Starting phenix.real_space_refine on Tue Mar 11 18:39:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1e_39724/03_2025/8z1e_39724.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1e_39724/03_2025/8z1e_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/cci-nas-00/data/ceres_data/8z1e_39724/03_2025/8z1e_39724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1e_39724/03_2025/8z1e_39724.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1e_39724/03_2025/8z1e_39724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1e_39724/03_2025/8z1e_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. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.37, per 1000 atoms: 0.67 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 899.6 milliseconds 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: 1.83 Time building geometry restraints manager: 1.76 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: 0.00 - 1.26: 8949 1.26 - 2.52: 122 2.52 - 3.78: 24 3.78 - 5.04: 9 5.04 - 6.30: 5 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: 1.040 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: 0.040 Set scattering table: 0.070 Process input model: 18.270 Find NCS groups from input model: 0.240 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: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.850 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 0.671 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: 0.2179 time to fit residues: 34.4750 Evaluate side-chains 122 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.132897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104874 restraints weight = 7402.370| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.59 r_work: 0.3023 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8531 (mtp180) cc_final: 0.8299 (ptm160) outliers start: 15 outliers final: 12 residues processed: 137 average time/residue: 0.1903 time to fit residues: 34.7201 Evaluate side-chains 126 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 85 GLN R 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.131568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.103830 restraints weight = 7510.484| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.58 r_work: 0.3011 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6675 Z= 0.230 Angle : 0.478 5.783 9109 Z= 0.250 Chirality : 0.037 0.131 1100 Planarity : 0.004 0.027 1097 Dihedral : 3.441 15.314 915 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.49 % Allowed : 20.64 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.30), residues: 822 helix: 2.29 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.19 (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 R 228 PHE 0.010 0.001 PHE R 253 TYR 0.011 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 146 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.8729 (m-80) REVERT: B 181 ASP cc_start: 0.7467 (t0) cc_final: 0.7146 (t0) REVERT: R 93 MET cc_start: 0.8459 (mmp) cc_final: 0.8217 (mmt) outliers start: 24 outliers final: 19 residues processed: 135 average time/residue: 0.1657 time to fit residues: 30.7810 Evaluate side-chains 132 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 0.0030 chunk 80 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 GLN R 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.105099 restraints weight = 7558.042| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.59 r_work: 0.3052 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1712 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= 0.185 Angle : 0.453 5.534 9109 Z= 0.235 Chirality : 0.036 0.132 1100 Planarity : 0.003 0.027 1097 Dihedral : 3.422 14.452 915 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.34 % Allowed : 22.09 % Favored : 74.56 % 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 (0.30), residues: 822 helix: 2.37 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.25 (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 R 228 PHE 0.009 0.001 PHE R 253 TYR 0.009 0.001 TYR R 158 ARG 0.003 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 136 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.8694 (m-80) REVERT: R 85 GLN cc_start: 0.8818 (mm110) cc_final: 0.8564 (mm110) REVERT: R 117 ASP cc_start: 0.8807 (m-30) cc_final: 0.8400 (m-30) outliers start: 23 outliers final: 17 residues processed: 125 average time/residue: 0.1669 time to fit residues: 28.9067 Evaluate side-chains 128 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 204 PHE Chi-restraints excluded: chain A residue 206 LEU 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 224 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.131808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.104795 restraints weight = 7424.696| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.51 r_work: 0.3037 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1774 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= 0.216 Angle : 0.471 6.291 9109 Z= 0.242 Chirality : 0.037 0.133 1100 Planarity : 0.003 0.027 1097 Dihedral : 3.423 14.899 915 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.92 % Allowed : 22.24 % 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: 2.34 (0.30), residues: 822 helix: 2.49 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.01 (0.45), 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 0.010 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 144 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 2.115 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9365 (OUTLIER) cc_final: 0.8714 (m-80) REVERT: R 85 GLN cc_start: 0.8763 (mm110) cc_final: 0.8464 (mm110) REVERT: R 117 ASP cc_start: 0.8792 (m-30) cc_final: 0.8405 (m-30) outliers start: 27 outliers final: 23 residues processed: 131 average time/residue: 0.2614 time to fit residues: 45.3130 Evaluate side-chains 137 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 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 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 224 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 10 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.130776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.103042 restraints weight = 7469.915| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.57 r_work: 0.3004 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6675 Z= 0.274 Angle : 0.505 7.842 9109 Z= 0.258 Chirality : 0.038 0.132 1100 Planarity : 0.003 0.027 1097 Dihedral : 3.508 15.829 915 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.94 % Allowed : 21.80 % 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: 2.20 (0.30), residues: 822 helix: 2.39 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.04 (0.45), 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 0.012 0.001 PHE R 253 TYR 0.014 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 to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.8735 (m-80) REVERT: R 117 ASP cc_start: 0.8830 (m-30) cc_final: 0.8441 (m-30) outliers start: 34 outliers final: 29 residues processed: 134 average time/residue: 0.1785 time to fit residues: 32.6250 Evaluate side-chains 144 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 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 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 