Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 08:41:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj5_36340/08_2023/8jj5_36340_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj5_36340/08_2023/8jj5_36340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj5_36340/08_2023/8jj5_36340.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj5_36340/08_2023/8jj5_36340.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj5_36340/08_2023/8jj5_36340_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj5_36340/08_2023/8jj5_36340_trim.pdb" } resolution = 3.5 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= -0.005 sd= 0.124 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 4460 2.51 5 N 1108 2.21 5 O 1290 1.98 5 H 6679 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 89": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 117": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 151": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 175": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 140": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 120": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 163": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 204": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 85": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 113": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 128": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 152": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 188": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 228": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 257": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 13594 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3893 Classifications: {'peptide': 248} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 237} Chain: "B" Number of atoms: 2224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2224 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain breaks: 1 Chain: "C" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3253 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 15, 'TRANS': 202} Chain: "D" Number of atoms: 4040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 4040 Classifications: {'peptide': 254} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 243} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.00, per 1000 atoms: 0.44 Number of scatterers: 13594 At special positions: 0 Unit cell: (94.5, 78.3, 145.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 O 1290 8.00 N 1108 7.00 C 4460 6.00 H 6679 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 158 " - pdb=" SG CYS A 217 " distance=2.02 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 189 " distance=2.02 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 204 " distance=2.02 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 110 " distance=2.04 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 152 " distance=2.05 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 218 " distance=2.01 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 190 " distance=2.04 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 205 " distance=2.02 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 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 201 " - " ASN B 28 " " NAG D 301 " - " ASN D 131 " " NAG E 1 " - " ASN A 169 " " NAG F 1 " - " ASN B 57 " " NAG G 1 " - " ASN C 139 " " NAG H 1 " - " ASN C 170 " Time building additional restraints: 11.80 Conformation dependent library (CDL) restraints added in 1.2 seconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 6 sheets defined 57.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 12 through 42 removed outlier: 3.504A pdb=" N LEU A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.677A pdb=" N GLY A 52 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A 53 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 87 removed outlier: 4.061A pdb=" N ALA A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE A 68 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 122 removed outlier: 5.670A pdb=" N ILE A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 135 removed outlier: 4.855A pdb=" N GLN A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 157 removed outlier: 3.564A pdb=" N LEU A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 172 through 178 removed outlier: 4.109A pdb=" N ALA A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 217 through 257 removed outlier: 3.623A pdb=" N ILE A 221 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'B' and resid 50 through 54 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 153 through 182 removed outlier: 3.705A pdb=" N VAL B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 75 removed outlier: 3.921A pdb=" N ARG C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 removed outlier: 4.023A pdb=" N ARG C 120 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 132 Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.525A pdb=" N ILE C 197 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 236 Proline residue: C 219 - end of helix Processing helix chain 'D' and resid 8 through 38 Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 53 through 83 Processing helix chain 'D' and resid 84 through 114 removed outlier: 4.611A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 removed outlier: 3.784A pdb=" N TYR D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 