Starting phenix.real_space_refine on Wed Feb 14 07:07:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f02_31394/02_2024/7f02_31394_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f02_31394/02_2024/7f02_31394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f02_31394/02_2024/7f02_31394.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f02_31394/02_2024/7f02_31394.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f02_31394/02_2024/7f02_31394_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f02_31394/02_2024/7f02_31394_updated.pdb" } resolution = 3.24 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= 0.047 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 3 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 5778 2.51 5 N 1505 2.21 5 O 1501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 54": "OD1" <-> "OD2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "B ASP 122": "OD1" <-> "OD2" Residue "C TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8835 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "B" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1848 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 11, 'TRANS': 219} Chain: "D" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "F" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.07, per 1000 atoms: 0.57 Number of scatterers: 8835 At special positions: 0 Unit cell: (98.176, 99.008, 118.976, 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 46 16.00 P 3 15.00 Mg 2 11.99 O 1501 8.00 N 1505 7.00 C 5778 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: 3.43 Conformation dependent library (CDL) restraints added in 1.8 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 6 sheets defined 56.8% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 40 through 47 removed outlier: 3.582A pdb=" N LEU A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 65 through 68 No H-bonds generated for 'chain 'A' and resid 65 through 68' Processing helix chain 'A' and resid 91 through 98 Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.569A pdb=" N ARG A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.609A pdb=" N GLN A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 173 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 14 Processing helix chain 'B' and resid 23 through 39 removed outlier: 3.960A pdb=" N PHE B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 43 through 46 No H-bonds generated for 'chain 'B' and resid 43 through 46' Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.775A pdb=" N GLU B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASP B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 83 No H-bonds generated for 'chain 'B' and resid 80 through 83' Processing helix chain 'B' and resid 89 through 104 removed outlier: 3.542A pdb=" N ALA B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET B 102 " --> pdb=" O MET B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 118 Proline residue: B 113 - end of helix removed outlier: 3.802A pdb=" N MET B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 removed outlier: 3.764A pdb=" N VAL B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET B 129 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 133 " --> pdb=" O MET B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 153 removed outlier: 3.687A pdb=" N GLY B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) Proline residue: B 146 - end of helix removed outlier: 3.535A pdb=" N LEU B 150 " --> pdb=" O PRO B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.904A pdb=" N ILE B 163 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 164 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 184 Proline residue: B 171 - end of helix removed outlier: 3.803A pdb=" N ILE B 174 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 177 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N MET B 180 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP B 181 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 203 removed outlier: 4.485A pdb=" N ILE B 195 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 197 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 198 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 219 Processing helix chain 'C' and resid 14 through 17 No H-bonds generated for 'chain 'C' and resid 14 through 17' Processing helix chain 'C' and resid 20 through 27 removed outlier: 4.615A pdb=" N TRP C 24 " --> pdb=" O TRP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 36 No H-bonds generated for 'chain 'C' and resid 33 through 36' Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.509A pdb=" N TRP C 66 " --> pdb=" O PRO C 62 