 274 Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 290 through 313 Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.505A pdb=" N ARG D 320 " --> pdb=" O ASP D 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34 removed outlier: 6.522A pdb=" N HIS A 6 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N CYS A 58 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 8 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLU A 60 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ILE A 10 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 34 removed outlier: 6.831A pdb=" N HIS B 6 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N CYS B 58 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 8 " --> pdb=" O CYS B 58 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU B 60 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ILE B 10 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA B 55 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N SER B 81 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE B 57 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE B 83 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 59 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 236 through 237 removed outlier: 3.751A pdb=" N ARG B 250 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 240 through 241 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 34 removed outlier: 6.526A pdb=" N HIS C 6 " --> pdb=" O HIS C 56 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N CYS C 58 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE C 8 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N GLU C 60 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ILE C 10 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 28 through 34 removed outlier: 6.722A pdb=" N HIS D 6 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N CYS D 58 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE D 8 " --> pdb=" O CYS D 58 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N GLU D 60 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ILE D 10 " --> pdb=" O GLU D 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 236 through 237 removed outlier: 3.755A pdb=" N ARG D 250 " --> pdb=" O ARG D 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 240 through 241 677 hydrogen bonds defined for protein. 2004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 228 hydrogen bonds 450 hydrogen bond angles 0 basepair planarities 91 basepair parallelities 140 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 7.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3274 1.34 - 1.46: 5506 1.46 - 1.58: 6286 1.58 - 1.69: 470 1.69 - 1.81: 84 Bond restraints: 15620 Sorted by residual: bond pdb=" C ILE B 201 " pdb=" N PRO B 202 " ideal model delta sigma weight residual 1.333 1.358 -0.025 1.01e-02 9.80e+03 6.09e+00 bond pdb=" C ILE A 201 " pdb=" N PRO A 202 " ideal model delta sigma weight residual 1.333 1.358 -0.024 1.01e-02 9.80e+03 5.81e+00 bond pdb=" C ILE C 201 " pdb=" N PRO C 202 " ideal model delta sigma weight residual 1.333 1.358 -0.024 1.01e-02 9.80e+03 5.67e+00 bond pdb=" O5' G E 60 " pdb=" C5' G E 60 " ideal model delta sigma weight residual 1.420 1.455 -0.035 1.50e-02 4.44e+03 5.55e+00 bond pdb=" O5' G F 169 " pdb=" C5' G F 169 " ideal model delta sigma weight residual 1.420 1.455 -0.035 1.50e-02 4.44e+03 5.52e+00 ... (remaining 15615 not shown) Histogram of bond angle deviations from ideal: 96.61 - 104.16: 912 104.16 - 111.72: 7185 111.72 - 119.27: 6577 119.27 - 126.82: 6748 126.82 - 134.38: 738 Bond angle restraints: 22160 Sorted by residual: angle pdb=" O3' DA G 26 " pdb=" P DC G 27 " pdb=" O5' DC G 27 " ideal model delta sigma weight residual 104.00 96.61 7.39 1.50e+00 4.44e-01 2.43e+01 angle pdb=" O3' U F 132 " pdb=" P G F 133 " pdb=" O5' G F 133 " ideal model delta sigma weight residual 104.00 110.87 -6.87 1.50e+00 4.44e-01 2.10e+01 angle pdb=" CA ASP C 25 " pdb=" CB ASP C 25 " pdb=" CG ASP C 25 " ideal model delta sigma weight residual 112.60 117.05 -4.45 1.00e+00 1.00e+00 1.98e+01 angle pdb=" CA ASP C 11 " pdb=" CB ASP C 11 " pdb=" CG ASP C 11 " ideal model delta sigma weight residual 112.60 116.86 -4.26 1.00e+00 1.00e+00 1.82e+01 angle pdb=" CA ASP D 105 " pdb=" CB ASP D 105 " pdb=" CG ASP D 105 " ideal model delta sigma weight residual 112.60 116.81 -4.21 1.00e+00 1.00e+00 1.77e+01 ... (remaining 