Starting phenix.real_space_refine on Sun Mar 10 16:16:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwl_14188/03_2024/7qwl_14188.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwl_14188/03_2024/7qwl_14188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwl_14188/03_2024/7qwl_14188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwl_14188/03_2024/7qwl_14188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwl_14188/03_2024/7qwl_14188.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwl_14188/03_2024/7qwl_14188.pdb" } resolution = 3.47 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= 0.004 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2082 2.51 5 N 519 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "C TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C ARG 247": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3258 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "C" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Time building chain proxies: 2.21, per 1000 atoms: 0.68 Number of scatterers: 3258 At special positions: 0 Unit cell: (105.8, 98.9, 31.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 636 8.00 N 519 7.00 C 2082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.05 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.05 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: 1.13 Conformation dependent library (CDL) restraints added in 1.4 seconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 50.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.961A pdb=" N VAL A 133 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 133 " --> pdb=" O SER C 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 Processing sheet with id=AA5, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 156 Processing sheet with id=AA7, first strand: chain 'A' and resid 165 through 170 removed outlier: 6.459A pdb=" N ILE A 165 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N GLN B 168 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA A 167 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N GLN B 170 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 169 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 165 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N GLN C 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA B 167 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N GLN C 170 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 169 " --> pdb=" O GLN C 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 173 through 175 removed outlier: 6.412A pdb=" N THR A 174 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 187 removed outlier: 6.464A pdb=" N ILE A 186 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE B 186 " --> pdb=" O ILE C 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AB2, first strand: chain 'A' and resid 194 through 198 removed outlier: 8.237A pdb=" N ILE A 195 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR B 198 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N TYR A 197 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.382A pdb=" N VAL A 202 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AB5, first strand: chain 'A' and resid 214 through 218 Processing sheet with id=AB6, first strand: chain 'A' and resid 221 through 236 removed outlier: 8.501A pdb=" N HIS A 222 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL B 225 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N ILE A 224 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N MET B 227 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N LEU A 226 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N GLN B 229 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N MET A 228 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR B 231 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 230 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 232 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 10.565A pdb=" N THR B 235 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N THR A 234 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N HIS B 222 " --> pdb=" O ASN C 223 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL C 225 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N ILE B 224 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N MET C 227 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N LEU B 226 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N GLN C 229 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N MET B 228 " --> pdb=" O GLN C 229 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N THR C 231 " --> pdb=" O MET B 228 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL B 230 " --> pdb=" O THR C 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 221 through 236 removed outlier: 8.501A pdb=" N HIS A 222 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL B 225 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N ILE A 224 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N MET B 227 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N LEU A 226 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N GLN B 229 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N MET A 228 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR B 231 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 230 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 232 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 10.565A pdb=" N THR B 235 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N THR A 234 