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 68' Processing helix chain 'C' and resid 71 through 83 removed outlier: 3.915A pdb=" N VAL C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 95 removed outlier: 3.673A pdb=" N ALA C 92 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 119 Proline residue: C 117 - end of helix Processing helix chain 'C' and resid 127 through 146 removed outlier: 4.113A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 184 Proline residue: C 171 - end of helix removed outlier: 3.644A pdb=" N TRP C 179 " --> pdb=" O TYR C 175 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 200 through 225 Processing helix chain 'C' and resid 233 through 236 Processing helix chain 'D' and resid 18 through 53 Proline residue: D 31 - end of helix removed outlier: 4.222A pdb=" N LEU D 47 " --> pdb=" O HIS D 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 48 Processing helix chain 'E' and resid 91 through 97 removed outlier: 3.734A pdb=" N LEU E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 114 Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 129 through 141 removed outlier: 4.001A pdb=" N ARG E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG E 134 " --> pdb=" O GLY E 130 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG E 139 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TRP E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 175 removed outlier: 3.774A pdb=" N GLN E 167 " --> pdb=" O ASP E 163 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ALA E 170 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 16 removed outlier: 3.588A pdb=" N ARG F 16 " --> pdb=" O ARG F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 38 removed outlier: 3.833A pdb=" N PHE F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) Proline residue: F 36 - end of helix Processing helix chain 'F' and resid 43 through 68 Proline residue: F 51 - end of helix removed outlier: 3.710A pdb=" N TRP F 55 " --> pdb=" O PRO F 51 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ARG F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 74 No H-bonds generated for 'chain 'F' and resid 71 through 74' Processing helix chain 'F' and resid 89 through 110 removed outlier: 4.374A pdb=" N LEU F 106 " --> pdb=" O MET F 102 " (cutoff:3.500A) Proline residue: F 107 - end of helix Processing helix chain 'F' and resid 112 through 119 Processing helix chain 'F' and resid 123 through 134 Processing helix chain 'F' and resid 137 through 151 Proline residue: F 146 - end of helix Processing helix chain 'F' and resid 159 through 183 Proline residue: F 167 - end of helix removed outlier: 4.036A pdb=" N ILE F 170 " --> pdb=" O LEU F 166 " (cutoff:3.500A) Proline residue: F 171 - end of helix Processing helix chain 'F' and resid 191 through 204 removed outlier: 3.584A pdb=" N ILE F 195 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU F 196 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 199 " --> pdb=" O ILE F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 219 Processing sheet with id= A, first strand: chain 'A' and resid 195 through 198 removed outlier: 6.707A pdb=" N TRP A 148 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N THR A 182 " --> pdb=" O TRP A 148 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU A 150 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 77 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASP A 151 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 79 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 7 through 9 removed outlier: 3.768A pdb=" N LEU A 7 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 20 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N CYS A 9 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N SER A 18 " --> pdb=" O CYS A 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'E' and resid 3 through 5 Processing sheet with id= D, first strand: chain 'E' and resid 178 through 181 removed outlier: 6.517A pdb=" N GLU E 28 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU E 181 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL E 30 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG E 195 " --> pdb=" O GLN E 31 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR E 33 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE E 197 " --> pdb=" O THR E 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'E' and resid 77 through 79 Processing sheet with id= F, first strand: chain 'E' and resid 7 through 9 removed outlier: 7.705A pdb=" N CYS E 9 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER E 18 " --> pdb=" O CYS E 9 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1353 1.31 - 1.43: 2403 1.43 - 1.56: 5199 