Starting phenix.real_space_refine on Sat Aug 3 01:30:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z1e_39724/08_2024/8z1e_39724.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z1e_39724/08_2024/8z1e_39724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z1e_39724/08_2024/8z1e_39724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z1e_39724/08_2024/8z1e_39724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z1e_39724/08_2024/8z1e_39724.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z1e_39724/08_2024/8z1e_39724.cif" } resolution = 3.12 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= 0.041 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 48 5.16 5 C 4322 2.51 5 N 1056 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 41": "OD1" <-> "OD2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 116": "OD1" <-> "OD2" Residue "R ASP 117": "OD1" <-> "OD2" Residue "R TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 302": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6516 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2168 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2174 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2174 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 4.32, per 1000 atoms: 0.66 Number of scatterers: 6516 At special positions: 0 Unit cell: (91.035, 91.035, 73.899, 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 48 16.00 O 1090 8.00 N 1056 7.00 C 4322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 109 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 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: 2.53 Conformation dependent library (CDL) restraints added in 1.3 seconds 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 3 sheets defined 85.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 34 through 65 Processing helix chain 'A' and resid 71 through 96 Processing helix chain 'A' and resid 105 through 140 removed outlier: 3.608A pdb=" N ALA A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 149 through 171 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 193 through 206 Processing helix chain 'A' and resid 207 through 221 removed outlier: 3.576A pdb=" N ILE A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 261 removed outlier: 3.706A pdb=" N ARG A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.878A pdb=" N GLY A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 286 removed outlier: 3.740A pdb=" N GLU A 277 " --> pdb=" O MET A 273 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 292 through 298 removed outlier: 4.253A pdb=" N ILE A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.901A pdb=" N ASP A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 317 " --> pdb=" O TYR A 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 65 Processing helix chain 'B' and resid 71 through 96 removed outlier: 3.531A pdb=" N LEU B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 141 removed outlier: 3.724A pdb=" N ALA B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.662A pdb=" N GLU B 148 " --> pdb=" O TRP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 176 Proline residue: B 173 - end of helix Processing helix chain 'B' and resid 190 through 192 No H-bonds generated for 'chain 'B' and resid 190 through 192' Processing helix chain 'B' and resid 193 through 206 Processing helix chain 'B' and resid 207 through 222 removed outlier: 3.507A pdb=" N ILE B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 261 removed outlier: 3.670A pdb=" N ARG B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Proline residue: B 249 - end of helix removed outlier: 3.979A pdb=" N GLY B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 286 removed outlier: 3.668A pdb=" N GLU B 277 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 292 through 298 removed outlier: 4.343A pdb=" N ILE B 296 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 317 removed outlier: 3.789A pdb=" N ASP B 308 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 317 " --> pdb=" O TYR B 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 65 Processing helix chain 'R' and resid 71 through 96 Processing helix chain 'R' and resid 105 through 140 removed outlier: 3.555A pdb=" N ALA R 124 " --> pdb=" O LEU R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 148 removed outlier: 3.651A pdb=" N GLU R 148 " --> pdb=" O TRP R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 176 Proline residue: R 173 - end of helix Processing helix chain 'R' and resid 190 through 192 No H-bonds generated for 'chain 'R' and resid 190 through 192' Processing helix chain 'R' and resid 193 through 206 Processing helix chain 'R' and resid 207 through 222 removed outlier: 3.604A pdb=" N ILE R 211 " --> pdb=" O GLY R 207 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR R 222 " --> pdb=" O