22155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.43: 8684 34.43 - 68.86: 630 68.86 - 103.29: 52 103.29 - 137.72: 0 137.72 - 172.15: 1 Dihedral angle restraints: 9367 sinusoidal: 5753 harmonic: 3614 Sorted by residual: dihedral pdb=" O4' U F 159 " pdb=" C1' U F 159 " pdb=" N1 U F 159 " pdb=" C2 U F 159 " ideal model delta sinusoidal sigma weight residual 232.00 59.85 172.15 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" C5' U E 86 " pdb=" C4' U E 86 " pdb=" C3' U E 86 " pdb=" O3' U E 86 " ideal model delta sinusoidal sigma weight residual 147.00 102.18 44.82 1 8.00e+00 1.56e-02 4.36e+01 dihedral pdb=" O4' U E 86 " pdb=" C4' U E 86 " pdb=" C3' U E 86 " pdb=" C2' U E 86 " ideal model delta sinusoidal sigma weight residual 24.00 -16.12 40.12 1 8.00e+00 1.56e-02 3.53e+01 ... (remaining 9364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2266 0.127 - 0.255: 298 0.255 - 0.382: 0 0.382 - 0.509: 0 0.509 - 0.636: 6 Chirality restraints: 2570 Sorted by residual: chirality pdb=" P DG J 12 " pdb=" OP1 DG J 12 " pdb=" OP2 DG J 12 " pdb=" O5' DG J 12 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DA H 3 " pdb=" OP1 DA H 3 " pdb=" OP2 DA H 3 " pdb=" O5' DA H 3 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DG I 5 " pdb=" OP1 DG I 5 " pdb=" OP2 DG I 5 " pdb=" O5' DG I 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.62 2.00e-01 2.50e+01 9.50e+00 ... (remaining 2567 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A F 157 " -0.035 2.00e-02 2.50e+03 1.42e-02 5.55e+00 pdb=" N9 A F 157 " 0.021 2.00e-02 2.50e+03 pdb=" C8 A F 157 " 0.008 2.00e-02 2.50e+03 pdb=" N7 A F 157 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A F 157 " 0.006 2.00e-02 2.50e+03 pdb=" C6 A F 157 " -0.006 2.00e-02 2.50e+03 pdb=" N6 A F 157 " -0.016 2.00e-02 2.50e+03 pdb=" N1 A F 157 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A F 157 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A F 157 " 0.008 2.00e-02 2.50e+03 pdb=" C4 A F 157 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U F 159 " 0.027 2.00e-02 2.50e+03 1.39e-02 4.32e+00 pdb=" N1 U F 159 " -0.026 2.00e-02 2.50e+03 pdb=" C2 U F 159 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U F 159 " -0.010 2.00e-02 2.50e+03 pdb=" N3 U F 159 " 0.010 2.00e-02 2.50e+03 pdb=" C4 U F 159 " 0.005 2.00e-02 2.50e+03 pdb=" O4 U F 159 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U F 159 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U F 159 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 27 " 0.027 2.00e-02 2.50e+03 1.22e-02 4.12e+00 pdb=" N9 DA I 27 " -0.028 2.00e-02 2.50e+03 pdb=" C8 DA I 27 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA I 27 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 27 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 27 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 27 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 27 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 27 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 27 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 27 " -0.002 2.00e-02 2.50e+03 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 14 2.27 - 2.92: 5194 2.92 - 3.58: 21613 3.58 - 4.24: 39550 4.24 - 4.90: 60383 Nonbonded interactions: 126754 Sorted by model distance: nonbonded pdb=" OG SER D 241 " pdb=" P DA G 26 " model vdw 1.608 3.400 nonbonded pdb=" OG SER B 241 " pdb=" P DT I 21 " model vdw 1.608 3.400 nonbonded pdb=" OE2 GLU A 60 " pdb="MG MG A 401 " model vdw 1.884 2.170 nonbonded pdb="MG MG C 401 " pdb=" O HOH C 501 " model vdw 1.922 2.170 nonbonded pdb=" O3' DT G 25 " pdb="MG MG A 401 " model vdw 2.066 2.170 ... (remaining 126749 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 138 or resid 140 through 321)) selection = (chain 'B' and (resid 5 through 138 or resid 140 through 238 or resid 251 throug \ h 321)) selection = (chain 'C' and (resid 5 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 138 or resid 140 through 321)) selection = (chain 'D' and (resid 5 through 138 or resid 140 through 238 or resid 251 throug \ h 321)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 53.500 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 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 : 0.008 0.039 15620 Z= 0.490 Angle : 1.311 7.391 22160 Z= 0.851 Chirality : 0.078 0.636 2570 Planarity : 0.004 0.052 1986 Dihedral : 19.845 172.147 7029 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 0.