Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 09:45:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6k_28886/04_2023/8f6k_28886.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6k_28886/04_2023/8f6k_28886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6k_28886/04_2023/8f6k_28886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6k_28886/04_2023/8f6k_28886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6k_28886/04_2023/8f6k_28886.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6k_28886/04_2023/8f6k_28886.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.017 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 Zn 4 6.06 5 S 12 5.16 5 C 5630 2.51 5 N 1470 2.21 5 O 1596 1.98 5 H 8586 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B ASP 213": "OD1" <-> "OD2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D GLU 252": "OE1" <-> "OE2" Residue "D PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 17298 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4226 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 6, 'TRANS': 272} Chain: "B" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4421 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "C" Number of atoms: 4226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4226 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 6, 'TRANS': 272} Chain: "D" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4421 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.78, per 1000 atoms: 0.45 Number of scatterers: 17298 At special positions: 0 Unit cell: (137.033, 102.505, 102.505, 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) Zn 4 29.99 S 12 16.00 O 1596 8.00 N 1470 7.00 C 5630 6.00 H 8586 1.00 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: 14.80 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 155 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 155 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 155 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 155 " 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 67.8% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 12 through 34 removed outlier: 3.659A pdb=" N ARG A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 63 removed outlier: 3.706A pdb=" N ILE A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 109 removed outlier: 4.149A pdb=" N ALA A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 removed outlier: 3.662A pdb=" N GLY A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 175 removed outlier: 4.414A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 180 through 208 removed outlier: 3.767A pdb=" N PHE A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.544A pdb=" N LEU A 222 " --> pdb=" O GLN A 218 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'B' and resid 15 through 23 Processing helix chain 'B' and resid 24 through 35 Processing helix chain 'B' and resid 38 through 65 removed outlier: 3.591A pdb=" N ILE B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 109 removed outlier: 3.719A pdb=" N LEU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 140 Processing helix chain 'B' and resid 141 through 144 Processing helix chain 'B' and resid 149 through 176 removed outlier: 3.667A pdb=" N LEU B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 217 removed outlier: 4.165A pdb=" N ASP B 181 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 269 removed outlier: 3.539A pdb=" N THR B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 34 removed outlier: 3.664A pdb=" N ARG C 16 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 31 " --> pdb=" O THR C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 63 removed outlier: 3.703A pdb=" N ILE C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE C 60 " --> pdb=" O ILE C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 109 removed outlier: 4.125A pdb=" N ALA C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE C 92 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 142 removed outlier: 3.666A pdb=" N GLY C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 175 removed outlier: 4.418A pdb=" N PHE C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 180 through 208 removed outlier: 3.767A pdb=" N PHE C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA C 185 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 224 removed outlier: 3.539A pdb=" N LEU C 222 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 275 Processing helix chain 'D' and resid 15 through 23 Processing helix chain 'D' and resid 24 through 35 Processing helix chain 'D' and resid 38 through 65 removed outlier: 3.591A pdb=" N ILE D 57 " --> pdb=" O LEU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 109 removed outlier: 3.732A pdb=" N LEU D 86 " --> pdb=" O PRO D 82 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 140 Processing helix chain 'D' and resid 141 through 144 Processing helix chain 'D' and resid 149 through 176 removed outlier: 3.667A pdb=" N LEU D 160 " --> pdb=" O TYR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 217 removed outlier: 4.165A pdb=" N ASP D 181 " --> pdb=" O TRP D 177 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY D 182 " --> pdb=" O TRP D 178 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 269 removed outlier: 3.535A pdb=" N THR D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 269 " --> pdb=" O ILE D 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 239 through 241 removed outlier: 4.026A pdb=" N THR A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 244 through 246 removed outlier: 6.297A pdb=" N VAL B 245 " --> pdb=" O GLU B 281 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 252 through 254 Processing sheet with id=AA4, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AA5, first strand: chain 'D' and resid 244 through 246 removed outlier: 6.294A pdb=" N VAL D 245 " --> pdb=" O GLU D 281 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 252 through 254 567 hydrogen bonds defined for protein. 