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.132216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.105022 restraints weight = 7448.692| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.55 r_work: 0.3029 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1907 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= 0.197 Angle : 0.470 7.246 9109 Z= 0.241 Chirality : 0.036 0.133 1100 Planarity : 0.003 0.027 1097 Dihedral : 3.490 16.541 915 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: 2.34 (0.30), residues: 822 helix: 2.50 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.05 (0.45), 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 0.010 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 149 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8431 (mmm160) cc_final: 0.8106 (mmm160) REVERT: A 204 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.8607 (m-80) REVERT: R 85 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8500 (mm110) REVERT: R 117 ASP cc_start: 0.8840 (m-30) cc_final: 0.8454 (m-30) REVERT: R 228 HIS cc_start: 0.7814 (OUTLIER) cc_final: 0.7082 (p90) outliers start: 28 outliers final: 24 residues processed: 137 average time/residue: 0.1705 time to fit residues: 31.7120 Evaluate side-chains 142 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 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 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 228 HIS Chi-restraints excluded: chain R residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.132088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.104800 restraints weight = 7498.277| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.56 r_work: 0.3027 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1948 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= 0.212 Angle : 0.488 6.860 9109 Z= 0.248 Chirality : 0.037 0.136 1100 Planarity : 0.003 0.027 1097 Dihedral : 3.522 18.628 915 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.22 % Allowed : 23.26 % 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: 2.33 (0.30), residues: 822 helix: 2.50 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.05 (0.44), 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 0.010 0.001 TYR A 313 ARG 0.003 0.000 ARG R 254 *********************** 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 to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8428 (mmm160) cc_final: 0.8103 (mmm160) REVERT: A 204 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8660 (m-80) REVERT: R 85 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8492 (mm110) REVERT: R 117 ASP cc_start: 0.8823 (m-30) cc_final: 0.8440 (m-30) REVERT: R 228 HIS cc_start: 0.7809 (OUTLIER) cc_final: 0.7071 (p90) outliers start: 29 outliers final: 25 residues processed: 134 average time/residue: 0.2196 time to fit residues: 38.6085 Evaluate side-chains 142 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 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 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 228 HIS Chi-restraints excluded: chain R residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.105800 restraints weight = 7544.840| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.51 r_work: 0.3049 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2003 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= 0.199 Angle : 0.477 8.301 9109 Z= 0.243 Chirality : 0.036 0.133 1100 Planarity : 0.003 0.027 1097 Dihedral : 3.482 15.265 915 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.36 % Allowed : 22.67 % 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: 2.37 (0.30), residues: 822 helix: 2.53 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.04 (0.44), residues: 186 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 0.009 0.001 PHE R 253 TYR 0.011 0.001 TYR R 240 ARG 0.002 0.000 ARG R 66 *********************** 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 150 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8368 (mmm160) cc_final: 0.8079 (mmm160) REVERT: A 204 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.8603 (m-80) REVERT: R 85 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8515 (mm110) REVERT: R 117 ASP cc_start: 0.8820 (m-30) cc_final: 0.8446 (m-30) REVERT: R 228 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7019 (p90) outliers start: 30 outliers final: 27 residues processed: 136 average time/residue: 0.1807 time to fit residues: 34.2645 Evaluate side-chains 148 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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 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 228 HIS Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 63 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104919 restraints weight = 7535.356| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.59 r_work: 0.3036 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2009 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= 0.219 Angle : 0.495 8.080 9109 Z= 0.251 Chirality : 0.037 0.133 1100 Planarity : 0.003 0.027 1097 Dihedral : 3.541 15.430 915 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.36 % Allowed : 23.40 % 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: 2.32 (0.30), residues: 822 helix: 2.48 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.03 (0.44), residues: 186 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 0.011 0.001 TYR A 313 ARG 0.003 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 to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8379 (mmm160) cc_final: 0.8084 (mmm160) REVERT: A 204 PHE cc_start: 0.9313 (OUTLIER) cc_final: 0.8646 (m-80) REVERT: R 85 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8513 (mm110) REVERT: R 117 ASP cc_start: 0.8828 (m-30) cc_final: 0.8460 (m-30) REVERT: R 228 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.7033 (p90) outliers start: 30 outliers final: 28 residues processed: 133 average time/residue: 0.1643 time to fit residues: 30.0768 Evaluate side-chains 146 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 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 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 283 LEU 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 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 228 HIS Chi-restraints excluded: chain R residue 238 THR Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 21 optimal weight: 0.0370 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.132956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.105649 restraints weight = 7625.771| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.58 r_work: 0.3038 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2036 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= 0.201 Angle : 0.493 8.783 9109 Z= 0.249 Chirality : 0.036 0.133 1100 Planarity : 0.003 0.027 1097 Dihedral : 3.542 15.495 915 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.51 % Allowed : 23.26 % 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: 2.34 (0.30), residues: 822 helix: 2.49 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.01 (0.44), residues: 186 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 0.009 0.001 PHE B 253 TYR 0.011 0.001 TYR A 313 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: 3744.11 seconds wall clock time: 64 minutes 51.60 seconds (3891.60 seconds total)