Starting phenix.real_space_refine on Wed Sep 17 07:05:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1e_39724/09_2025/8z1e_39724.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1e_39724/09_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_39724/09_2025/8z1e_39724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1e_39724/09_2025/8z1e_39724.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1e_39724/09_2025/8z1e_39724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1e_39724/09_2025/8z1e_39724.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 5, 'GLU:plan': 1, 'ARG:plan': 1} 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: {'ASP:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1} 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: {'ASP:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 1.97, per 1000 atoms: 0.30 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: 0.56 Conformation dependent library (CDL) restraints added in 408.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.21 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: 0.86 Time building geometry restraints manager: 0.77 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: 1.360 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 8.190 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.820 ------------------------------------------------------------------------------- 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 6678 Z= 0.092 Angle : 0.432 6.302 9115 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 : 4.26 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG B 254 TYR 0.009 0.001 TYR B 313 PHE 0.006 0.001 PHE A 162 TRP 0.025 0.001 TRP A 145 HIS 0.000 0.000 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 6675) covalent geometry : angle 0.43173 ( 9109) SS BOND : bond 0.00216 ( 3) SS BOND : angle 0.54147 ( 6) hydrogen bonds : bond 0.22410 ( 504) hydrogen bonds : angle 6.20989 ( 1500) *********************** 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 : 0.218 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: 0.0883 time to fit residues: 14.0560 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 : 0.246 ------------------------------------------------------------------------------- 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 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.0030 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.132131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.103894 restraints weight = 7533.585| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.61 r_work: 0.3015 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6678 Z= 0.146 Angle : 0.488 5.843 9115 Z= 0.262 Chirality : 0.037 0.135 1100 Planarity : 0.004 0.026 1097 Dihedral : 3.520 19.234 918 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.33 % Allowed : 19.91 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.30), residues: 822 helix: 2.16 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.14 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 66 TYR 0.011 0.001 TYR R 240 PHE 0.011 0.001 PHE A 253 TRP 0.009 0.001 TRP A 145 HIS 0.001 0.000 HIS R 228 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6675) covalent geometry : angle 0.48765 ( 9109) SS BOND : bond 0.00625 ( 3) SS BOND : angle 1.06890 ( 6) hydrogen bonds : bond 0.05373 ( 504) hydrogen bonds : angle 3.81509 ( 1500) *********************** 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: 16 poor density : 128 time to evaluate : 0.239 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 138 average time/residue: 0.0854 time to fit residues: 15.6899 Evaluate side-chains 127 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 58 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 GLN B 216 ASN R 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.104356 restraints weight = 7488.220| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.59 r_work: 0.3023 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6678 Z= 0.132 Angle : 0.464 5.823 9115 Z= 0.243 Chirality : 0.037 0.129 1100 Planarity : 0.004 0.030 1097 Dihedral : 3.428 14.787 915 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.49 % Allowed : 20.78 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.30), residues: 822 helix: 2.32 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.19 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 66 TYR 0.010 0.001 TYR A 240 PHE 0.009 0.001 PHE R 253 TRP 0.009 0.001 TRP B 230 HIS 0.001 0.000 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6675) covalent geometry : angle 0.46379 ( 9109) SS BOND : bond 0.00542 ( 3) SS BOND : angle 1.09412 ( 6) hydrogen bonds : bond 0.04541 ( 504) hydrogen bonds : angle 3.56011 ( 1500) *********************** 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 144 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.8729 (m-80) REVERT: R 93 MET cc_start: 0.8452 (mmp) cc_final: 0.8220 (mmt) REVERT: R 117 ASP cc_start: 0.8851 (m-30) cc_final: 0.8511 (m-30) outliers start: 24 outliers final: 18 residues processed: 132 average time/residue: 0.0703 time to fit residues: 12.9568 Evaluate side-chains 133 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 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 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 160 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 78 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 0.0870 chunk 55 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 ASN R 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.132631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104976 restraints weight = 7556.451| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.59 r_work: 0.3050 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6678 Z= 0.127 Angle : 0.467 5.704 9115 Z= 0.243 Chirality : 0.036 0.132 1100 Planarity : 0.003 0.028 1097 Dihedral : 3.431 14.562 915 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.20 % Allowed : 22.