1.56 - 1.69: 2 1.69 - 1.81: 87 Bond restraints: 9044 Sorted by residual: bond pdb=" C11 3PE C 302 " pdb=" O13 3PE C 302 " ideal model delta sigma weight residual 1.408 1.486 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" O3 PO4 E 301 " pdb=" P PO4 E 301 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.86e+00 bond pdb=" O3 PO4 A 301 " pdb=" P PO4 A 301 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" O4 PO4 A 301 " pdb=" P PO4 A 301 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 8.87e+00 bond pdb=" O2 PO4 E 301 " pdb=" P PO4 E 301 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.65e+00 ... (remaining 9039 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.56: 233 105.56 - 112.71: 4903 112.71 - 119.86: 3102 119.86 - 127.01: 3920 127.01 - 134.16: 174 Bond angle restraints: 12332 Sorted by residual: angle pdb=" N VAL C 35 " pdb=" CA VAL C 35 " pdb=" C VAL C 35 " ideal model delta sigma weight residual 113.53 106.37 7.16 9.80e-01 1.04e+00 5.34e+01 angle pdb=" N ILE C 56 " pdb=" CA ILE C 56 " pdb=" C ILE C 56 " ideal model delta sigma weight residual 112.98 107.81 5.17 1.25e+00 6.40e-01 1.71e+01 angle pdb=" C12 3PE C 302 " pdb=" C11 3PE C 302 " pdb=" O13 3PE C 302 " ideal model delta sigma weight residual 108.28 119.53 -11.25 3.00e+00 1.11e-01 1.41e+01 angle pdb=" N ILE C 194 " pdb=" CA ILE C 194 " pdb=" C ILE C 194 " ideal model delta sigma weight residual 113.71 110.29 3.42 9.50e-01 1.11e+00 1.30e+01 angle pdb=" N TYR C 54 " pdb=" CA TYR C 54 " pdb=" C TYR C 54 " ideal model delta sigma weight residual 111.81 107.00 4.81 1.44e+00 4.82e-01 1.12e+01 ... (remaining 12327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4772 17.86 - 35.73: 432 35.73 - 53.59: 86 53.59 - 71.46: 15 71.46 - 89.32: 6 Dihedral angle restraints: 5311 sinusoidal: 2087 harmonic: 3224 Sorted by residual: dihedral pdb=" CA TRP C 39 " pdb=" C TRP C 39 " pdb=" N GLY C 40 " pdb=" CA GLY C 40 " ideal model delta harmonic sigma weight residual 180.00 154.50 25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA THR E 166 " pdb=" C THR E 166 " pdb=" N GLN E 167 " pdb=" CA GLN E 167 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA LEU B 131 " pdb=" C LEU B 131 " pdb=" N THR B 132 " pdb=" CA THR B 132 " ideal model delta harmonic sigma weight residual 180.00 159.01 20.99 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 5308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1035 0.041 - 0.081: 314 0.081 - 0.122: 95 0.122 - 0.163: 9 0.163 - 0.203: 2 Chirality restraints: 1455 Sorted by residual: chirality pdb=" CB THR A 182 " pdb=" CA THR A 182 " pdb=" OG1 THR A 182 " pdb=" CG2 THR A 182 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB THR E 182 " pdb=" CA THR E 182 " pdb=" OG1 THR E 182 " pdb=" CG2 THR E 182 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.46e-01 chirality pdb=" CA ILE A 180 " pdb=" N ILE A 180 " pdb=" C ILE A 180 " pdb=" CB ILE A 180 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.11e-01 ... (remaining 1452 not shown) Planarity restraints: 1521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 123 " -0.017 2.00e-02 2.50e+03 1.28e-02 4.10e+00 pdb=" CG TRP C 123 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP C 123 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 123 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 123 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 123 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 123 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 123 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 123 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 123 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 89 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO F 90 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO F 90 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 90 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 22 " -0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO C 23 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 23 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 23 " -0.025 5.00e-02 4.00e+02 ... (remaining 1518 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 32 2.50 - 3.10: 6302 3.10 - 3.70: 13183 3.70 - 4.30: 19158 4.30 - 4.90: 32363 Nonbonded interactions: 71038 Sorted by model distance: nonbonded pdb=" NE2 HIS E 81 " pdb="MG MG E 300 " model vdw 1.895 2.250 nonbonded pdb=" NE2 HIS A 81 " pdb="MG MG A 300 " model vdw 1.895 2.250 nonbonded pdb="MG MG A 300 " pdb=" O1 PO4 A 301 " model vdw 2.030 2.170 nonbonded pdb=" OG1 THR E 41 " pdb="MG MG E 300 " model vdw 2.061 2.170 nonbonded pdb=" OG1 THR A 41 " pdb="MG MG A 300 " model vdw 2.062 2.170 ... (remaining 71033 