VAL R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 261 removed outlier: 3.590A pdb=" N ARG R 235 " --> pdb=" O SER R 231 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR R 238 " --> pdb=" O GLY R 234 " (cutoff:3.500A) Proline residue: R 249 - end of helix removed outlier: 3.882A pdb=" N GLY R 258 " --> pdb=" O ARG R 254 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 286 removed outlier: 3.816A pdb=" N GLU R 277 " --> pdb=" O MET R 273 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU R 284 " --> pdb=" O THR R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 291 removed outlier: 3.545A pdb=" N ILE R 290 " --> pdb=" O MET R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 298 removed outlier: 4.340A pdb=" N ILE R 296 " --> pdb=" O PRO R 292 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA R 297 " --> pdb=" O LEU R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 317 removed outlier: 3.894A pdb=" N ASP R 308 " --> pdb=" O THR R 304 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG R 317 " --> pdb=" O TYR R 313 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 180 removed outlier: 3.702A pdb=" N SER A 179 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 179 through 180 removed outlier: 3.794A pdb=" N SER B 179 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 179 through 180 removed outlier: 3.760A pdb=" N SER R 179 " --> pdb=" O GLN R 188 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1977 1.34 - 1.46: 1574 1.46 - 1.58: 3049 1.58 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 6675 Sorted by residual: bond pdb=" N GLY R 271 " pdb=" CA GLY R 271 " ideal model delta sigma weight residual 1.449 1.468 -0.019 1.45e-02 4.76e+03 1.71e+00 bond pdb=" N GLY A 271 " pdb=" CA GLY A 271 " ideal model delta sigma weight residual 1.449 1.468 -0.019 1.45e-02 4.76e+03 1.64e+00 bond pdb=" N GLY B 271 " pdb=" CA GLY B 271 " ideal model delta sigma weight residual 1.449 1.467 -0.018 1.45e-02 4.76e+03 1.56e+00 bond pdb=" C GLY B 271 " pdb=" N ILE B 272 " ideal model delta sigma weight residual 1.335 1.324 0.011 1.20e-02 6.94e+03 8.42e-01 bond pdb=" C GLY A 271 " pdb=" N ILE A 272 " ideal model delta sigma weight residual 1.335 1.324 0.011 1.20e-02 6.94e+03 8.34e-01 ... (remaining 6670 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.71: 153 106.71 - 113.54: 3726 113.54 - 120.37: 2446 120.37 - 127.20: 2713 127.20 - 134.03: 71 Bond angle restraints: 9109 Sorted by residual: angle pdb=" N THR A 68 " pdb=" CA THR A 68 " pdb=" C THR A 68 " ideal model delta sigma weight residual 109.39 106.41 2.98 1.59e+00 3.96e-01 3.50e+00 angle pdb=" CA LEU R 42 " pdb=" CB LEU R 42 " pdb=" CG LEU R 42 " ideal model delta sigma weight residual 116.30 122.60 -6.30 3.50e+00 8.16e-02 3.24e+00 angle pdb=" N ARG B 226 " pdb=" CA ARG B 226 " pdb=" C ARG B 226 " ideal model delta sigma weight residual 110.80 114.31 -3.51 2.13e+00 2.20e-01 2.72e+00 angle pdb=" CA ASP B 116 " pdb=" CB ASP B 116 " pdb=" CG ASP B 116 " ideal model delta sigma weight residual 112.60 114.23 -1.63 1.00e+00 1.00e+00 2.67e+00 angle pdb=" N ARG R 226 " pdb=" CA ARG R 226 " pdb=" C ARG R 226 " ideal model delta sigma weight residual 110.80 114.24 -3.44 2.13e+00 2.20e-01 2.61e+00 ... (remaining 9104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.63: 3218 12.63 - 25.26: 396 25.26 - 37.89: 165 37.89 - 50.52: 58 50.52 - 63.16: 17 Dihedral angle restraints: 3854 sinusoidal: 1418 harmonic: 2436 Sorted by residual: dihedral pdb=" CB CYS R 109 " pdb=" SG CYS R 109 " pdb=" SG CYS R 187 " pdb=" CB CYS R 187 " ideal model delta sinusoidal sigma weight residual -86.00 -149.16 63.16 1 1.00e+01 1.00e-02 5.26e+01 dihedral pdb=" CB CYS B 109 " pdb=" SG CYS B 109 " pdb=" SG CYS B 187 " pdb=" CB CYS B 187 " ideal model delta sinusoidal sigma weight residual -86.00 -146.22 60.22 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CA ASP R 133 " pdb=" CB ASP R 133 " pdb=" CG ASP R 133 " pdb=" OD1 ASP R 133 " ideal model delta sinusoidal sigma weight residual -30.00 -84.34 54.34 1 2.00e+01 2.50e-03 1.00e+01 ... (remaining 3851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 703 0.026 - 0.052: 242 0.052 - 0.077: 129 0.077 - 0.103: 16 0.103 - 0.129: 10 Chirality restraints: 1100 Sorted by residual: chirality pdb=" CA ILE R 189 " pdb=" N ILE R 189 " pdb=" C ILE R 189 " pdb=" CB ILE R 189 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE A 189 " pdb=" N ILE A 189 " pdb=" C ILE A 189 " pdb=" CB ILE A 189 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE B 189 " pdb=" N ILE B 189 " pdb=" C ILE B 189 " pdb=" CB ILE B 189 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 1097 not shown) Planarity restraints: 1097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 145 " -0.010 2.00e-02 2.50e+03 9.40e-03 2.21e+00 pdb=" CG TRP A 145 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 