1689 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: 5.82 Time building geometry restraints manager: 15.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8582 1.03 - 1.23: 8 1.23 - 1.42: 3670 1.42 - 1.62: 5178 1.62 - 1.81: 20 Bond restraints: 17458 Sorted by residual: bond pdb=" N VAL A 11 " pdb=" CA VAL A 11 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 bond pdb=" N VAL C 11 " pdb=" CA VAL C 11 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 bond pdb=" N VAL A 11 " pdb=" H VAL A 11 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" N VAL C 11 " pdb=" H VAL C 11 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" N ASP C 279 " pdb=" CA ASP C 279 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.73e-01 ... (remaining 17453 not shown) Histogram of bond angle deviations from ideal: 100.75 - 107.39: 666 107.39 - 114.04: 20744 114.04 - 120.69: 5935 120.69 - 127.34: 4040 127.34 - 133.99: 89 Bond angle restraints: 31474 Sorted by residual: angle pdb=" N VAL B 273 " pdb=" CA VAL B 273 " pdb=" C VAL B 273 " ideal model delta sigma weight residual 112.80 109.64 3.16 1.15e+00 7.56e-01 7.54e+00 angle pdb=" N VAL D 273 " pdb=" CA VAL D 273 " pdb=" C VAL D 273 " ideal model delta sigma weight residual 112.80 109.65 3.15 1.15e+00 7.56e-01 7.51e+00 angle pdb=" N HIS C 73 " pdb=" CA HIS C 73 " pdb=" CB HIS C 73 " ideal model delta sigma weight residual 114.27 110.56 3.71 1.64e+00 3.72e-01 5.12e+00 angle pdb=" N ALA D 116 " pdb=" CA ALA D 116 " pdb=" CB ALA D 116 " ideal model delta sigma weight residual 113.65 110.37 3.28 1.47e+00 4.63e-01 4.98e+00 angle pdb=" N HIS A 73 " pdb=" CA HIS A 73 " pdb=" CB HIS A 73 " ideal model delta sigma weight residual 114.27 110.64 3.63 1.64e+00 3.72e-01 4.91e+00 ... (remaining 31469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 6378 16.81 - 33.62: 501 33.62 - 50.43: 88 50.43 - 67.24: 21 67.24 - 84.05: 18 Dihedral angle restraints: 7006 sinusoidal: 3198 harmonic: 3808 Sorted by residual: dihedral pdb=" CA ASP B 70 " pdb=" C ASP B 70 " pdb=" N HIS B 71 " pdb=" CA HIS B 71 " ideal model delta harmonic sigma weight residual -180.00 -157.56 -22.44 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ASP D 70 " pdb=" C ASP D 70 " pdb=" N HIS D 71 " pdb=" CA HIS D 71 " ideal model delta harmonic sigma weight residual 180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA HIS D 71 " pdb=" C HIS D 71 " pdb=" N ASP D 72 " pdb=" CA ASP D 72 " ideal model delta harmonic sigma weight residual -180.00 -159.68 -20.32 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 7003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1012 0.029 - 0.059: 319 0.059 - 0.088: 101 0.088 - 0.117: 26 0.117 - 0.147: 12 Chirality restraints: 1470 Sorted by residual: chirality pdb=" CA VAL A 67 " pdb=" N VAL A 67 " pdb=" C VAL A 67 " pdb=" CB VAL A 67 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA VAL C 67 " pdb=" N VAL C 67 " pdb=" C VAL C 67 " pdb=" CB VAL C 67 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ILE D 283 " pdb=" N ILE D 283 " pdb=" C ILE D 283 " pdb=" CB ILE D 283 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 1467 not shown) Planarity restraints: 2582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 67 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.27e+00 pdb=" N PRO A 68 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 67 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO B 68 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 68 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 68 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 287 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.10e+00 pdb=" N PRO D 288 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 288 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 288 " -0.020 5.00e-02 4.00e+02 ... (remaining 2579 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 941 2.20 - 2.80: 35960 2.80 - 3.40: 47133 3.40 - 4.00: 58732 4.00 - 4.60: 91886 Nonbonded interactions: 234652 Sorted by model distance: nonbonded pdb=" HE2 HIS D 71 " pdb=" O TYR D 75 " model vdw 1.595 1.850 nonbonded pdb=" O LEU D 251 " pdb=" H ALA D 287 " model vdw 1.597 1.850 nonbonded pdb=" O LEU B 251 " pdb=" H ALA B 287 " model vdw 1.608 1.850 nonbonded pdb=" OD1 ASP B 51 " pdb=" HE2 HIS B 155 " model vdw 1.617 1.850 nonbonded pdb=" OD1 ASP D 51 " pdb=" HE2 HIS D 155 " model vdw 1.618 1.850 ... (remaining 234647 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 'B' and (resid 11 through 65 or (resid 66 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 67 and (n \ ame N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (re \ sid 68 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 69 and (name N or name CA or name C or name O or name CB )) or ( \ resid 70 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name OD2)) or (resid 71 and (name N or name CA or name C or name O or n \ ame CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 72 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name OD2)) or (resid 73 and (name N or name CA or name C or name O or name CB o \ r name CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 74 