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 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } 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 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: 1.890 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: 7.170 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.780 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.004 0.078 9044 Z= 0.265 Angle : 0.693 11.254 12332 Z= 0.366 Chirality : 0.042 0.203 1455 Planarity : 0.005 0.046 1521 Dihedral : 14.417 89.323 3227 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.68 % Favored : 91.14 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: -1.36 (0.26), residues: 1118 helix: -0.16 (0.21), residues: 677 sheet: -0.94 (0.75), residues: 58 loop : -2.15 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 123 HIS 0.006 0.001 HIS E 96 PHE 0.021 0.001 PHE A 97 TYR 0.006 0.001 TYR F 124 ARG 0.007 0.000 ARG F 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 HIS cc_start: 0.8110 (t70) cc_final: 0.7732 (t70) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2254 time to fit residues: 66.1527 Evaluate side-chains 190 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 28 optimal weight: 0.3980 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 0.0470 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9044 Z= 0.173 Angle : 0.600 6.393 12332 Z= 0.298 Chirality : 0.040 0.143 1455 Planarity : 0.004 0.046 1521 Dihedral : 7.214 71.814 1247 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.96 % Allowed : 10.80 % Favored : 87.24 % 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: -1.04 (0.26), residues: 1118 helix: 0.21 (0.22), residues: 674 sheet: -1.01 (0.73), residues: 58 loop : -2.20 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 123 HIS 0.003 0.001 HIS A 73 PHE 0.023 0.001 PHE B 3 TYR 0.006 0.001 TYR F 124 ARG 0.004 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 196 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 HIS cc_start: 0.8337 (t70) cc_final: 0.7903 (t70) REVERT: F 110 ILE cc_start: 0.8494 (tp) cc_final: 0.8224 (mm) outliers start: 18 outliers final: 9 residues processed: 202 average time/residue: 0.2271 time to fit residues: 61.5460 Evaluate side-chains 193 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 184 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 72 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9044 Z= 0.327 Angle : 0.658 6.595 12332 Z= 0.331 Chirality : 0.044 0.168 1455 Planarity : 0.005 0.050 1521 Dihedral : 7.049 70.847 1247 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 2.73 % Allowed : 15.38 % Favored : 81.90 % 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: -1.20 (0.26), residues: 1118 helix: 0.07 (0.21), residues: 683 sheet: -1.18 (0.72), residues: 58 loop : -2.28 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 39 HIS 0.008 0.001 HIS A 73 PHE 0.013 0.002 PHE C 207 TYR 0.019 0.002 TYR F 124 ARG 0.004 0.000 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 220 GLN cc_start: 0.7315 (mt0) cc_final: 0.6426 (tm-30) REVERT: C 25 LEU cc_start: 0.8133 (tp) cc_final: 0.7897 (tp) REVERT: F 10 GLU cc_start: 0.7779 (tp30) cc_final: 0.7328 (tp30) REVERT: F 100 HIS cc_start: 0.8452 (t70) cc_final: 0.8125 (t-90) outliers start: 25 outliers final: 22 residues processed: 201 average time/residue: 0.2230 time to fit residues: 60.0703 Evaluate side-chains 202 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 180 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 189 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0980 chunk 52 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.0010 chunk 53 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9044 Z= 0.156 Angle : 0.588 11.757 12332 Z= 0.285 Chirality : 0.040 0.154 1455 Planarity : 0.004 0.053 1521 Dihedral : 6.510 70.388 1247 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.84 % Allowed : 16.79 % Favored : 80.37 % 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: -0.85 (0.27), residues: 1118 helix: 0.38 (0.22), residues: 677 sheet: -1.23 (0.72), residues: 58 loop : -2.14 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 234 HIS 0.004 0.001 HIS A 73 PHE 0.016 0.001 PHE B 3 TYR 0.004 0.001 TYR F 192 ARG 0.002 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7493 (mt-10) REVERT: B 2 MET cc_start: 0.6255 (tpt) cc_final: 0.5940 (ttm) REVERT: B 135 LEU cc_start: 0.9081 (tp) cc_final: 0.8845 (tt) REVERT: B 220 GLN cc_start: 0.7199 (mt0) cc_final: 0.6354 (tm-30) REVERT: C 25 LEU cc_start: 0.8024 (tp) cc_final: 0.7817 (tp) REVERT: E 182 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.7943 (p) REVERT: F 10 GLU cc_start: 0.7665 (tp30) cc_final: 