Starting phenix.real_space_refine on Sun Mar 17 08:58:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6k_28886/03_2024/8f6k_28886.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6k_28886/03_2024/8f6k_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_28886/03_2024/8f6k_28886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6k_28886/03_2024/8f6k_28886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6k_28886/03_2024/8f6k_28886.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6k_28886/03_2024/8f6k_28886.pdb" } resolution = 3.46 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= 0.000 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-dev-5265/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: 7.79, 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: 13.92 Conformation dependent library (CDL) restraints added in 1.9 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: 1.15 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: 5.69 Time building geometry restraints manager: 14.38 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: 7389 16.81 - 33.62: 540 33.62 - 50.43: 127 50.43 - 67.24: 72 67.24 - 84.05: 18 Dihedral angle restraints: 8146 sinusoidal: 4338 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 8143 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: 3.410 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: 0.260 Extract box with map and model: 10.690 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 60.140 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.880 ------------------------------------------------------------------------------- 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 % Allowed : 0.66 % Favored : 99.34 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 178 HIS 0.006 0.001 HIS B 73 PHE 0.012 0.001 PHE A 161 TYR 0.016 0.001 TYR A 156 ARG 0.001 0.000 ARG C 210 *********************** 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 : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 THR cc_start: 0.7696 (m) cc_final: 0.7275 (m) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.3385 time to fit residues: 82.1481 Evaluate side-chains 121 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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: 5.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 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: 0.5980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7292 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8872 Z= 0.215 Angle : 0.529 4.892 12088 Z= 0.294 Chirality : 0.036 0.142 1470 Planarity : 0.004 0.043 1512 Dihedral : 4.558 21.663 1214 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.34 % Favored : 94.22 % Rotamer: Outliers : 1.87 % Allowed : 7.05 % Favored : 91.08 % 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: 0.26 (0.27), residues: 1124 helix: 1.69 (0.20), residues: 780 sheet: -3.81 (0.44), residues: 86 loop : -3.20 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 178 HIS 0.008 0.001 HIS D 71 PHE 0.011 0.001 PHE A 277 TYR 0.010 0.001 TYR C 156 ARG 0.002 0.000 ARG B 16 *********************** 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 156 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.7139 (t70) cc_final: 0.6652 (t0) outliers start: 17 outliers final: 15 residues processed: 150 average time/residue: 0.3306 time to fit residues: 74.6752 Evaluate side-chains 139 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 190 CYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 256 ASN 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: 0.9990 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 27 optimal weight: 0.0070 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1556 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= 0.192 Angle : 0.511 5.358 12088 Z= 0.283 Chirality : 0.035 0.143 1470 Planarity : 0.004 0.042 1512 Dihedral : 4.542 21.903 1214 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.32 % Favored : 93.24 % Rotamer: Outliers : 1.65 % Allowed : 9.58 % Favored : 88.77 % 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: 0.42 (0.27), residues: 1124 helix: 1.81 (0.20), residues: 784 sheet: -3.68 (0.44), residues: 86 loop : -3.27 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 178 HIS 0.007 0.001 HIS D 71 PHE 0.012 0.001 PHE A 277 TYR 0.010 0.001 TYR B 102 ARG 0.001 0.000 ARG B 217 *********************** 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 155 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ASP cc_start: 0.7138 (t70) cc_final: 0.6662 (t0) outliers start: 15 outliers final: 15 residues processed: 151 average time/residue: 0.3272 time to fit residues: 75.3430 Evaluate side-chains 137 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 256 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 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: B 73 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8872 Z= 0.182 Angle : 0.497 4.860 12088 Z= 0.276 Chirality : 0.035 0.144 1470 Planarity : 0.003 0.040 1512 Dihedral : 4.468 21.637 1214 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.49 % Favored : 93.06 % Rotamer: Outliers : 1.43 % Allowed : 11.12 % Favored : 87.44 % 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: 0.57 (0.27), residues: 1124 helix: 1.92 (0.20), residues: 784 sheet: -3.53 (0.45), residues: 86 loop : -3.26 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 178 HIS 0.006 0.001 HIS B 71 PHE 0.010 0.001 PHE A 277 TYR 0.009 0.001 TYR B 102 ARG 0.001 0.000 ARG C 210 *********************** 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 144 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 HIS cc_start: 0.5644 (m-70) cc_final: 0.4973 (m-70) REVERT: B 213 ASP cc_start: 0.7084 (t70) cc_final: 0.6628 (t0) outliers start: 13 outliers final: 13 residues processed: 140 average time/residue: 0.3204 time to fit residues: 68.3067 Evaluate side-chains 133 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 256 ASN 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: 8.