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.30), residues: 822 helix: 2.48 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.97 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 66 TYR 0.010 0.001 TYR A 240 PHE 0.009 0.001 PHE R 253 TRP 0.009 0.001 TRP R 230 HIS 0.001 0.000 HIS R 228 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6675) covalent geometry : angle 0.46633 ( 9109) SS BOND : bond 0.00580 ( 3) SS BOND : angle 1.23977 ( 6) hydrogen bonds : bond 0.04176 ( 504) hydrogen bonds : angle 3.47969 ( 1500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.8711 (m-80) REVERT: R 117 ASP cc_start: 0.8832 (m-30) cc_final: 0.8446 (m-30) outliers start: 22 outliers final: 19 residues processed: 129 average time/residue: 0.0730 time to fit residues: 13.0444 Evaluate side-chains 135 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 204 PHE Chi-restraints excluded: chain R residue 206 LEU 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 43 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.104749 restraints weight = 7631.103| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.55 r_work: 0.3030 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6678 Z= 0.137 Angle : 0.474 6.777 9115 Z= 0.244 Chirality : 0.037 0.134 1100 Planarity : 0.003 0.027 1097 Dihedral : 3.425 15.085 915 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.07 % Allowed : 22.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.30), residues: 822 helix: 2.48 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.97 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 66 TYR 0.011 0.001 TYR A 240 PHE 0.010 0.001 PHE R 253 TRP 0.009 0.001 TRP R 230 HIS 0.001 0.000 HIS R 228 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 6675) covalent geometry : angle 0.47344 ( 9109) SS BOND : bond 0.00590 ( 3) SS BOND : angle 1.09868 ( 6) hydrogen bonds : bond 0.04191 ( 504) hydrogen bonds : angle 3.44906 ( 1500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 204 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.8718 (m-80) REVERT: R 117 ASP cc_start: 0.8821 (m-30) cc_final: 0.8455 (m-30) outliers start: 28 outliers final: 25 residues processed: 131 average time/residue: 0.0734 time to fit residues: 13.2273 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 : 0.263 ------------------------------------------------------------------------------- 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 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 99 MET Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 211 ILE Chi-restraints excluded: chain R residue 224 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 50 optimal weight: 0.2980 chunk 79 optimal weight: 0.0020 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.106154 restraints weight = 7568.430| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.59 r_work: 0.3045 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6678 Z= 0.114 Angle : 0.458 6.910 9115 Z= 0.235 Chirality : 0.036 0.132 1100 Planarity : 0.003 0.027 1097 Dihedral : 3.412 15.069 915 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.07 % Allowed : 22.38 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.30), residues: 822 helix: 2.59 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -1.95 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 66 TYR 0.008 0.001 TYR A 240 PHE 0.008 0.001 PHE R 253 TRP 0.009 0.001 TRP R 230 HIS 0.001 0.000 HIS R 228 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6675) covalent geometry : angle 0.45716 ( 9109) SS BOND : bond 0.00527 ( 3) SS BOND : angle 1.07514 ( 6) hydrogen bonds : bond 0.03824 ( 504) hydrogen bonds : angle 3.38057 ( 1500) *********************** 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 148 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8580 (mm110) REVERT: A 183 ARG cc_start: 0.8401 (mmm160) cc_final: 0.8104 (mmm160) REVERT: A 204 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8585 (m-80) REVERT: R 117 ASP cc_start: 0.8867 (m-30) cc_final: 0.8516 (m-30) outliers start: 28 outliers final: 21 residues processed: 137 average time/residue: 0.0739 time to fit residues: 13.7261 Evaluate side-chains 140 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 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 99 MET Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 211 ILE Chi-restraints excluded: chain R residue 224 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.102040 restraints weight = 7527.008| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.56 r_work: 0.2984 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6678 Z= 0.211 Angle : 0.556 7.269 9115 Z= 0.282 Chirality : 0.040 0.153 1100 Planarity : 0.004 0.031 1097 Dihedral : 3.609 17.716 915 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.23 % Allowed : 21.