Starting phenix.real_space_refine on Tue Jan 14 10:59:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1e_39724/01_2025/8z1e_39724.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1e_39724/01_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_39724/01_2025/8z1e_39724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1e_39724/01_2025/8z1e_39724.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1e_39724/01_2025/8z1e_39724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1e_39724/01_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 4.29, per 1000 atoms: 0.66 Number of scatterers: 6516 At special positions: 0 Unit cell: (91.035, 91.035, 73.899, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1090 8.00 N 1056 7.00 C 4322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 109 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.64 Conformation dependent library (CDL) restraints added in 956.9 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: 0.60 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: 1.92 Time building geometry restraints manager: 1.88 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.130 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.460 ------------------------------------------------------------------------------- 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 : 0.730 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: 0.2099 time to fit residues: 33.3740 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 : 0.727 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104874 restraints weight = 7402.368| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.59 r_work: 0.3024 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.684 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8529 (mtp180) cc_final: 0.8298 (ptm160) outliers start: 15 outliers final: 12 residues processed: 137 average time/residue: 0.1892 time to fit residues: 34.3353 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 : 0.664 ------------------------------------------------------------------------------- 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: 0.8980 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.130830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.103018 restraints weight = 7515.729| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.58 r_work: 0.3023 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6675 Z= 0.261 Angle : 0.495 5.955 9109 Z= 0.258 Chirality : 0.038 0.139 1100 Planarity : 0.004 0.027 1097 Dihedral : 3.471 15.787 915 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.78 % Allowed : 20.93 % Favored : 75.29 % 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: 2.09 (0.30), residues: 822 helix: 2.23 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.22 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 230 HIS 0.001 0.000 HIS R 228 PHE 0.011 0.001 PHE R 253 TYR 0.013 0.001 TYR R 240 ARG 0.006 0.000 ARG R 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.8818 (m-80) REVERT: A 222 TYR cc_start: 0.9212 (m-80) cc_final: 0.8500 (m-80) REVERT: B 181 ASP cc_start: 0.7471 (t0) cc_final: 0.7164 (t0) REVERT: R 93 MET cc_start: 0.8406 (mmp) cc_final: 0.8150 (mmt) REVERT: R 117 ASP cc_start: 0.8767 (m-30) cc_final: 0.8416 (m-30) outliers start: 26 outliers final: 20 residues processed: 139 average time/residue: 0.1746 time to fit residues: 32.5052 Evaluate side-chains 135 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain R residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 14 optimal weight: 0.0470 chunk 80 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.132452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104815 restraints weight = 7568.419| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.59 r_work: 0.3026 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1733 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= 0.189 Angle : 0.459 5.618 9109 Z= 0.239 Chirality : 0.036 0.131 1100 Planarity : 0.003 0.027 1097 Dihedral : 3.456 15.785 915 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.63 % Allowed : 21.80 % 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: 2.22 (0.30), residues: 822 helix: 2.34 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.27 (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 0.008 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 136 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.8719 (m-80) REVERT: B 51 SER cc_start: 0.8872 (m) cc_final: 0.7992 (p) REVERT: R 85 GLN cc_start: 0.8844 (mm110) cc_final: 0.8621 (mm110) REVERT: R 117 ASP cc_start: 0.8860 (m-30) cc_final: 0.8485 (m-30) outliers start: 25 outliers final: 18 residues processed: 122 average time/residue: 0.1702 time to fit residues: 28.4108 Evaluate side-chains 128 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 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 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 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: 0.5980 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.131763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104266 restraints weight = 7433.451| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.57 r_work: 0.3022 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6675 Z= 0.219 Angle : 0.478 6.929 9109 Z= 0.245 Chirality : 0.037 0.133 1100 Planarity : 0.003 0.027 1097 Dihedral : 3.458 15.750 915 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.65 % Allowed : 21.22 % 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: 2.29 (0.30), residues: 822 helix: 2.46 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.03 (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 0.010 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 148 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.8721 (m-80) REVERT: R 85 GLN cc_start: 0.8785 (mm110) cc_final: 0.8507 (mm110) REVERT: R 117 ASP cc_start: 0.8856 (m-30) cc_final: 0.8496 (m-30) outliers start: 32 outliers final: 24 residues processed: 133 average time/residue: 0.1750 time to fit residues: 31.7361 Evaluate side-chains 137 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 B residue 99 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 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 238 THR 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: 1.9990 chunk 54 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.129551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.102422 restraints weight = 7492.922| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.50 r_work: 0.3019 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6675 Z= 0.320 Angle : 0.537 9.661 9109 Z= 0.273 Chirality : 0.039 0.143 1100 Planarity : 0.004 0.028 1097 Dihedral : 3.590 16.807 915 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.38 % Allowed : 21.66 % 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: 2.03 (0.30), residues: 822 helix: 2.27 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.14 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 230 HIS 0.002 0.000 HIS R 228 PHE 0.013 0.001 PHE R 253 TYR 0.016 0.002 TYR A 240 ARG 0.004 0.000 ARG R 254 *********************** 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 157 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9396 (OUTLIER) cc_final: 0.8774 (m-80) REVERT: R 117 ASP cc_start: 0.8798 (m-30) cc_final: 