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N TYR C 236 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR B 235 " --> pdb=" O TYR C 236 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 240 through 252 removed outlier: 6.851A pdb=" N VAL A 251 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASP B 252 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 251 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASP C 252 " --> pdb=" O VAL B 251 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 180 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: 0.78 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 938 1.33 - 1.45: 521 1.45 - 1.57: 1817 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 3312 Sorted by residual: bond pdb=" CB THR C 215 " pdb=" OG1 THR C 215 " ideal model delta sigma weight residual 1.433 1.387 0.046 1.60e-02 3.91e+03 8.14e+00 bond pdb=" CZ ARG B 247 " pdb=" NH2 ARG B 247 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.62e+00 bond pdb=" CZ ARG C 247 " pdb=" NH2 ARG C 247 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.10e+00 bond pdb=" CZ ARG C 180 " pdb=" NH2 ARG C 180 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.55e+00 bond pdb=" CZ ARG A 247 " pdb=" NH2 ARG A 247 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.54e+00 ... (remaining 3307 not shown) Histogram of bond angle deviations from ideal: 98.72 - 104.79: 67 104.79 - 110.87: 857 110.87 - 116.94: 1240 116.94 - 123.01: 1998 123.01 - 129.09: 341 Bond angle restraints: 4503 Sorted by residual: angle pdb=" N GLU C 246 " pdb=" CA GLU C 246 " pdb=" C GLU C 246 " ideal model delta sigma weight residual 109.07 122.14 -13.07 1.52e+00 4.33e-01 7.39e+01 angle pdb=" N GLU C 246 " pdb=" CA GLU C 246 " pdb=" CB GLU C 246 " ideal model delta sigma weight residual 111.66 98.72 12.94 1.67e+00 3.59e-01 6.01e+01 angle pdb=" OD1 ASN A 164 " pdb=" CG ASN A 164 " pdb=" ND2 ASN A 164 " ideal model delta sigma weight residual 122.60 115.11 7.49 1.00e+00 1.00e+00 5.61e+01 angle pdb=" OD1 ASN C 164 " pdb=" CG ASN C 164 " pdb=" ND2 ASN C 164 " ideal model delta sigma weight residual 122.60 116.24 6.36 1.00e+00 1.00e+00 4.04e+01 angle pdb=" C ILE A 219 " pdb=" CA ILE A 219 " pdb=" CB ILE A 219 " ideal model delta sigma weight residual 111.06 116.62 -5.56 8.80e-01 1.29e+00 3.99e+01 ... (remaining 4498 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.07: 1830 16.07 - 32.13: 122 32.13 - 48.19: 25 48.19 - 64.26: 9 64.26 - 80.32: 9 Dihedral angle restraints: 1995 sinusoidal: 777 harmonic: 1218 Sorted by residual: dihedral pdb=" C ASN B 183 " pdb=" N ASN B 183 " pdb=" CA ASN B 183 " pdb=" CB ASN B 183 " ideal model delta harmonic sigma weight residual -122.60 -137.49 14.89 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" CA ASN B 183 " pdb=" C ASN B 183 " pdb=" N ILE B 184 " pdb=" CA ILE B 184 " ideal model delta harmonic sigma weight residual -180.00 -150.77 -29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ILE B 152 " pdb=" C ILE B 152 " pdb=" N THR B 153 " pdb=" CA THR B 153 " ideal model delta harmonic sigma weight residual 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 1992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 337 0.110 - 0.220: 156 0.220 - 0.329: 38 0.329 - 0.439: 10 0.439 - 0.549: 2 Chirality restraints: 543 Sorted by residual: chirality pdb=" CA ASN B 183 " pdb=" N ASN B 183 " pdb=" C ASN B 183 " pdb=" CB ASN B 183 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.54e+00 chirality pdb=" CA ASN A 183 " pdb=" N ASN A 183 " pdb=" C ASN A 183 " pdb=" CB ASN A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA GLN A 138 " pdb=" N GLN A 138 " pdb=" C GLN A 138 " pdb=" CB GLN A 138 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 540 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 135 " -0.134 2.00e-02 2.50e+03 8.25e-02 1.36e+02 pdb=" CG TYR B 135 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 135 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR B 135 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR B 135 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR B 135 " 0.069 2.00e-02 2.50e+03 pdb=" CZ TYR B 135 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR B 135 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 135 " -0.129 2.00e-02 2.50e+03 8.01e-02 1.28e+02 pdb=" CG TYR A 135 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 135 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR A 135 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR A 135 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A 135 " 0.072 2.00e-02 2.50e+03 pdb=" CZ TYR A 135 " 0.027 2.00e-02 2.50e+03 pdb=" OH TYR A 135 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 143 " 0.153 2.00e-02 2.50e+03 7.96e-02 1.27e+02 pdb=" CG TYR C 143 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR C 143 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR C 143 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 TYR C 143 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR C 143 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR C 143 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 143 " 0.107 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1602 2.98 - 3.46: 2809 3.46 - 3.94: 5234 3.94 - 4.42: 5555 4.42 - 4.90: 10249 Nonbonded interactions: 25449 Sorted by model distance: nonbonded pdb=" OE1 GLU A 161 " pdb=" OG SER B 120 " model vdw 2.501 2.440 nonbonded pdb=" OE1 GLU B 161 " pdb=" OG SER C 120 " model vdw 2.526 2.440 nonbonded pdb=" OD2 ASP C 212 " pdb=" OG1 THR C 215 " model vdw 2.550 2.440 nonbonded