0.7297 (tp30) REVERT: F 100 HIS cc_start: 0.8403 (t70) cc_final: 0.8010 (t70) REVERT: F 110 ILE cc_start: 0.8196 (tp) cc_final: 0.7908 (pt) outliers start: 26 outliers final: 17 residues processed: 201 average time/residue: 0.2174 time to fit residues: 59.2257 Evaluate side-chains 199 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 189 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 0.0070 chunk 92 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9044 Z= 0.207 Angle : 0.604 8.296 12332 Z= 0.293 Chirality : 0.041 0.139 1455 Planarity : 0.004 0.052 1521 Dihedral : 6.334 69.693 1247 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.05 % Allowed : 17.12 % Favored : 79.83 % 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: -0.76 (0.27), residues: 1118 helix: 0.43 (0.22), residues: 676 sheet: -1.05 (0.72), residues: 58 loop : -2.08 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 123 HIS 0.005 0.001 HIS A 73 PHE 0.014 0.001 PHE B 28 TYR 0.011 0.001 TYR F 124 ARG 0.002 0.000 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7491 (mt-10) REVERT: B 135 LEU cc_start: 0.8999 (tp) cc_final: 0.8767 (tt) REVERT: B 220 GLN cc_start: 0.7203 (mt0) cc_final: 0.6339 (tm-30) REVERT: C 25 LEU cc_start: 0.8097 (tp) cc_final: 0.7867 (tp) REVERT: F 10 GLU cc_start: 0.7606 (tp30) cc_final: 0.7307 (tp30) REVERT: F 100 HIS cc_start: 0.8442 (t70) cc_final: 0.8065 (t70) REVERT: F 110 ILE cc_start: 0.8199 (tp) cc_final: 0.7941 (pt) REVERT: F 206 LEU cc_start: 0.8442 (mp) cc_final: 0.8239 (mt) outliers start: 28 outliers final: 23 residues processed: 201 average time/residue: 0.2248 time to fit residues: 61.2717 Evaluate side-chains 205 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 189 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 108 optimal weight: 0.0370 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9044 Z= 0.284 Angle : 0.639 7.162 12332 Z= 0.314 Chirality : 0.043 0.202 1455 Planarity : 0.005 0.052 1521 Dihedral : 6.408 69.944 1247 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.93 % Allowed : 17.56 % Favored : 78.52 % 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: -0.93 (0.27), residues: 1118 helix: 0.28 (0.21), residues: 680 sheet: -1.04 (0.72), residues: 58 loop : -2.15 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 39 HIS 0.007 0.001 HIS A 73 PHE 0.013 0.001 PHE B 142 TYR 0.016 0.001 TYR F 124 ARG 0.003 0.000 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 179 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7477 (mt-10) REVERT: B 135 LEU cc_start: 0.9062 (tp) cc_final: 0.8798 (tt) REVERT: B 220 GLN cc_start: 0.7325 (mt0) cc_final: 0.6454 (tm-30) REVERT: C 25 LEU cc_start: 0.8148 (tp) cc_final: 0.7913 (tp) REVERT: C 54 TYR cc_start: 0.6467 (OUTLIER) cc_final: 0.6240 (t80) REVERT: C 229 GLU cc_start: 0.7109 (tt0) cc_final: 0.6818 (tt0) REVERT: F 10 GLU cc_start: 0.7696 (tp30) cc_final: 0.7407 (tp30) REVERT: F 206 LEU cc_start: 0.8479 (mp) cc_final: 0.8275 (mt) outliers start: 36 outliers final: 30 residues processed: 197 average time/residue: 0.2178 time to fit residues: 58.1243 Evaluate side-chains 214 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 183 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9044 Z= 0.256 Angle : 0.623 7.662 12332 Z= 0.305 Chirality : 0.042 0.175 1455 Planarity : 0.004 0.053 1521 Dihedral : 6.356 70.585 1247 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.71 % Allowed : 18.87 % Favored : 77.43 % 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: -0.86 (0.27), residues: 1118 helix: 0.35 (0.21), residues: 679 sheet: -0.97 (0.72), residues: 58 loop : -2.15 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 123 HIS 0.006 0.001 HIS A 73 PHE 0.017 0.001 PHE B 28 TYR 0.013 0.001 TYR F 124 ARG 0.003 0.000 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 188 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: B 135 LEU cc_start: 0.9033 (tp) cc_final: 0.8772 (tt) REVERT: B 220 GLN cc_start: 0.7291 (mt0) cc_final: 0.6463 (tm-30) REVERT: C 25 LEU cc_start: 0.8112 (tp) cc_final: 0.7908 (tp) REVERT: C 54 TYR cc_start: 0.6487 (OUTLIER) cc_final: 0.6253 (t80) REVERT: C 229 GLU cc_start: 0.7198 (tt0) cc_final: 0.6862 (tt0) REVERT: F 10 GLU cc_start: 0.7673 (tp30) cc_final: 0.7453 (tp30) outliers start: 34 outliers final: 28 residues processed: 204 average time/residue: 0.2217 time to fit residues: 61.1599 Evaluate side-chains 215 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 186 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 10 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9044 Z= 0.175 Angle : 0.600 9.646 12332 Z= 0.290 Chirality : 0.041 0.157 1455 Planarity : 0.004 0.054 1521 Dihedral : 6.175 71.532 