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.49 % Allowed : 2.07 % Favored : 97.43 % 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: -1.68 (0.20), residues: 1243 helix: -0.83 (0.15), residues: 805 sheet: -1.25 (0.36), residues: 162 loop : -1.19 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.005 TRP A 169 HIS 0.010 0.002 HIS D 256 PHE 0.017 0.002 PHE C 228 TYR 0.017 0.002 TYR D 307 ARG 0.025 0.002 ARG D 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: A 261 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8458 (tpt-90) REVERT: A 268 MET cc_start: 0.8680 (ttp) cc_final: 0.8458 (ttp) REVERT: A 299 MET cc_start: 0.9323 (mtp) cc_final: 0.9112 (mtp) REVERT: B 99 ASN cc_start: 0.8400 (m-40) cc_final: 0.8060 (m-40) REVERT: B 298 MET cc_start: 0.9398 (tpt) cc_final: 0.8624 (tpt) REVERT: C 268 MET cc_start: 0.8765 (mtm) cc_final: 0.8562 (mtm) REVERT: D 108 MET cc_start: 0.8901 (tpp) cc_final: 0.8671 (mmt) REVERT: D 239 TYR cc_start: 0.9156 (t80) cc_final: 0.8926 (t80) REVERT: D 268 MET cc_start: 0.8979 (ttp) cc_final: 0.8776 (ttm) outliers start: 5 outliers final: 0 residues processed: 94 average time/residue: 1.8633 time to fit residues: 187.7380 Evaluate side-chains 62 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 0.0270 chunk 128 optimal weight: 5.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN C 287 ASN D 93 GLN D 99 ASN D 287 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15620 Z= 0.227 Angle : 0.593 6.256 22160 Z= 0.331 Chirality : 0.039 0.195 2570 Planarity : 0.004 0.032 1986 Dihedral : 21.951 160.762 4602 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 0.59 % Allowed : 4.84 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.23), residues: 1243 helix: 1.94 (0.17), residues: 809 sheet: -0.85 (0.36), residues: 160 loop : -0.73 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 276 HIS 0.005 0.001 HIS B 256 PHE 0.012 0.002 PHE B 112 TYR 0.020 0.002 TYR A 215 ARG 0.006 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: B 107 ARG cc_start: 0.8530 (ttt90) cc_final: 0.8234 (ttm-80) REVERT: B 298 MET cc_start: 0.9356 (tpt) cc_final: 0.8949 (tpt) REVERT: C 258 SER cc_start: 0.9407 (m) cc_final: 0.9020 (p) REVERT: D 108 MET cc_start: 0.8878 (tpp) cc_final: 0.8627 (mmt) outliers start: 6 outliers final: 0 residues processed: 67 average time/residue: 1.6311 time to fit residues: 119.1709 Evaluate side-chains 60 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 93 GLN C 287 ASN D 6 HIS D 99 ASN D 287 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15620 Z= 0.301 Angle : 0.544 6.080 22160 Z= 0.303 Chirality : 0.039 0.190 2570 Planarity : 0.004 0.064 1986 Dihedral : 22.118 161.150 4598 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.79 % Allowed : 5.03 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.24), residues: 1243 helix: 2.54 (0.18), residues: 808 sheet: -0.59 (0.37), residues: 163 loop : -0.66 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 46 HIS 0.005 0.001 HIS B 256 PHE 0.012 0.002 PHE C 316 TYR 0.016 0.002 TYR A 215 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 1.357 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9378 (tpt) cc_final: 0.8909 (tpt) REVERT: B 99 ASN cc_start: 0.8167 (m-40) cc_final: 0.7858 (m-40) REVERT: B 107 ARG cc_start: 0.8642 (ttt90) cc_final: 0.8320 (ttm-80) REVERT: C 54 HIS cc_start: 0.8363 (m-70) cc_final: 0.8058 (m90) REVERT: D 99 ASN cc_start: 0.7977 (m-40) cc_final: 0.7769 (m-40) REVERT: D 108 MET cc_start: 0.8889 (tpp) cc_final: 0.8614 (mmt) REVERT: D 261 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8548 (ttm-80) REVERT: D 304 GLN cc_start: 0.9215 (tt0) cc_final: 0.8944 (mt0) outliers start: 8 outliers final: 0 residues processed: 70 average time/residue: 1.6632 time to fit residues: 127.5592 Evaluate side-chains 60 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 261 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 66 optimal weight: 0.0670 chunk 14 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 93 GLN C 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15620 Z= 0.177 Angle : 0.490 5.866 22160 Z= 0.274 Chirality : 0.035 0.179 2570 Planarity : 0.004 0.036 1986 Dihedral : 22.087 162.241 4598 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.59 % Allowed : 6.02 % Favored : 93.39 % 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: 2.52 (0.24), residues: 1243 helix: 2.78 (0.18), residues: 807 sheet: -0.21 (0.39), residues: 