0.8390 (m-30) REVERT: R 228 HIS cc_start: 0.7718 (OUTLIER) cc_final: 0.6977 (p90) outliers start: 37 outliers final: 30 residues processed: 138 average time/residue: 0.1679 time to fit residues: 31.2585 Evaluate side-chains 146 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 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 B residue 46 MET Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain 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 228 HIS 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: 0.6980 chunk 73 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.131074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.103686 restraints weight = 7455.140| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.56 r_work: 0.3009 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1868 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= 0.227 Angle : 0.492 7.545 9109 Z= 0.253 Chirality : 0.037 0.132 1100 Planarity : 0.003 0.028 1097 Dihedral : 3.575 18.049 915 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.65 % Allowed : 22.24 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.30), residues: 822 helix: 2.36 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.19 (0.43), 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 0.012 0.001 TYR R 313 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 146 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8664 (m-80) REVERT: R 117 ASP cc_start: 0.8858 (m-30) cc_final: 0.8472 (m-30) REVERT: R 216 ASN cc_start: 0.8800 (t0) cc_final: 0.8598 (t0) outliers start: 32 outliers final: 27 residues processed: 132 average time/residue: 0.1758 time to fit residues: 31.7150 Evaluate side-chains 142 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 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 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 238 THR Chi-restraints excluded: chain R residue 314 LEU 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: 0.5980 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 79 optimal weight: 0.0970 chunk 71 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.132935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.106264 restraints weight = 7495.217| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.51 r_work: 0.3055 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1967 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= 0.176 Angle : 0.475 7.509 9109 Z= 0.244 Chirality : 0.036 0.135 1100 Planarity : 0.003 0.028 1097 Dihedral : 3.576 19.457 915 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.92 % Allowed : 22.97 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.30), residues: 822 helix: 2.49 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.14 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 230 HIS 0.001 0.000 HIS R 228 PHE 0.009 0.001 PHE B 162 TYR 0.011 0.001 TYR R 313 ARG 0.003 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 143 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8505 (mm110) REVERT: A 204 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8570 (m-80) REVERT: R 85 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8463 (mm110) REVERT: R 117 ASP cc_start: 0.8795 (m-30) cc_final: 0.8365 (m-30) outliers start: 27 outliers final: 24 residues processed: 131 average time/residue: 0.1648 time to fit residues: 29.8203 Evaluate side-chains 139 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 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 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 314 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.132779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106239 restraints weight = 7558.551| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.51 r_work: 0.3052 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2012 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= 0.189 Angle : 0.474 7.220 9109 Z= 0.242 Chirality : 0.036 0.134 1100 Planarity : 0.003 0.028 1097 Dihedral : 3.520 15.282 915 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.17 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: 2.32 (0.30), residues: 822 helix: 2.49 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.09 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 230 HIS 0.001 0.000 HIS R 228 PHE 0.009 0.001 PHE B 253 TYR 0.011 0.001 TYR R 313 ARG 0.003 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 144 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8531 (mm110) REVERT: A 204 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8554 (m-80) REVERT: R 85 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8521 (mm110) REVERT: R 117 ASP cc_start: 0.8817 (m-30) cc_final: 0.8449 (m-30) outliers start: 27 outliers final: 22 residues processed: 133 average time/residue: 0.1608 time to fit residues: 29.2759 Evaluate side-chains 137 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 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 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.132261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.104574 restraints weight = 7551.826| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.58 r_work: 0.3026 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6675 Z= 0.224 Angle : 0.490 7.449 9109 Z= 0.249 Chirality : 0.037 0.132 1100 Planarity : 0.003 0.028 1097 Dihedral : 3.575 15.692 915 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.78 % Allowed : 24.27 % Favored : 71.95 % 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: 2.28 (0.30), residues: 822 helix: 2.46 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.09 (0.43), 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 0.012 0.001 TYR A 240 ARG 0.002 0.000 ARG R 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8560 (m-80) REVERT: R 85 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8513 (mm110) REVERT: R 117 ASP cc_start: 0.8855 (m-30) cc_final: 0.8502 (m-30) REVERT: R 183 ARG cc_start: 0.8549 (mmm160) cc_final: 0.8047 (mmm160) REVERT: R 228 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.7053 (p90) outliers start: 26 outliers final: 23 residues processed: 128 average time/residue: 0.1756 time to fit residues: 30.2650 Evaluate side-chains 139 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 B residue 149 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 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 228 HIS 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: 0.5980 chunk 58 optimal weight: 0.5980 chunk 67 optimal weight: 0.0870 chunk 21 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.132217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.105166 restraints weight = 7648.925| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.54 r_work: 0.3060 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2061 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= 0.175 Angle : 0.474 8.453 9109 Z= 0.241 Chirality : 0.036 0.133 1100 Planarity : 0.003 0.028 1097 Dihedral : 3.551 15.564 915 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: 2.39 (0.30), residues: 822 helix: 2.54 (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 0.011 0.001 TRP R 230 HIS 0.001 0.000 HIS R 228 PHE 0.008 0.001 PHE R 253 TYR 0.011 0.001 TYR R 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: 3535.69 seconds wall clock time: 64 minutes 17.75 seconds (3857.75 seconds total)