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2)) or (resid 75 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ or name OH )) or (resid 76 and (name N or name CA or name C or nam \ e O )) or (resid 77 and (name N or name CA or name C or name O or name CB or nam \ e CG or name ND1 or name CD2 or name CE1 or name NE2)) or resid 78 through 287 o \ r (resid 288 and (name N or name CA or name C or name O or name CB or name CG or \ name CD )) or (resid 289 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2)) or resid 301)) selection = chain 'C' selection = (chain 'D' and (resid 11 through 65 or (resid 66 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 67 and (n \ ame N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (re \ sid 68 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 69 and (name N or name CA or name C or name O or name CB )) or ( \ resid 70 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name OD2)) or (resid 71 and (name N or name CA or name C or name O or n \ ame CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 72 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name OD2)) or (resid 73 and (name N or name CA or name C or name O or name CB o \ r name CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 74 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2)) or (resid 75 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ or name OH )) or (resid 76 and (name N or name CA or name C or nam \ e O )) or (resid 77 and (name N or name CA or name C or name O or name CB or nam \ e CG or name ND1 or name CD2 or name CE1 or name NE2)) or resid 78 through 287 o \ r (resid 288 and (name N or name CA or name C or name O or name CB or name CG or \ name CD )) or (resid 289 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2)) or resid 301)) } 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: 4.540 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: 0.290 Extract box with map and model: 11.380 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 60.800 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 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 : 0.002 0.031 8872 Z= 0.152 Angle : 0.499 4.773 12088 Z= 0.285 Chirality : 0.034 0.147 1470 Planarity : 0.003 0.038 1512 Dihedral : 14.249 84.047 3098 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.96 % Favored : 93.51 % Rotamer Outliers : 0.00 % 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: -0.45 (0.26), residues: 1124 helix: 1.06 (0.20), residues: 776 sheet: -4.09 (0.45), residues: 76 loop : -3.13 (0.33), residues: 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.3394 time to fit residues: 82.1959 Evaluate side-chains 121 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.536 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 8872 Z= 0.262 Angle : 0.555 5.043 12088 Z= 0.309 Chirality : 0.037 0.143 1470 Planarity : 0.004 0.042 1512 Dihedral : 4.715 23.351 1214 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.14 % Favored : 93.42 % Rotamer Outliers : 1.87 % 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: 0.15 (0.27), residues: 1124 helix: 1.57 (0.20), residues: 786 sheet: -3.94 (0.43), residues: 86 loop : -3.19 (0.35), residues: 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 145 average time/residue: 0.3457 time to fit residues: 76.0360 Evaluate side-chains 138 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.378 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2055 time to fit residues: 7.1266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 0.0270 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 0.0870 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 overall best weight: 0.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN C 163 ASN C 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 8872 Z= 0.164 Angle : 0.499 5.005 12088 Z= 0.275 Chirality : 0.034 0.144 1470 Planarity : 0.003 0.037 1512 Dihedral : 4.494 22.495 1214 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.69 % Favored : 93.86 % Rotamer Outliers : 0.55 % 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: 0.47 (0.27), residues: 1124 helix: 1.85 (0.20), residues: 784 sheet: -3.67 (0.44), residues: 86 loop : -3.26 (0.35), residues: 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 143 average time/residue: 0.3344 time to fit residues: 72.5374 Evaluate side-chains 125 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 1.465 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1982 time to fit residues: 3.5763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 240 GLN C 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 8872 Z= 0.185 Angle : 0.497 4.839 12088 Z= 0.276 Chirality : 0.035 0.143 1470 Planarity : 0.003 0.037 1512 Dihedral : 4.455 21.680 1214 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.96 % Favored : 93.59 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.28), residues: 1124 helix: 1.93 (0.20), residues: 784 sheet: -3.56 (0.45), residues: 86 loop : -3.26 (0.35), residues: 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 131 average time/residue: 0.3318 time to fit residues: 65.7970 Evaluate side-chains 119 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 1.353 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1787 time to fit residues: 2.3152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 0.3980 chunk 95 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 73 HIS C 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8872 Z= 0.227 Angle : 0.524 4.773 12088 Z= 0.291 Chirality : 0.036 0.145 1470 Planarity : 0.003 0.037 1512 Dihedral : 4.556 21.978 1214 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.76 % Favored : 92.97 % Rotamer Outliers : 0.88 % 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: 0.51 (0.27), residues: 1124 helix: 1.90 (0.20), residues: 780 sheet: -3.54 (0.45), residues: 86 loop : -3.32 (0.35), residues: 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 132 average time/residue: 0.3763 time to fit residues: 73.5074 Evaluate side-chains 125 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.532 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1935 time to fit residues: 4.6457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 8872 Z= 0.171 Angle : 0.497 4.777 12088 Z= 0.274 Chirality : 0.034 0.143 1470 Planarity : 0.003 0.034 1512 Dihedral : 4.435 22.353 1214 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.85 % Favored : 92.97 % Rotamer Outliers : 0.33 % 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: 0.70 (0.28), residues: 1124 helix: 2.05 (0.20), residues: 780 sheet: -3.42 (0.46), residues: 86 loop : -3.27 (0.36), residues: 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 135 average time/residue: 0.3868 time to fit residues: 77.0210 Evaluate side-chains 124 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 1.573 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.2006 time to fit residues: 2.9101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.0370 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN C 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 8872 Z= 0.147 Angle : 0.493 4.771 12088 Z= 0.269 Chirality : 0.034 0.160 1470 Planarity : 0.003 0.033 1512 Dihedral : 4.324 22.191 1214 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.23 % Favored : 93.59 % Rotamer Outliers : 0.55 % 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: 0.90 (0.28), residues: 1124 helix: 2.20 (0.20), residues: 780 sheet: -3.31 (0.47), residues: 86 loop : -3.21 (0.36), residues: 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 134 average time/residue: 0.4048 time to fit residues: 77.8621 Evaluate side-chains 120 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 1.495 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1871 time to fit residues: 3.1850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 8872 Z= 0.305 Angle : 0.573 4.792 12088 Z= 0.320 Chirality : 0.038 0.208 1470 Planarity : 0.004 0.040 1512 Dihedral : 4.780 26.384 1214 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.12 % Favored : 92.53 % Rotamer Outliers : 0.88 % 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: 1124 helix: 1.91 (0.19), residues: 784 sheet: -3.61 (0.45), residues: 86 loop : -3.28 (0.36), residues: 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 133 average time/residue: 0.4132 time to fit residues: 78.5301 Evaluate side-chains 123 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 1.511 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2056 time to fit residues: 2.6080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8872 Z= 0.201 Angle : 0.533 4.803 12088 Z= 0.292 Chirality : 0.035 0.173 1470 Planarity : 0.003 0.034 1512 Dihedral : 4.650 24.288 1214 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.56 % Favored : 92.08 % Rotamer Outliers : 0.44 % 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: 1124 helix: 2.10 (0.20), residues: 780 sheet: -3.43 (0.45), residues: 86 loop : -3.24 (0.36), residues: 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 1.557 Fit side-chains 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: 131 average time/residue: 0.4025 time to fit residues: 75.4847 Evaluate side-chains 125 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 1.437 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1931 time to fit residues: 2.6782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 0.2980 chunk 9 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 8872 Z= 0.148 Angle : 0.509 4.661 12088 Z= 0.276 Chirality : 0.034 0.153 1470 Planarity : 0.003 0.034 1512 Dihedral : 4.423 22.385 1214 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.49 % Favored : 93.15 % Rotamer Outliers : 0.00 % 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: 1.06 (0.28), residues: 1124 helix: 2.29 (0.20), residues: 784 sheet: -3.28 (0.47), residues: 86 loop : -3.12 (0.37), residues: 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Residue ALA 263 is missing expected H atoms. Skipping. Residue ALA 287 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.4161 time to fit residues: 75.8685 Evaluate side-chains 121 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.493 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 0.0870 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.187651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.149087 restraints weight = 35527.336| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.63 r_work: 0.3593 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 8872 Z= 0.172 Angle : 0.518 4.816 12088 Z= 0.282 Chirality : 0.035 0.155 1470 Planarity : 0.003 0.034 1512 Dihedral : 4.429 22.024 1214 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.12 % Favored : 92.53 % Rotamer Outliers : 0.55 % 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: 1.05 (0.28), residues: 1124 helix: 2.31 (0.19), residues: 780 sheet: -3.30 (0.47), residues: 86 loop : -3.12 (0.37), residues: 258 =============================================================================== Job complete usr+sys time: 3947.76 seconds wall clock time: 70 minutes 31.24 seconds (4231.24 seconds total)