pdb=" OD2 ASP A 212 " pdb=" OG1 THR A 215 " model vdw 2.559 2.440 nonbonded pdb=" OD2 ASP B 212 " pdb=" OG1 THR B 215 " model vdw 2.579 2.440 ... (remaining 25444 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' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.460 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.900 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.010 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.012 0.046 3312 Z= 0.796 Angle : 2.274 13.066 4503 Z= 1.512 Chirality : 0.135 0.549 543 Planarity : 0.015 0.083 558 Dihedral : 13.778 80.320 1206 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.28 % Favored : 88.22 % Rotamer: Outliers : 1.06 % Allowed : 2.65 % Favored : 96.30 % Cbeta Deviations : 3.59 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.004 HIS A 239 PHE 0.047 0.013 PHE A 171 TYR 0.153 0.031 TYR C 143 ARG 0.002 0.001 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7814 (mttt) cc_final: 0.7568 (mtpt) REVERT: A 241 GLU cc_start: 0.7171 (tt0) cc_final: 0.6929 (tt0) REVERT: B 122 ASP cc_start: 0.7749 (t0) cc_final: 0.6593 (t0) REVERT: C 139 LYS cc_start: 0.8698 (mttt) cc_final: 0.8349 (mmmt) outliers start: 4 outliers final: 0 residues processed: 105 average time/residue: 0.1661 time to fit residues: 20.6595 Evaluate side-chains 69 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 155 ASN B 138 GLN B 154 ASN B 155 ASN B 245 GLN C 155 ASN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3312 Z= 0.226 Angle : 0.739 6.771 4503 Z= 0.406 Chirality : 0.053 0.140 543 Planarity : 0.003 0.013 558 Dihedral : 7.999 23.513 447 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 5.56 % Allowed : 9.52 % Favored : 84.92 % 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: -3.09 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 239 PHE 0.008 0.001 PHE C 237 TYR 0.029 0.002 TYR A 143 ARG 0.002 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7411 (mt-10) REVERT: B 178 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6566 (tptp) REVERT: B 212 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8402 (p0) REVERT: C 178 LYS cc_start: 0.7204 (mttp) cc_final: 0.6769 (tptt) REVERT: C 192 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7534 (mtp) REVERT: C 210 MET cc_start: 0.7511 (mtp) cc_final: 0.7108 (mtt) REVERT: C 234 THR cc_start: 0.8640 (t) cc_final: 0.8369 (m) outliers start: 21 outliers final: 13 residues processed: 92 average time/residue: 0.1857 time to fit residues: 20.2122 Evaluate side-chains 84 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 26 optimal weight: 0.0770 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN B 154 ASN B 245 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3312 Z= 0.427 Angle : 0.761 5.379 4503 Z= 0.427 Chirality : 0.056 0.162 543 Planarity : 0.003 0.013 558 Dihedral : 8.207 23.785 447 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 8.20 % Allowed : 10.58 % Favored : 81.22 % 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: -3.04 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 239 PHE 0.013 0.002 PHE B 171 TYR 0.022 0.003 TYR C 143 ARG 0.002 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 65 time to evaluate : 0.396 Fit side-chains REVERT: B 178 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.6412 (tptp) REVERT: B 212 ASP cc_start: 0.8981 (OUTLIER) cc_final: 0.8567 (p0) REVERT: C 178 LYS cc_start: 0.7350 (mttp) cc_final: 0.6695 (tptp) outliers start: 31 outliers final: 23 residues processed: 82 average time/residue: 0.1614 time to fit residues: 15.6524 Evaluate side-chains 87 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 62 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 247 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3312 Z= 0.226 Angle : 0.627 5.825 4503 Z= 0.354 Chirality : 0.052 0.158 543 Planarity : 0.002 0.013 558 Dihedral : 7.467 21.121 447 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 8.20 % Allowed : 13.49 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 239 PHE 0.006 0.001 PHE B 171 TYR 0.020 0.002 TYR B 143 ARG 0.001 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 64 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: B 178 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6409 (tptp) REVERT: B 212 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8600 (p0) REVERT: C 178 LYS cc_start: 0.7209 (mttp) cc_final: 0.6603 (tptt) outliers start: 31 outliers final: 18 residues processed: 79 average time/residue: 0.1943 time to fit residues: 18.1807 Evaluate side-chains 79 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 3312 Z= 0.537 Angle : 0.746 5.172 4503 Z= 0.426 Chirality : 0.056 0.156 543 Planarity : 0.003 0.015 558 Dihedral : 8.058 22.829 447 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 6.61 % Allowed : 14.55 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 239 PHE 0.015 0.002 PHE B 171 TYR 0.025 0.003 TYR B 143 ARG 0.002 0.001 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 60 time to evaluate : 0.395 Fit side-chains REVERT: B 212 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8608 (p0) REVERT: B 247 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7692 (ttm170) REVERT: C 178 LYS cc_start: 0.7240 (mttp) cc_final: 0.6627 (tptp) outliers start: 25 outliers final: 21 residues processed: 74 average time/residue: 0.1935 time to fit residues: 16.8320 Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 57 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 182 ASN B 229 GLN C 182 ASN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3312 