Starting phenix.real_space_refine on Tue Jun 25 02:25:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z1e_39724/06_2024/8z1e_39724.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z1e_39724/06_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_39724/06_2024/8z1e_39724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z1e_39724/06_2024/8z1e_39724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z1e_39724/06_2024/8z1e_39724.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z1e_39724/06_2024/8z1e_39724.pdb" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 4.00, per 1000 atoms: 0.61 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: 2.67 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: 0.57 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: 1.82 Time building geometry restraints manager: 2.82 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 2.440 nonbonded pdb=" O THR R 68 " pdb=" OG1 THR R 68 " model vdw 2.298 2.440 nonbonded pdb=" O THR B 68 " pdb=" OG1 THR B 68 " model vdw 2.309 2.440 nonbonded pdb=" OG1 THR A 149 " pdb=" OD1 ASN A 152 " model vdw 2.342 2.440 nonbonded pdb=" OG SER B 88 " pdb=" NH2 ARG B 287 " model vdw 2.369 2.520 ... (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 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: 0.810 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: 3.710 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.800 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.510 ------------------------------------------------------------------------------- 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 : 0.640 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: 0.1922 time to fit residues: 30.5023 Evaluate side-chains 122 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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: 1.9990 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 0.0070 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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: 0.1141 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= 0.193 Angle : 0.474 5.713 9109 Z= 0.253 Chirality : 0.037 0.134 1100 Planarity : 0.004 0.026 1097 Dihedral : 3.476 19.376 918 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.47 % Allowed : 20.35 % Favored : 77.18 % 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: 2.14 (0.30), residues: 822 helix: 2.25 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.13 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 145 HIS 0.001 0.000 HIS A 146 PHE 0.011 0.001 PHE A 253 TYR 0.010 0.001 TYR R 158 ARG 0.004 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: 17 poor density : 127 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8219 (mtp180) cc_final: 0.7903 (ptm160) outliers start: 17 outliers final: 14 residues processed: 136 average time/residue: 0.1870 time to fit residues: 33.7994 Evaluate side-chains 127 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 238 THR 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: 2.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 GLN R 85 GLN R 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6675 Z= 0.273 Angle : 0.502 5.988 9109 Z= 0.260 Chirality : 0.038 0.139 1100 Planarity : 0.004 0.029 1097 Dihedral : 3.518 15.648 915 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.51 % Allowed : 21.37 % Favored : 74.13 % 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: 2.16 (0.30), residues: 822 helix: 2.31 (0.20), residues: 639 sheet: None (None), residues: 0 loop : -1.91 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 230 HIS 0.002 0.000 HIS R 228 PHE 0.011 0.001 PHE R 253 TYR 0.015 0.001 TYR A 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 157 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8274 (m-30) cc_final: 0.7999 (m-30) REVERT: A 204 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.8696 (m-80) REVERT: A 222 TYR cc_start: 0.8974 (m-80) cc_final: 0.8249 (m-80) REVERT: B 216 ASN cc_start: 0.8545 (t0) cc_final: 0.8335 (t0) REVERT: B 270 PHE cc_start: 0.8353 (m-80) cc_final: 0.8123 (m-10) REVERT: R 85 GLN cc_start: 0.8530 (mm110) cc_final: 0.8301 (mm-40) REVERT: R 93 MET cc_start: 0.8018 (mmp) cc_final: 0.7749 (mmt) outliers start: 31 outliers final: 22 residues processed: 140 average time/residue: 0.2192 time to fit residues: 41.6789 Evaluate side-chains 138 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 227 ASP Chi-restraints excluded: chain B residue 99 MET 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 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 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: 0.9990 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7802 moved from start: 0.1709 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= 0.190 Angle : 0.464 5.593 9109 Z= 0.240 Chirality : 0.036 0.134 1100 Planarity : 0.003 0.026 1097 Dihedral : 3.494 15.565 915 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.63 % Allowed : 22.53 % Favored : 73.84 % 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: 2.36 (0.30), residues: 822 helix: 2.49 (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 0.009 0.001 PHE R 253 TYR 0.010 0.001 TYR R 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 139 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8322 (m-30) cc_final: 0.8018 (m-30) REVERT: A 204 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.8544 (m-80) REVERT: B 188 GLN cc_start: 0.8199 (pt0) cc_final: 0.7768 (pt0) REVERT: B 189 ILE cc_start: 0.8426 (tt) cc_final: 0.8218 (mt) REVERT: R 85 GLN cc_start: 0.8494 (mm110) cc_final: 0.8174 (mm-40) outliers start: 25 outliers final: 21 residues processed: 