1247 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.16 % Allowed : 19.41 % Favored : 77.43 % 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: -0.65 (0.27), residues: 1118 helix: 0.51 (0.22), residues: 682 sheet: -0.85 (0.72), residues: 58 loop : -2.09 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 55 HIS 0.005 0.001 HIS A 73 PHE 0.016 0.001 PHE B 70 TYR 0.006 0.001 TYR F 124 ARG 0.004 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: B 135 LEU cc_start: 0.8871 (tp) cc_final: 0.8615 (tt) REVERT: B 220 GLN cc_start: 0.7247 (mt0) cc_final: 0.6453 (tm-30) REVERT: C 25 LEU cc_start: 0.8067 (tp) cc_final: 0.7851 (tp) REVERT: C 54 TYR cc_start: 0.6442 (OUTLIER) cc_final: 0.6228 (t80) REVERT: C 123 TRP cc_start: 0.8169 (t-100) cc_final: 0.7948 (t-100) REVERT: C 229 GLU cc_start: 0.7059 (tt0) cc_final: 0.6731 (tt0) REVERT: F 10 GLU cc_start: 0.7635 (tp30) cc_final: 0.7413 (tp30) outliers start: 29 outliers final: 24 residues processed: 204 average time/residue: 0.2182 time to fit residues: 60.1352 Evaluate side-chains 209 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 184 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 chunk 103 optimal weight: 0.5980 chunk 60 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 106 optimal weight: 0.0980 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9044 Z= 0.165 Angle : 0.595 9.146 12332 Z= 0.287 Chirality : 0.040 0.149 1455 Planarity : 0.004 0.053 1521 Dihedral : 6.032 72.852 1247 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.73 % Allowed : 20.17 % Favored : 77.10 % 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: -0.40 (0.27), residues: 1118 helix: 0.72 (0.22), residues: 675 sheet: -0.77 (0.72), residues: 58 loop : -1.95 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 55 HIS 0.004 0.001 HIS A 73 PHE 0.018 0.001 PHE B 3 TYR 0.005 0.001 TYR F 124 ARG 0.007 0.000 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: B 135 LEU cc_start: 0.8728 (tp) cc_final: 0.8486 (tt) REVERT: B 220 GLN cc_start: 0.7150 (mt0) cc_final: 0.6353 (tm-30) REVERT: C 25 LEU cc_start: 0.8072 (tp) cc_final: 0.7871 (tp) REVERT: C 54 TYR cc_start: 0.6417 (OUTLIER) cc_final: 0.6196 (t80) REVERT: C 229 GLU cc_start: 0.7051 (tt0) cc_final: 0.6746 (tt0) outliers start: 25 outliers final: 20 residues processed: 203 average time/residue: 0.2226 time to fit residues: 61.6135 Evaluate side-chains 212 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 0.2980 chunk 102 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9044 Z= 0.195 Angle : 0.616 9.338 12332 Z= 0.299 Chirality : 0.041 0.148 1455 Planarity : 0.004 0.053 1521 Dihedral : 6.042 73.370 1247 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.62 % Allowed : 20.72 % Favored : 76.66 % 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: -0.38 (0.27), residues: 1118 helix: 0.73 (0.22), residues: 674 sheet: -0.72 (0.72), residues: 58 loop : -1.94 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 123 HIS 0.005 0.001 HIS A 73 PHE 0.031 0.001 PHE B 3 TYR 0.008 0.001 TYR F 124 ARG 0.004 0.000 ARG A 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7299 (mt-10) REVERT: B 135 LEU cc_start: 0.8750 (tp) cc_final: 0.8512 (tt) REVERT: B 220 GLN cc_start: 0.7282 (mt0) cc_final: 0.6480 (tm-30) REVERT: C 25 LEU cc_start: 0.8111 (tp) cc_final: 0.7905 (tp) REVERT: C 54 TYR cc_start: 0.6413 (OUTLIER) cc_final: 0.6203 (t80) REVERT: C 229 GLU cc_start: 0.7133 (tt0) cc_final: 0.6814 (tt0) outliers start: 24 outliers final: 21 residues processed: 197 average time/residue: 0.2191 time to fit residues: 58.3798 Evaluate side-chains 205 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.2980 chunk 37 optimal weight: 0.0670 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** F 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.120961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.106163 restraints weight = 14272.036| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.22 r_work: 0.3299 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9044 Z= 0.243 Angle : 0.643 9.256 12332 Z= 0.314 Chirality : 0.042 0.152 1455 Planarity : 0.004 0.052 1521 Dihedral : 6.140 73.273 1247 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.84 % Allowed : 21.05 % Favored : 76.12 % 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: -0.55 (0.27), residues: 1118 helix: 0.53 (0.21), residues: 690 sheet: -0.65 (0.73), residues: 58 loop : -1.98 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 123 HIS 0.006 0.001 HIS A 73 PHE 0.035 0.001 PHE B 3 TYR 0.011 0.001 TYR F 124 ARG 0.004 0.000 ARG A 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2244.56 seconds wall clock time: 41 minutes 0.43 seconds (2460.43 seconds total)