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 26 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: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8872 Z= 0.279 Angle : 0.553 5.141 12088 Z= 0.308 Chirality : 0.037 0.148 1470 Planarity : 0.004 0.045 1512 Dihedral : 4.734 22.807 1214 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.41 % Favored : 93.42 % Rotamer: Outliers : 2.31 % Allowed : 12.22 % Favored : 85.46 % 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: 0.29 (0.27), residues: 1124 helix: 1.67 (0.20), residues: 790 sheet: -3.61 (0.45), residues: 86 loop : -3.37 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 178 HIS 0.008 0.002 HIS D 71 PHE 0.011 0.001 PHE A 277 TYR 0.011 0.001 TYR B 102 ARG 0.003 0.000 ARG B 217 *********************** 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 143 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 HIS cc_start: 0.4744 (OUTLIER) cc_final: 0.4533 (m-70) outliers start: 21 outliers final: 18 residues processed: 138 average time/residue: 0.3291 time to fit residues: 68.3506 Evaluate side-chains 137 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8872 Z= 0.219 Angle : 0.523 4.626 12088 Z= 0.290 Chirality : 0.035 0.147 1470 Planarity : 0.004 0.040 1512 Dihedral : 4.637 22.455 1214 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.58 % Favored : 93.06 % Rotamer: Outliers : 2.86 % Allowed : 13.00 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 1124 helix: 1.80 (0.20), residues: 786 sheet: -3.56 (0.45), residues: 86 loop : -3.39 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 178 HIS 0.007 0.001 HIS B 71 PHE 0.011 0.001 PHE A 277 TYR 0.010 0.001 TYR B 102 ARG 0.002 0.000 ARG B 217 *********************** 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 155 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.306 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: D 73 HIS cc_start: 0.5625 (m-70) cc_final: 0.4840 (m-70) outliers start: 26 outliers final: 22 residues processed: 150 average time/residue: 0.3333 time to fit residues: 74.6618 Evaluate side-chains 136 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8872 Z= 0.178 Angle : 0.513 4.630 12088 Z= 0.280 Chirality : 0.034 0.143 1470 Planarity : 0.003 0.041 1512 Dihedral : 4.483 22.576 1214 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.67 % Favored : 92.97 % Rotamer: Outliers : 2.20 % Allowed : 13.88 % Favored : 83.92 % 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: 0.61 (0.28), residues: 1124 helix: 1.96 (0.20), residues: 786 sheet: -3.44 (0.46), residues: 86 loop : -3.33 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 178 HIS 0.006 0.001 HIS A 77 PHE 0.010 0.001 PHE A 277 TYR 0.011 0.001 TYR C 156 ARG 0.001 0.000 ARG C 210 *********************** 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 143 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 17 residues processed: 141 average time/residue: 0.3461 time to fit residues: 72.6813 Evaluate side-chains 134 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 256 ASN 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: 0.9990 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8872 Z= 0.284 Angle : 0.563 4.673 12088 Z= 0.313 Chirality : 0.037 0.145 1470 Planarity : 0.004 0.043 1512 Dihedral : 4.727 21.799 1214 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.12 % Favored : 92.53 % Rotamer: Outliers : 2.31 % Allowed : 14.21 % Favored : 83.48 % 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: 0.33 (0.27), residues: 1124 helix: 1.72 (0.20), residues: 790 sheet: -3.67 (0.44), residues: 86 loop : -3.36 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 178 HIS 0.007 0.002 HIS B 71 PHE 0.010 0.001 PHE A 277 TYR 0.011 0.001 TYR B 102 ARG 0.002 0.000 ARG D 217 *********************** 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 141 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 139 average time/residue: 0.3487 time to fit residues: 73.9343 Evaluate side-chains 129 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8872 Z= 0.165 Angle : 0.514 4.626 12088 Z= 0.280 Chirality : 0.034 0.143 1470 Planarity : 0.003 0.038 1512 Dihedral : 4.461 23.177 1214 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.21 % Favored : 92.44 % Rotamer: Outliers : 2.09 % Allowed : 15.09 % Favored : 82.82 % 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: 0.71 (0.28), residues: 1124 helix: 2.00 (0.20), residues: 790 sheet: -3.49 (0.45), residues: 86 loop : -3.24 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 178 HIS 0.005 0.001 HIS B 71 PHE 0.009 0.001 PHE D 91 TYR 0.011 0.001 TYR B 75 ARG 0.001 0.000 ARG A 210 *********************** 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 151 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.273 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: 19 outliers final: 17 residues processed: 150 average time/residue: 0.3304 time to fit residues: 74.4089 Evaluate side-chains 136 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 0.0010 chunk 26 optimal weight: 1.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8872 Z= 0.161 Angle : 0.509 4.629 12088 Z= 0.277 Chirality : 0.034 0.152 1470 Planarity : 0.003 0.040 1512 Dihedral : 4.348 21.973 1214 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.67 % Favored : 92.97 % Rotamer: Outliers : 2.09 % Allowed : 15.09 % Favored : 82.82 % 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: 0.91 (0.28), residues: 1124 helix: 2.15 (0.20), residues: 790 sheet: -3.38 (0.46), residues: 86 loop : -3.20 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 178 HIS 0.005 0.001 HIS D 71 PHE 0.009 0.001 PHE D 91 TYR 0.011 0.001 TYR C 156 ARG 0.001 0.000 ARG D 210 ********************** 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 143 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.359 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: 19 outliers final: 16 residues processed: 141 average time/residue: 0.3625 time to fit residues: 75.2050 Evaluate side-chains 136 residues out of total 908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 8 ASP Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.0470 chunk 12 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 ASN ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.186058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.147219 restraints weight = 35300.868| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.65 r_work: 0.3554 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2490 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= 0.190 Angle : 0.520 4.765 12088 Z= 0.284 Chirality : 0.035 0.146 1470 Planarity : 0.004 0.039 1512 Dihedral : 4.406 22.080 1214 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.21 % Favored : 92.44 % Rotamer: Outliers : 1.54 % Allowed : 15.86 % Favored : 82.60 % 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: 0.83 (0.28), residues: 1124 helix: 2.13 (0.20), residues: 786 sheet: -3.48 (0.45), residues: 86 loop : -3.23 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 178 HIS 0.006 0.001 HIS B 71 PHE 0.009 0.001 PHE D 91 TYR 0.013 0.001 TYR A 156 ARG 0.004 0.000 ARG B 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3826.27 seconds wall clock time: 68 minutes 4.58 seconds (4084.58 seconds total)