149 loop : -0.60 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 46 HIS 0.004 0.001 HIS B 256 PHE 0.010 0.001 PHE B 112 TYR 0.013 0.001 TYR A 215 ARG 0.003 0.000 ARG D 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9331 (tpt) cc_final: 0.9014 (tpt) REVERT: B 107 ARG cc_start: 0.8594 (ttt90) cc_final: 0.8386 (ttm-80) REVERT: C 54 HIS cc_start: 0.8407 (m-70) cc_final: 0.8138 (m90) REVERT: C 150 ASN cc_start: 0.9279 (OUTLIER) cc_final: 0.8897 (t0) outliers start: 6 outliers final: 1 residues processed: 67 average time/residue: 1.4781 time to fit residues: 108.6563 Evaluate side-chains 62 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 258 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15620 Z= 0.238 Angle : 0.503 6.310 22160 Z= 0.277 Chirality : 0.036 0.180 2570 Planarity : 0.004 0.035 1986 Dihedral : 22.132 162.140 4598 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.59 % Allowed : 6.42 % Favored : 92.99 % 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: 2.68 (0.24), residues: 1243 helix: 2.89 (0.18), residues: 807 sheet: -0.02 (0.39), residues: 148 loop : -0.57 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 46 HIS 0.003 0.001 HIS B 256 PHE 0.012 0.002 PHE B 112 TYR 0.012 0.001 TYR A 215 ARG 0.002 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9345 (tpt) cc_final: 0.8993 (tpt) REVERT: B 107 ARG cc_start: 0.8660 (ttt90) cc_final: 0.8362 (ttm-80) REVERT: C 54 HIS cc_start: 0.8453 (m-70) cc_final: 0.8206 (m90) REVERT: D 268 MET cc_start: 0.8752 (ttm) cc_final: 0.8508 (ttm) outliers start: 6 outliers final: 2 residues processed: 64 average time/residue: 1.5050 time to fit residues: 105.7243 Evaluate side-chains 62 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 258 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 113 optimal weight: 0.0870 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 overall best weight: 2.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 15620 Z= 0.320 Angle : 0.533 8.783 22160 Z= 0.291 Chirality : 0.038 0.188 2570 Planarity : 0.004 0.035 1986 Dihedral : 22.228 161.331 4598 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.69 % Allowed : 6.81 % Favored : 92.50 % 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: 2.69 (0.24), residues: 1243 helix: 2.89 (0.18), residues: 807 sheet: 0.03 (0.39), residues: 148 loop : -0.58 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 46 HIS 0.004 0.001 HIS D 256 PHE 0.013 0.002 PHE B 112 TYR 0.016 0.001 TYR D 215 ARG 0.003 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9343 (tpt) cc_final: 0.8996 (tpt) REVERT: B 107 ARG cc_start: 0.8689 (ttt90) cc_final: 0.8326 (ttm-80) REVERT: C 54 HIS cc_start: 0.8483 (m-70) cc_final: 0.8243 (m90) REVERT: D 268 MET cc_start: 0.8732 (ttm) cc_final: 0.8475 (ttm) outliers start: 7 outliers final: 3 residues processed: 62 average time/residue: 1.5693 time to fit residues: 106.3309 Evaluate side-chains 60 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 191 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 54 optimal weight: 0.0010 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15620 Z= 0.193 Angle : 0.490 8.058 22160 Z= 0.270 Chirality : 0.035 0.177 2570 Planarity : 0.004 0.035 1986 Dihedral : 22.197 161.861 4598 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.59 % Allowed : 7.11 % Favored : 92.30 % 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: 2.80 (0.24), residues: 1243 helix: 2.96 (0.18), residues: 808 sheet: 0.05 (0.40), residues: 150 loop : -0.48 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 46 HIS 0.003 0.000 HIS B 256 PHE 0.010 0.001 PHE B 112 TYR 0.011 0.001 TYR D 307 ARG 0.005 0.000 ARG D 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.9163 (m-80) cc_final: 0.8952 (m-80) REVERT: A 298 MET cc_start: 0.9341 (tpt) cc_final: 0.9098 (tpt) REVERT: B 107 ARG cc_start: 0.8643 (ttt90) cc_final: 0.8360 (ttm-80) REVERT: C 54 HIS cc_start: 0.8493 (m-70) cc_final: 0.8268 (m90) REVERT: D 153 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: D 206 GLU cc_start: 0.7618 (mp0) cc_final: 0.7330 (mm-30) outliers start: 6 outliers final: 2 residues processed: 66 average time/residue: 1.4967 time to fit residues: 108.5283 Evaluate side-chains 65 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 191 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15620 Z= 0.236 Angle : 0.499 8.878 22160 Z= 0.273 Chirality : 0.035 0.178 2570 Planarity : 0.004 0.035 