145 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 145 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 145 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 145 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 145 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 145 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 145 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 145 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 189 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.18e+00 pdb=" N PRO A 190 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 190 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 190 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 189 " 0.017 5.00e-02 4.00e+02 2.63e-02 1.11e+00 pdb=" N PRO R 190 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 190 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 190 " 0.015 5.00e-02 4.00e+02 ... (remaining 1094 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1743 2.80 - 3.32: 6469 3.32 - 3.85: 10754 3.85 - 4.37: 12684 4.37 - 4.90: 22082 Nonbonded interactions: 53732 Sorted by model distance: nonbonded pdb=" O THR A 68 " pdb=" OG1 THR A 68 " model vdw 2.273 3.040 nonbonded pdb=" O THR R 68 " pdb=" OG1 THR R 68 " model vdw 2.298 3.040 nonbonded pdb=" O THR B 68 " pdb=" OG1 THR B 68 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR A 149 " pdb=" OD1 ASN A 152 " model vdw 2.342 3.040 nonbonded pdb=" OG SER B 88 " pdb=" NH2 ARG B 287 " model vdw 2.369 3.120 ... (remaining 53727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 34 through 180 or (resid 181 and (name N or name CA or nam \ e C or name O or name CB )) or resid 182 through 313 or (resid 314 and (name N o \ r name CA or name C or name O or name CB )) or resid 315 through 318)) selection = (chain 'R' and (resid 34 through 180 or (resid 181 and (name N or name CA or nam \ e C or name O or name CB )) or resid 182 through 313 or (resid 314 and (name N o \ r name CA or name C or name O or name CB )) or resid 315 through 318)) } 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: 1.160 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.230 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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 0.022 6675 Z= 0.132 Angle : 0.432 6.302 9109 Z= 0.230 Chirality : 0.033 0.129 1100 Planarity : 0.003 0.027 1097 Dihedral : 14.556 57.659 2273 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.44 % Allowed : 20.64 % Favored : 78.92 % 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: 0.87 (0.30), residues: 822 helix: 1.27 (0.20), residues: 675 sheet: None (None), residues: 0 loop : -2.67 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 145 HIS 0.000 0.000 HIS B 228 PHE 0.006 0.001 PHE A 162 TYR 0.009 0.001 TYR B 313 ARG 0.007 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 150 ARG cc_start: 0.7119 (tmt170) cc_final: 0.6762 (tmt170) outliers start: 3 outliers final: 1 residues processed: 121 average time/residue: 0.1937 time to fit residues: 30.7185 Evaluate side-chains 122 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6675 Z= 0.184 Angle : 0.472 5.697 9109 Z= 0.255 Chirality : 0.036 0.131 1100 Planarity : 0.004 0.026 1097 Dihedral : 3.459 19.808 918 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.18 % Allowed : 20.20 % Favored : 77.62 % 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: 2.17 (0.30), residues: 822 helix: 2.27 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.09 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 145 HIS 0.001 0.000 HIS A 147 PHE 0.010 0.001 PHE A 253 TYR 0.009 0.001 TYR R 158 ARG 0.005 0.000 ARG R 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8277 (mtp180) cc_final: 0.8005 (ptm160) REVERT: R 85 GLN cc_start: 0.8543 (mm110) cc_final: 0.8287 (mm-40) outliers start: 15 outliers final: 12 residues processed: 137 average time/residue: 0.1811 time to fit residues: 32.7942 Evaluate side-chains 126 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 204 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6675 Z= 0.201 Angle : 0.463 5.884 9109 Z= 0.242 Chirality : 0.037 0.132 1100 Planarity : 0.004 0.029 1097 Dihedral : 3.414 14.739 915 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.63 % Allowed : 20.20 % Favored : 76.16 % 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: 2.26 (0.31), residues: 822 helix: 2.35 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.18 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 230 HIS 0.001 0.000 HIS A 146 PHE 0.010 0.001 PHE R 253 TYR 0.010 0.001 TYR R 240 ARG 0.006 0.000 ARG R 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8487 (m-80) REVERT: B 181 ASP cc_start: 0.7269 (t0) cc_final: 0.7038 (t0) REVERT: B 188 GLN cc_start: 0.8249 (pt0) cc_final: 0.8023 (pt0) REVERT: R 85 GLN cc_start: 0.8392 (mm110) cc_final: 0.8032 (mm110) REVERT: R 117 ASP cc_start: 0.8433 (m-30) cc_final: 0.8045 (m-30) outliers start: 25 outliers final: 20 residues processed: 132 average time/residue: 0.1695 time to fit residues: 30.8748 Evaluate side-chains 134 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain R residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6675 Z= 0.209 Angle : 0.467 5.585 9109 Z= 0.242 Chirality : 0.036 0.132 1100 Planarity : 0.003 0.027 1097 Dihedral : 3.416 14.900 915 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.49 % Allowed : 22.53 % Favored : 73.98 % 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: 2.33 (0.30), residues: 822 helix: 2.47 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.94 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 230 HIS 0.001 0.000 HIS R 228 PHE 0.010 0.001 PHE R 253 TYR 0.011 0.001 TYR A 240 ARG 0.004 0.000 ARG R 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8494 (m-80) REVERT: R 85 GLN cc_start: 0.8398 (mm110) cc_final: 0.7975 (mm-40) REVERT: R 117 ASP cc_start: 0.8475 (m-30) cc_final: 0.8040 (m-30) outliers start: 24 outliers final: 20 residues processed: 128 average time/residue: 0.1581 time to fit residues: 27.5479 Evaluate side-chains 135 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 245 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 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 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6675 Z= 0.211 Angle : 0.472 7.356 9109 Z= 0.242 Chirality : 0.036 0.134 1100 Planarity : 0.003 0.027 1097 Dihedral : 3.427 14.995 915 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.51 % Allowed : 21.51 % Favored : 73.98 % 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: 2.36 (0.30), residues: 822 helix: 2.50 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.96 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 230 HIS 0.001 0.000 HIS R 228 PHE 0.010 0.001 PHE R 253 TYR 0.011 0.001 TYR A 240 ARG 0.003 0.000 ARG R 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8491 (m-80) REVERT: R 85 GLN cc_start: 0.8424 (mm110) cc_final: 0.7970 (mm-40) REVERT: R 117 ASP cc_start: 0.8484 (m-30) cc_final: 0.8037 (m-30) outliers start: 31 outliers final: 25 residues processed: 131 average time/residue: 0.1664 time to fit residues: 30.0229 Evaluate side-chains 139 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 211 ILE Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 245 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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: 0.7791 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6675 Z= 0.187 Angle : 0.470 8.155 9109 Z= 0.241 Chirality : 0.036 0.134 1100 Planarity : 0.003 0.026 1097 Dihedral : 3.439 15.597 915 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.65 % Allowed : 21.37 % Favored : 73.98 % 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: 2.43 (0.30), residues: 822 helix: 2.55 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.95 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 230 HIS 0.001 0.000 HIS R 228 PHE 0.009 0.001 PHE R 253 TYR 0.010 0.001 TYR A 240 ARG 0.003 0.000 ARG R 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8361 (m-80) REVERT: B 188 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7808 (pt0) REVERT: R 85 GLN cc_start: 0.8398 (mm110) cc_final: 0.7921 (mm-40) REVERT: R 117 ASP cc_start: 0.8505 (m-30) cc_final: 0.8043 (m-30) outliers start: 32 outliers final: 27 residues processed: 135 average time/residue: 0.1730 time to fit residues: 31.1787 Evaluate side-chains 144 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 211 ILE Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain R residue 245 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 9.9990 chunk 44 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6675 Z= 0.195 Angle : 0.469 7.424 9109 Z= 0.239 Chirality : 0.036 0.134 1100 Planarity : 0.003 0.027 1097 Dihedral : 3.443 16.213 915 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.65 % Allowed : 21.66 % Favored : 73.69 % 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: 2.36 (0.31), residues: 822 helix: 2.44 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.21 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 230 HIS 0.001 0.000 HIS A 147 PHE 0.010 0.001 PHE R 253 TYR 0.010 0.001 TYR A 240 ARG 0.003 0.000 ARG R 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7906 (mmm160) REVERT: A 204 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: R 85 GLN cc_start: 0.8373 (mm110) cc_final: 0.7914 (mm-40) REVERT: R 117 ASP cc_start: 0.8517 (m-30) cc_final: 0.8066 (m-30) outliers start: 32 outliers final: 28 residues processed: 137 average time/residue: 0.1815 time to fit residues: 33.9645 Evaluate side-chains 147 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 211 