Z= 0.244 Angle : 0.637 6.493 4503 Z= 0.356 Chirality : 0.052 0.189 543 Planarity : 0.002 0.013 558 Dihedral : 7.407 23.856 447 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 5.82 % Allowed : 16.40 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.36), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 239 PHE 0.007 0.001 PHE B 171 TYR 0.020 0.002 TYR A 143 ARG 0.001 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 65 time to evaluate : 0.395 Fit side-chains REVERT: B 178 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6363 (tptp) REVERT: B 209 TYR cc_start: 0.8717 (m-80) cc_final: 0.8461 (m-80) REVERT: B 212 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8540 (p0) REVERT: C 178 LYS cc_start: 0.7187 (mttp) cc_final: 0.6442 (tptp) outliers start: 22 outliers final: 18 residues processed: 77 average time/residue: 0.1874 time to fit residues: 17.0090 Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3312 Z= 0.258 Angle : 0.652 7.278 4503 Z= 0.357 Chirality : 0.052 0.137 543 Planarity : 0.002 0.015 558 Dihedral : 7.291 22.739 447 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 6.88 % Allowed : 14.81 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.37), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 239 PHE 0.015 0.002 PHE C 237 TYR 0.019 0.002 TYR B 143 ARG 0.001 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 65 time to evaluate : 0.405 Fit side-chains REVERT: B 178 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6421 (tptp) REVERT: B 209 TYR cc_start: 0.8720 (m-80) cc_final: 0.8454 (m-80) REVERT: B 212 ASP cc_start: 0.8832 (OUTLIER) cc_final: 0.8528 (p0) REVERT: C 178 LYS cc_start: 0.7145 (mttp) cc_final: 0.6335 (tptt) outliers start: 26 outliers final: 16 residues processed: 80 average time/residue: 0.1747 time to fit residues: 16.7755 Evaluate side-chains 81 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3312 Z= 0.152 Angle : 0.604 8.189 4503 Z= 0.329 Chirality : 0.051 0.136 543 Planarity : 0.002 0.013 558 Dihedral : 6.758 19.690 447 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.23 % Allowed : 17.46 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.38), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 239 PHE 0.012 0.001 PHE C 237 TYR 0.018 0.002 TYR A 143 ARG 0.001 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 0.421 Fit side-chains REVERT: A 140 ARG cc_start: 0.6500 (ppt170) cc_final: 0.6090 (tmm160) REVERT: B 178 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6366 (tptp) REVERT: C 178 LYS cc_start: 0.6919 (mttp) cc_final: 0.6404 (tptt) outliers start: 16 outliers final: 13 residues processed: 79 average time/residue: 0.1700 time to fit residues: 16.1202 Evaluate side-chains 79 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.0270 chunk 34 optimal weight: 0.0670 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3312 Z= 0.173 Angle : 0.609 7.538 4503 Z= 0.337 Chirality : 0.051 0.131 543 Planarity : 0.002 0.013 558 Dihedral : 6.606 19.792 447 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.44 % Allowed : 18.25 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.38), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 239 PHE 0.022 0.002 PHE B 237 TYR 0.017 0.002 TYR A 143 ARG 0.001 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.359 Fit side-chains REVERT: A 140 ARG cc_start: 0.6482 (ppt170) cc_final: 0.6085 (tmm160) REVERT: B 178 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6461 (tptp) REVERT: B 209 TYR cc_start: 0.8444 (m-80) cc_final: 0.8138 (m-80) REVERT: C 178 LYS cc_start: 0.6902 (mttp) cc_final: 0.6368 (tptt) outliers start: 13 outliers final: 12 residues processed: 70 average time/residue: 0.1657 time to fit residues: 13.9306 Evaluate side-chains 75 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3312 Z= 0.278 Angle : 0.640 7.781 4503 Z= 0.356 Chirality : 0.052 0.131 543 Planarity : 0.002 0.013 558 Dihedral : 6.929 20.609 447 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 4.23 % Allowed : 16.93 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.38), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 239 PHE 0.022 0.002 PHE B 237 TYR 0.020 0.002 TYR B 125 ARG 0.002 0.000 ARG C 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.312 Fit side-chains REVERT: A 140 ARG cc_start: 0.6728 (ppt170) cc_final: 0.6139 (tmm160) REVERT: B 178 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6404 (tptp) REVERT: B 209 TYR cc_start: 0.8528 (m-80) cc_final: 0.8233 (m-80) REVERT: C 140 ARG cc_start: 0.6335 (mmp-170) cc_final: 0.6092 (mmp80) REVERT: C 178 LYS cc_start: 0.6980 (mttp) cc_final: 0.6399 (tptt) outliers start: 16 outliers final: 15 residues processed: 69 average time/residue: 0.1722 time to fit residues: 14.2100 Evaluate side-chains 76 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.118990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.103169 restraints weight = 4386.755| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.26 r_work: 0.3812 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3312 Z= 0.334 Angle : 0.663 6.256 4503 Z= 0.371 Chirality : 0.053 0.131 543 Planarity : 0.003 0.013 558 Dihedral : 7.161 20.875 447 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 4.50 % Allowed : 16.67 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.38), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 239 PHE 0.021 0.002 PHE B 237 TYR 0.025 0.002 TYR B 125 ARG 0.002 0.000 ARG C 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1276.00 seconds wall clock time: 23 minutes 58.74 seconds (1438.74 seconds total)