1986 Dihedral : 22.195 162.044 4598 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.39 % Allowed : 7.31 % Favored : 92.30 % 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: 2.86 (0.24), residues: 1243 helix: 3.01 (0.18), residues: 807 sheet: 0.08 (0.40), residues: 150 loop : -0.44 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 46 HIS 0.003 0.001 HIS D 256 PHE 0.012 0.002 PHE B 112 TYR 0.012 0.001 TYR D 307 ARG 0.002 0.000 ARG D 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9336 (tpt) cc_final: 0.9017 (tpt) REVERT: B 107 ARG cc_start: 0.8674 (ttt90) cc_final: 0.8340 (ttm-80) REVERT: C 54 HIS cc_start: 0.8517 (m-70) cc_final: 0.8280 (m90) REVERT: D 153 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: D 268 MET cc_start: 0.8798 (ttm) cc_final: 0.8596 (ttm) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 1.5595 time to fit residues: 109.1868 Evaluate side-chains 63 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 191 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15620 Z= 0.156 Angle : 0.486 8.643 22160 Z= 0.268 Chirality : 0.034 0.172 2570 Planarity : 0.004 0.035 1986 Dihedral : 22.197 162.272 4598 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.49 % Allowed : 7.60 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.24), residues: 1243 helix: 3.03 (0.18), residues: 809 sheet: 0.09 (0.40), residues: 146 loop : -0.43 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 46 HIS 0.003 0.001 HIS A 145 PHE 0.010 0.001 PHE B 112 TYR 0.014 0.001 TYR A 215 ARG 0.004 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.9334 (tpt) cc_final: 0.9056 (tpt) REVERT: B 107 ARG cc_start: 0.8647 (ttt90) cc_final: 0.8381 (ttm-80) REVERT: C 54 HIS cc_start: 0.8510 (m-70) cc_final: 0.8278 (m90) REVERT: D 153 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8193 (tm-30) REVERT: D 268 MET cc_start: 0.8758 (ttm) cc_final: 0.8544 (ttm) outliers start: 5 outliers final: 2 residues processed: 67 average time/residue: 1.7687 time to fit residues: 128.6523 Evaluate side-chains 65 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 191 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15620 Z= 0.150 Angle : 0.465 8.226 22160 Z= 0.256 Chirality : 0.033 0.165 2570 Planarity : 0.003 0.035 1986 Dihedral : 22.102 164.213 4598 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.39 % Allowed : 7.90 % Favored : 91.71 % 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: 3.01 (0.24), residues: 1243 helix: 3.11 (0.18), residues: 809 sheet: 0.13 (0.40), residues: 146 loop : -0.39 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 46 HIS 0.002 0.000 HIS B 256 PHE 0.010 0.001 PHE B 112 TYR 0.013 0.001 TYR C 74 ARG 0.002 0.000 ARG D 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.760 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.9080 (mtm) cc_final: 0.8839 (mtp) REVERT: A 298 MET cc_start: 0.9335 (tpt) cc_final: 0.9097 (tpt) REVERT: B 107 ARG cc_start: 0.8618 (ttt90) cc_final: 0.8413 (ttm-80) REVERT: C 54 HIS cc_start: 0.8516 (m-70) cc_final: 0.8302 (m90) REVERT: C 258 SER cc_start: 0.9290 (OUTLIER) cc_final: 0.8914 (t) REVERT: D 153 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8138 (tm-30) outliers start: 4 outliers final: 1 residues processed: 72 average time/residue: 1.6656 time to fit residues: 131.5159 Evaluate side-chains 67 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 191 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 31 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 115 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.080162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.053580 restraints weight = 86719.256| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.23 r_work: 0.2539 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 15620 Z= 0.147 Angle : 0.467 9.087 22160 Z= 0.256 Chirality : 0.033 0.160 2570 Planarity : 0.003 0.035 1986 Dihedral : 22.065 165.456 4598 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.49 % Allowed : 8.29 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.24), residues: 1243 helix: 3.17 (0.18), residues: 809 sheet: 0.21 (0.40), residues: 146 loop : -0.38 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 46 HIS 0.002 0.000 HIS B 256 PHE 0.010 0.001 PHE B 112 TYR 0.011 0.001 TYR D 307 ARG 0.005 0.000 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3573.49 seconds wall clock time: 64 minutes 29.38 seconds (3869.38 seconds total)