ILE Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 245 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.0370 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6675 Z= 0.184 Angle : 0.476 8.102 9109 Z= 0.241 Chirality : 0.036 0.133 1100 Planarity : 0.003 0.026 1097 Dihedral : 3.469 17.730 915 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.07 % Allowed : 22.67 % Favored : 73.26 % 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: 2.42 (0.31), residues: 822 helix: 2.48 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.22 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 230 HIS 0.001 0.000 HIS A 147 PHE 0.010 0.001 PHE A 162 TYR 0.010 0.001 TYR A 240 ARG 0.002 0.000 ARG R 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8168 (mmm160) cc_final: 0.7810 (mmm160) REVERT: A 204 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: B 183 ARG cc_start: 0.8231 (mmm160) cc_final: 0.7946 (mmm160) REVERT: R 85 GLN cc_start: 0.8359 (mm110) cc_final: 0.7894 (mm-40) REVERT: R 117 ASP cc_start: 0.8524 (m-30) cc_final: 0.8096 (m-30) outliers start: 28 outliers final: 25 residues processed: 133 average time/residue: 0.1604 time to fit residues: 29.1688 Evaluate side-chains 142 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 211 ILE Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain R residue 245 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6675 Z= 0.197 Angle : 0.476 7.879 9109 Z= 0.242 Chirality : 0.036 0.133 1100 Planarity : 0.003 0.026 1097 Dihedral : 3.473 15.108 915 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.92 % Allowed : 23.11 % Favored : 72.97 % 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: 2.38 (0.31), residues: 822 helix: 2.45 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.21 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 230 HIS 0.001 0.000 HIS A 147 PHE 0.009 0.001 PHE R 253 TYR 0.011 0.001 TYR R 240 ARG 0.002 0.000 ARG R 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8175 (mmm160) cc_final: 0.7820 (mmm160) REVERT: A 204 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.8347 (m-80) REVERT: R 85 GLN cc_start: 0.8357 (mm110) cc_final: 0.7885 (mm-40) REVERT: R 117 ASP cc_start: 0.8507 (m-30) cc_final: 0.8042 (m-30) outliers start: 27 outliers final: 26 residues processed: 133 average time/residue: 0.1589 time to fit residues: 29.0981 Evaluate side-chains 146 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 211 ILE Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain R residue 245 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 0.0980 chunk 74 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6675 Z= 0.193 Angle : 0.481 8.318 9109 Z= 0.243 Chirality : 0.036 0.133 1100 Planarity : 0.003 0.026 1097 Dihedral : 3.487 15.051 915 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.07 % Allowed : 22.82 % Favored : 73.11 % 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: 2.39 (0.31), residues: 822 helix: 2.46 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.21 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 230 HIS 0.002 0.000 HIS A 147 PHE 0.009 0.001 PHE R 253 TYR 0.010 0.001 TYR A 240 ARG 0.002 0.000 ARG R 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8193 (mmm160) cc_final: 0.7845 (mmm160) REVERT: A 204 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8323 (m-80) REVERT: R 85 GLN cc_start: 0.8355 (mm110) cc_final: 0.7882 (mm-40) REVERT: R 117 ASP cc_start: 0.8510 (m-30) cc_final: 0.8051 (m-30) REVERT: R 183 ARG cc_start: 0.8285 (mmm160) cc_final: 0.7605 (mmm160) outliers start: 28 outliers final: 27 residues processed: 134 average time/residue: 0.1636 time to fit residues: 29.8803 Evaluate side-chains 146 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 211 ILE Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain R residue 245 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 46 optimal weight: 0.2980 chunk 73 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS B 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.106287 restraints weight = 7408.799| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.56 r_work: 0.3056 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6675 Z= 0.193 Angle : 0.485 8.116 9109 Z= 0.245 Chirality : 0.036 0.136 1100 Planarity : 0.003 0.026 1097 Dihedral : 3.495 16.463 915 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.36 % Allowed : 22.82 % Favored : 72.82 % 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: 2.40 (0.31), residues: 822 helix: 2.47 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.20 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 230 HIS 0.002 0.000 HIS A 147 PHE 0.009 0.001 PHE R 253 TYR 0.010 0.001 TYR A 240 ARG 0.002 0.000 ARG R 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1647.59 seconds wall clock time: 29 minutes 52.71 seconds (1792.71 seconds total)