126 average time/residue: 0.1623 time to fit residues: 27.9054 Evaluate side-chains 131 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 187 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain B residue 46 MET 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 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 227 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7807 moved from start: 0.1789 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= 0.217 Angle : 0.476 7.099 9109 Z= 0.244 Chirality : 0.037 0.133 1100 Planarity : 0.003 0.027 1097 Dihedral : 3.496 15.731 915 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.92 % Allowed : 22.67 % Favored : 73.40 % 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: 2.37 (0.30), residues: 822 helix: 2.50 (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 0.010 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 139 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8359 (m-30) cc_final: 0.8020 (m-30) REVERT: A 204 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8547 (m-80) REVERT: B 188 GLN cc_start: 0.8230 (pt0) cc_final: 0.7993 (pt0) REVERT: R 85 GLN cc_start: 0.8405 (mm110) cc_final: 0.8019 (mm-40) REVERT: R 117 ASP cc_start: 0.8443 (m-30) cc_final: 0.8035 (m-30) outliers start: 27 outliers final: 25 residues processed: 126 average time/residue: 0.1716 time to fit residues: 29.2886 Evaluate side-chains 134 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 188 GLN Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 227 ASP 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 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 227 ASP 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: 1.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 0.0470 chunk 75 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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: 0.7792 moved from start: 0.1882 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= 0.183 Angle : 0.464 7.749 9109 Z= 0.237 Chirality : 0.036 0.133 1100 Planarity : 0.003 0.025 1097 Dihedral : 3.475 16.008 915 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.09 % Allowed : 21.95 % 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: 2.50 (0.31), residues: 822 helix: 2.59 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.88 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 230 HIS 0.001 0.000 HIS R 228 PHE 0.009 0.001 PHE R 253 TYR 0.009 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 150 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 115 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8391 (m-30) cc_final: 0.8054 (m-30) REVERT: A 204 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8519 (m-80) REVERT: R 85 GLN cc_start: 0.8412 (mm110) cc_final: 0.8003 (mm-40) REVERT: R 117 ASP cc_start: 0.8476 (m-30) cc_final: 0.8055 (m-30) outliers start: 35 outliers final: 27 residues processed: 133 average time/residue: 0.1637 time to fit residues: 29.8709 Evaluate side-chains 139 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 188 GLN 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 227 ASP 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 227 ASP 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 227 ASP Chi-restraints excluded: chain R residue 238 THR 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: 0.5980 chunk 65 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7792 moved from start: 0.1952 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= 0.201 Angle : 0.475 6.899 9109 Z= 0.241 Chirality : 0.036 0.134 1100 Planarity : 0.003 0.025 1097 Dihedral : 3.512 17.431 915 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.94 % Allowed : 22.82 % Favored : 72.24 % 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: 2.52 (0.31), residues: 822 helix: 2.60 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.88 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 230 HIS 0.001 0.000 HIS R 228 PHE 0.015 0.001 PHE B 162 TYR 0.007 0.001 TYR B 251 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 148 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 114 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8412 (m-30) cc_final: 0.8081 (m-30) REVERT: A 204 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: R 85 GLN cc_start: 0.8412 (mm110) cc_final: 0.7980 (mm-40) REVERT: R 117 ASP cc_start: 0.8469 (m-30) cc_final: 0.8055 (m-30) REVERT: R 228 HIS cc_start: 0.7708 (OUTLIER) cc_final: 0.6882 (p90) outliers start: 34 outliers final: 30 residues processed: 129 average time/residue: 0.1637 time to fit residues: 28.6817 Evaluate side-chains 146 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 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 160 VAL Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 188 GLN 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 227 ASP 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 204 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 227 ASP 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 99 MET 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 227 ASP Chi-restraints excluded: chain R residue 228 HIS 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: 0.0980 chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 61 optimal weight: 0.0020 chunk 71 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 overall best weight: 0.3588 ------------------------------------------------------------------------------- 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: 0.7763 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6675 Z= 0.142 Angle : 0.447 7.290 9109 Z= 0.228 Chirality : 0.035 0.133 1100 Planarity : 0.003 0.025 1097 Dihedral : 3.444 17.595 915 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.92 % Allowed : 23.55 % Favored : 72.53 % 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: 2.72 (0.31), residues: 822 helix: 2.74 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -1.76 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 230 HIS 0.000 0.000 HIS R 228 PHE 0.007 0.001 PHE R 253 TYR 0.009 0.001 TYR A 158 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 146 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8393 (mm110) cc_final: 0.8183 (mm110) REVERT: A 117 ASP cc_start: 0.8454 (m-30) cc_final: 0.8109 (m-30) REVERT: A 204 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8258 (m-80) REVERT: B 93 MET cc_start: 0.8270 (tpp) cc_final: 0.8060 (mmp) REVERT: R 85 GLN cc_start: 0.8411 (mm110) cc_final: 0.8063 (mm-40) REVERT: R 93 MET cc_start: 0.8030 (mmp) cc_final: 0.7739 (mmt) REVERT: R 117 ASP cc_start: 0.8566 (m-30) cc_final: 0.8069 (m-30) outliers start: 27 outliers final: 24 residues processed: 132 average time/residue: 0.1706 time to fit residues: 30.3731 Evaluate side-chains 141 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 211 ILE Chi-restraints excluded: chain A residue 227 ASP 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 227 ASP 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 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 227 ASP Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 46 optimal weight: 0.0570 chunk 36 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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: 0.7777 moved from start: 0.2091 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= 0.177 Angle : 0.462 6.953 9109 Z= 0.233 Chirality : 0.036 0.130 1100 Planarity : 0.003 0.028 1097 Dihedral : 3.435 15.012 915 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.63 % Allowed : 24.13 % Favored : 72.24 % 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: 2.60 (0.31), residues: 822 helix: 2.60 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.09 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 230 HIS 0.000 0.000 HIS R 228 PHE 0.008 0.001 PHE R 253 TYR 0.010 0.001 TYR A 240 ARG 0.003 0.000 ARG B 225 *********************** 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 144 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8393 (mm110) cc_final: 0.8167 (mm110) REVERT: A 117 ASP cc_start: 0.8455 (m-30) cc_final: 0.8097 (m-30) REVERT: A 204 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8415 (m-80) REVERT: B 93 MET cc_start: 0.8275 (tpp) cc_final: 0.8052 (mmp) REVERT: R 85 GLN cc_start: 0.8423 (mm110) cc_final: 0.8042 (mm-40) REVERT: R 93 MET cc_start: 0.8071 (mmp) cc_final: 0.7824 (mmp) REVERT: R 117 ASP cc_start: 0.8562 (m-30) cc_final: 0.8091 (m-30) outliers start: 25 outliers final: 24 residues processed: 131 average time/residue: 0.1736 time to fit residues: 31.3682 Evaluate side-chains 144 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 211 ILE Chi-restraints excluded: chain A residue 227 ASP 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 227 ASP 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 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 227 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: 0.8980 chunk 74 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7779 moved from start: 0.2102 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 : 0.473 8.514 9109 Z= 0.237 Chirality : 0.036 0.132 1100 Planarity : 0.003 0.025 1097 Dihedral : 3.461 15.051 915 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.78 % Allowed : 23.98 % Favored : 72.24 % 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: 2.60 (0.31), residues: 822 helix: 2.60 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.10 (0.49), residues: 168 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 B 225 ********************** 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 142 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8392 (mm110) cc_final: 0.8160 (mm110) REVERT: A 117 ASP cc_start: 0.8459 (m-30) cc_final: 0.8102 (m-30) REVERT: A 204 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8389 (m-80) REVERT: B 93 MET cc_start: 0.8283 (tpp) cc_final: 0.8057 (mmp) REVERT: R 85 GLN cc_start: 0.8422 (mm110) cc_final: 0.8032 (mm-40) REVERT: R 117 ASP cc_start: 0.8560 (m-30) cc_final: 0.8058 (m-30) outliers start: 26 outliers final: 24 residues processed: 130 average time/residue: 0.1558 time to fit residues: 28.0760 Evaluate side-chains 140 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 211 ILE Chi-restraints excluded: chain A residue 227 ASP 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 227 ASP 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 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 227 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: 1.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.105381 restraints weight = 7440.412| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.49 r_work: 0.3040 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6675 Z= 0.235 Angle : 0.504 8.626 9109 Z= 0.252 Chirality : 0.037 0.145 1100 Planarity : 0.003 0.025 1097 Dihedral : 3.525 16.212 915 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.07 % Allowed : 23.84 % Favored : 72.09 % 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: 2.53 (0.31), residues: 822 helix: 2.59 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.80 (0.47), 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 0.013 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: 1666.51 seconds wall clock time: 30 minutes 28.12 seconds (1828.12 seconds total)