157 removed outlier: 3.802A pdb=" N GLY D 145 " --> pdb=" O TRP D 141 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR D 147 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 218 through 257 Proline residue: D 225 - end of helix removed outlier: 3.606A pdb=" N ALA D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 44 through 46 Processing sheet with id=AA2, first strand: chain 'B' and resid 70 through 76 removed outlier: 3.549A pdb=" N SER B 126 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 70 through 76 Processing sheet with id=AA4, first strand: chain 'C' and resid 40 through 43 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 106 removed outlier: 5.948A pdb=" N LYS C 101 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL C 65 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 103 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 60 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR C 166 " --> pdb=" O GLN C 179 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLN C 179 " --> pdb=" O TYR C 166 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU C 168 " --> pdb=" O GLN C 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 106 removed outlier: 5.948A pdb=" N LYS C 101 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL C 65 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 103 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 60 " --> pdb=" O VAL C 169 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1164 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: 4.72 Time building geometry restraints manager: 12.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 1444 1.04 - 1.23: 6047 1.23 - 1.43: 2326 1.43 - 1.63: 3865 1.63 - 1.82: 84 Bond restraints: 13766 Sorted by residual: bond pdb=" N ARG D 9 " pdb=" H ARG D 9 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" CZ ARG D 9 " pdb=" NH2 ARG D 9 " ideal model delta sigma weight residual 1.330 1.231 0.099 1.30e-02 5.92e+03 5.75e+01 bond pdb=" N TRP D 246 " pdb=" H TRP D 246 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N GLY C 225 " pdb=" H GLY C 225 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" CD2 PHE C 220 " pdb=" HD2 PHE C 220 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 13761 not shown) Histogram of bond angle deviations from ideal: 96.33 - 104.41: 314 104.41 - 112.49: 14653 112.49 - 120.56: 6883 120.56 - 128.64: 2847 128.64 - 136.71: 70 Bond angle restraints: 24767 Sorted by residual: angle pdb=" CA PHE D 11 " pdb=" CB PHE D 11 " pdb=" CG PHE D 11 " ideal model delta sigma weight residual 113.80 121.20 -7.40 1.00e+00 1.00e+00 5.47e+01 angle pdb=" CA PHE D 92 " pdb=" CB PHE D 92 " pdb=" CG PHE D 92 " ideal model delta sigma weight residual 113.80 121.09 -7.29 1.00e+00 1.00e+00 5.31e+01 angle pdb=" CA PHE D 253 " pdb=" CB PHE D 253 " pdb=" CG PHE D 253 " ideal model delta sigma weight residual 113.80 120.90 -7.10 1.00e+00 1.00e+00 5.04e+01 angle pdb=" CA ASN D 19 " pdb=" CB ASN D 19 " pdb=" CG ASN D 19 " ideal model delta sigma weight residual 112.60 119.63 -7.03 1.00e+00 1.00e+00 4.94e+01 angle pdb=" CA ASN D 84 " pdb=" CB ASN D 84 " pdb=" CG ASN D 84 " ideal model delta sigma weight residual 112.60 119.62 -7.02 1.00e+00 1.00e+00 4.92e+01 ... (remaining 24762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4940 17.66 - 35.33: 394 35.33 - 52.99: 82 52.99 - 70.66: 59 70.66 - 88.32: 22 Dihedral angle restraints: 5497 sinusoidal: 2470 harmonic: 3027 Sorted by residual: dihedral pdb=" C SER D 42 " pdb=" N SER D 42 " pdb=" CA SER D 42 " pdb=" CB SER D 42 " ideal model delta harmonic sigma weight residual -122.60 -138.41 15.81 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" CA ASP D 39 " pdb=" C ASP D 39 " pdb=" N GLN D 40 " pdb=" CA GLN D 40 " ideal model delta harmonic sigma weight residual -180.00 -150.05 -29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA TYR D 41 " pdb=" C TYR D 41 " pdb=" N SER D 42 " pdb=" CA SER D 42 " ideal model delta harmonic sigma weight residual 180.00 -151.16 -28.84 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 5494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 877 0.154 - 0.308: 156 0.308 - 0.462: 33 0.462 - 0.617: 55 0.617 - 0.771: 22 Chirality restraints: 1143 Sorted by residual: chirality pdb=" C1 MAN G 5 " pdb=" O6 BMA G 3 " pdb=" C2 MAN G 5 " pdb=" O5 MAN G 5 " both_signs ideal model delta sigma weight residual False 2.40 2.09 0.31 2.00e-02 2.50e+03 2.33e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.43e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.27e+01 ... (remaining 1140 not shown) Planarity restraints: 2014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 230 " 0.199 2.00e-02 2.50e+03 1.35e-01 7.34e+02 pdb=" CG TRP A 230 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP A 230 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 230 " 0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP A 230 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TRP A 230 " 0.051 2.00e-02 2.50e+03 pdb=" CE3 TRP A 230 " -0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 230 " 0.071 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 230 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 230 " 0.117 2.00e-02 2.50e+03 pdb=" HD1 TRP A 230 " 0.027 2.00e-02 2.50e+03 pdb=" HE1 TRP A 230 " -0.340 2.00e-02 2.50e+03 pdb=" HE3 TRP A 230 " -0.253 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 230 " 0.046 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 230 " -0.124 2.00e-02 2.50e+03 pdb=" HH2 TRP A 230 " 0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 113 " 0.909 9.50e-02 1.11e+02 3.41e-01 6.41e+02 pdb=" NE ARG D 113 " 0.133 2.00e-02 2.50e+03 pdb=" CZ ARG D 113 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG D 113 " -0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG D 113 " -0.093 2.00e-02 2.50e+03 pdb="HH11 ARG D 113 " -0.265 2.00e-02 2.50e+03 pdb="HH12 ARG D 113 " 0.333 2.00e-02 2.50e+03 pdb="HH21 ARG D 113 " 0.022 2.00e-02 2.50e+03 pdb="HH22 ARG D 113 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 48 " 0.326 2.00e-02 2.50e+03 1.24e-01 4.60e+02 pdb=" CG TYR A 48 " -0.108 2.00e-02 2.50e+03 pdb=" CD1 TYR A 48 " -0.108 2.00e-02 2.50e+03 pdb=" CD2 TYR A 48 " -0.121 2.00e-02 2.50e+03 pdb=" CE1 TYR A 48 " -0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR A 48 " -0.044 2.00e-02 2.50e+03 pdb=" CZ TYR A 48 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR A 48 " 0.166 2.00e-02 2.50e+03 pdb=" HD1 TYR A 48 " -0.055 2.00e-02 2.50e+03 pdb=" HD2 TYR A 48 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 TYR A 48 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 48 " 0.027 2.00e-02 2.50e+03 ... (remaining 2011 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 867 2.18 - 2.78: 23757 2.78 - 3.39: 38509 3.39 - 3.99: 49776 3.99 - 4.60: 72615 Nonbonded interactions: 185524 Sorted by model distance: nonbonded pdb=" HG SER A 162 " pdb=" OD1 ASP A 166 " model vdw 1.572 1.850 nonbonded pdb=" HH TYR D 129 " pdb=" OD1 ASP D 151 " model vdw 1.600 1.850 nonbonded pdb=" OE2 GLU C 43 " pdb=" HH TYR C 132 " model vdw 1.601 1.850 nonbonded pdb=" HH TYR A 135 " pdb=" OD1 ASP A 150 " model vdw 1.607 1.850 nonbonded pdb=" O PHE D 35 " pdb=" HG SER D 38 " model vdw 1.611 1.850 ... (remaining 185519 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 'E' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.200 Extract box with map and model: 2.970 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 45.440 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 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 : 0.021 0.170 7087 Z= 1.372 Angle : 2.181 11.766 9657 Z= 1.445 Chirality : 0.194 0.771 1143 Planarity : 0.021 0.278 1192 Dihedral : 15.541 88.323 2439 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.88 % Favored : 91.00 % Rotamer Outliers : 1.22 % Cbeta Deviations : 4.87 % 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: -2.93 (0.25), residues: 856 helix: -1.78 (0.20), residues: 452 sheet: -0.70 (0.66), residues: 47 loop : -2.19 (0.31), residues: 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 276 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 281 average time/residue: 0.4151 time to fit residues: 152.3000 Evaluate side-chains 194 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 1.390 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.5378 time to fit residues: 2.7949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 GLN C 177 GLN D 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.080 7087 Z= 0.394 Angle : 0.880 8.771 9657 Z= 0.464 Chirality : 0.047 0.241 1143 Planarity : 0.006 0.072 1192 Dihedral : 8.608 85.344 939 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.91 (0.27), residues: 856 helix: -0.71 (0.23), residues: 461 sheet: -1.07 (0.56), residues: 59 loop : -1.98 (0.33), residues: 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 203 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 210 average time/residue: 0.3659 time to fit residues: 104.0943 Evaluate side-chains 195 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1740 time to fit residues: 5.6091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 7087 Z= 0.257 Angle : 0.760 7.705 9657 Z= 0.398 Chirality : 0.043 0.204 1143 Planarity : 0.005 0.053 1192 Dihedral : 7.364 76.409 939 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.24 (0.28), residues: 856 helix: -0.01 (0.24), residues: 451 sheet: -0.96 (0.58), residues: 64 loop : -1.85 (0.33), residues: 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 189 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 194 average time/residue: 0.3804 time to fit residues: 99.9920 Evaluate side-chains 173 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 168 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1622 time to fit residues: 2.7987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 76 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 7087 Z= 0.186 Angle : 0.686 7.193 9657 Z= 0.349 Chirality : 0.041 0.168 1143 Planarity : 0.004 0.051 1192 Dihedral : 6.650 72.645 939 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 2.03 % 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: -0.57 (0.29), residues: 856 helix: 0.53 (0.24), residues: 452 sheet: -0.39 (0.66), residues: 59 loop : -1.57 (0.33), residues: 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 182 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 190 average time/residue: 0.3951 time to fit residues: 99.3946 Evaluate side-chains 175 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 169 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1747 time to fit residues: 3.0440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7087 Z= 0.183 Angle : 0.649 7.354 9657 Z= 0.331 Chirality : 0.040 0.180 1143 Planarity : 0.004 0.042 1192 Dihedral : 6.322 69.437 939 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 1.08 % 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: -0.39 (0.28), residues: 856 helix: 0.66 (0.24), residues: 453 sheet: -0.43 (0.63), residues: 59 loop : -1.45 (0.33), residues: 344 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 182 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 184 average time/residue: 0.3939 time to fit residues: 96.6376 Evaluate side-chains 171 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 166 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1622 time to fit residues: 2.6659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 7087 Z= 0.190 Angle : 0.635 7.298 9657 Z= 0.327 Chirality : 0.041 0.178 1143 Planarity : 0.004 0.042 1192 Dihedral : 6.067 65.761 939 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 0.81 % 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: -0.24 (0.28), residues: 856 helix: 0.79 (0.24), residues: 452 sheet: -0.63 (0.58), residues: 65 loop : -1.33 (0.33), residues: 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 183 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 186 average time/residue: 0.4086 time to fit residues: 100.7663 Evaluate side-chains 173 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 169 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1714 time to fit residues: 2.5024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7087 Z= 0.213 Angle : 0.640 7.457 9657 Z= 0.330 Chirality : 0.041 0.187 1143 Planarity : 0.004 0.039 1192 Dihedral : 5.881 60.640 939 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 1.08 % 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: -0.20 (0.29), residues: 856 helix: 0.79 (0.24), residues: 453 sheet: -0.66 (0.58), residues: 70 loop : -1.24 (0.34), residues: 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 178 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 181 average time/residue: 0.4031 time to fit residues: 96.3567 Evaluate side-chains 171 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.051 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1498 time to fit residues: 2.3949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7087 Z= 0.227 Angle : 0.645 7.686 9657 Z= 0.334 Chirality : 0.041 0.196 1143 Planarity : 0.004 0.039 1192 Dihedral : 5.745 56.699 939 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 0.54 % 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: -0.21 (0.29), residues: 856 helix: 0.75 (0.24), residues: 453 sheet: -0.67 (0.58), residues: 71 loop : -1.21 (0.34), residues: 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 182 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 185 average time/residue: 0.4194 time to fit residues: 104.0410 Evaluate side-chains 175 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1993 time to fit residues: 2.3739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 7087 Z= 0.187 Angle : 0.630 7.816 9657 Z= 0.324 Chirality : 0.040 0.205 1143 Planarity : 0.004 0.039 1192 Dihedral : 5.488 52.177 939 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 0.68 % 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: 0.07 (0.29), residues: 856 helix: 0.99 (0.25), residues: 454 sheet: -0.50 (0.58), residues: 71 loop : -1.10 (0.35), residues: 331 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 184 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 186 average time/residue: 0.4169 time to fit residues: 102.3344 Evaluate side-chains 179 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 177 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1565 time to fit residues: 2.0186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 0.2980 chunk 83 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 7087 Z= 0.187 Angle : 0.628 7.937 9657 Z= 0.323 Chirality : 0.041 0.217 1143 Planarity : 0.004 0.038 1192 Dihedral : 5.304 47.944 939 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.68 % 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: 0.08 (0.29), residues: 856 helix: 0.97 (0.25), residues: 454 sheet: -0.27 (0.60), residues: 67 loop : -1.12 (0.34), residues: 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 184 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 186 average time/residue: 0.4239 time to fit residues: 105.6171 Evaluate side-chains 181 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 178 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1936 time to fit residues: 2.3337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN D 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.194061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.179098 restraints weight = 36130.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.183919 restraints weight = 15584.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.186841 restraints weight = 8298.824| |-----------------------------------------------------------------------------| r_work (final): 0.4640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.6346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 7087 Z= 0.216 Angle : 0.644 8.096 9657 Z= 0.331 Chirality : 0.041 0.203 1143 Planarity : 0.004 0.036 1192 Dihedral : 5.230 44.330 939 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 0.41 % 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: -0.01 (0.29), residues: 856 helix: 0.86 (0.25), residues: 460 sheet: -0.44 (0.58), residues: 71 loop : -1.10 (0.35), residues: 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3286.16 seconds wall clock time: 59 minutes 2.12 seconds (3542.12 seconds total)