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.30), residues: 822 helix: 2.32 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.11 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 254 TYR 0.017 0.002 TYR A 240 PHE 0.016 0.001 PHE A 162 TRP 0.010 0.001 TRP R 230 HIS 0.002 0.000 HIS R 228 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 6675) covalent geometry : angle 0.55556 ( 9109) SS BOND : bond 0.00661 ( 3) SS BOND : angle 1.08708 ( 6) hydrogen bonds : bond 0.04769 ( 504) hydrogen bonds : angle 3.54552 ( 1500) *********************** 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 158 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8450 (mmm160) cc_final: 0.8114 (mmm160) REVERT: A 204 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.8800 (m-80) REVERT: B 240 TYR cc_start: 0.8545 (m-80) cc_final: 0.8266 (m-80) REVERT: R 117 ASP cc_start: 0.8820 (m-30) cc_final: 0.8446 (m-30) REVERT: R 228 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.7029 (p90) outliers start: 36 outliers final: 31 residues processed: 140 average time/residue: 0.0802 time to fit residues: 15.1842 Evaluate side-chains 155 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 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 228 HIS 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 54 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS B 188 GLN B 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.132299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.105036 restraints weight = 7554.474| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.57 r_work: 0.3029 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6678 Z= 0.131 Angle : 0.486 7.728 9115 Z= 0.248 Chirality : 0.036 0.134 1100 Planarity : 0.003 0.028 1097 Dihedral : 3.555 18.674 915 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.78 % Allowed : 23.98 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.30), residues: 822 helix: 2.46 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.12 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 66 TYR 0.013 0.001 TYR R 313 PHE 0.010 0.001 PHE A 162 TRP 0.010 0.001 TRP R 230 HIS 0.001 0.000 HIS R 228 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6675) covalent geometry : angle 0.48547 ( 9109) SS BOND : bond 0.00581 ( 3) SS BOND : angle 1.01255 ( 6) hydrogen bonds : bond 0.04035 ( 504) hydrogen bonds : angle 3.44483 ( 1500) *********************** 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: 26 poor density : 120 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8391 (mmm160) cc_final: 0.8097 (mmm160) REVERT: A 204 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.8602 (m-80) REVERT: R 117 ASP cc_start: 0.8848 (m-30) cc_final: 0.8447 (m-30) outliers start: 26 outliers final: 24 residues processed: 135 average time/residue: 0.0719 time to fit residues: 13.4806 Evaluate side-chains 142 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.0020 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS B 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.104942 restraints weight = 7611.000| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.58 r_work: 0.3033 rms_B_bonded: 2.28 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: 0.8290 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6678 Z= 0.131 Angle : 0.496 9.059 9115 Z= 0.251 Chirality : 0.037 0.145 1100 Planarity : 0.003 0.029 1097 Dihedral : 3.548 16.393 915 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.92 % Allowed : 23.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.30), residues: 822 helix: 2.47 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.09 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 66 TYR 0.013 0.001 TYR R 313 PHE 0.009 0.001 PHE R 253 TRP 0.011 0.001 TRP R 230 HIS 0.001 0.000 HIS R 228 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6675) covalent geometry : angle 0.49556 ( 9109) SS BOND : bond 0.00547 ( 3) SS BOND : angle 0.97180 ( 6) hydrogen bonds : bond 0.04014 ( 504) hydrogen bonds : angle 3.41476 ( 1500) *********************** 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 138 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8406 (mmm160) cc_final: 0.8095 (mmm160) REVERT: A 204 PHE cc_start: 0.9313 (OUTLIER) cc_final: 0.8601 (m-80) REVERT: R 117 ASP cc_start: 0.8826 (m-30) cc_final: 0.8454 (m-30) outliers start: 27 outliers final: 26 residues processed: 125 average time/residue: 0.0717 time to fit residues: 12.4187 Evaluate side-chains 138 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 46 MET Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 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 B 188 GLN B 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104945 restraints weight = 7454.500| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.57 r_work: 0.3034 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 6678 Z= 0.138 Angle : 0.496 8.398 9115 Z= 0.251 Chirality : 0.037 0.142 1100 Planarity : 0.003 0.029 1097 Dihedral : 3.571 17.332 915 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.92 % Allowed : 23.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.30), residues: 822 helix: 2.47 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.07 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 66 TYR 0.012 0.001 TYR R 313 PHE 0.010 0.001 PHE R 253 TRP 0.011 0.001 TRP R 230 HIS 0.001 0.000 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6675) covalent geometry : angle 0.49553 ( 9109) SS BOND : bond 0.00567 ( 3) SS BOND : angle 0.92473 ( 6) hydrogen bonds : bond 0.04062 ( 504) hydrogen bonds : angle 3.42323 ( 1500) ********************** 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 138 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8368 (mmm160) cc_final: 0.8064 (mmm160) REVERT: A 204 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.8594 (m-80) REVERT: R 117 ASP cc_start: 0.8828 (m-30) cc_final: 0.8460 (m-30) outliers start: 27 outliers final: 26 residues processed: 126 average time/residue: 0.0720 time to fit residues: 12.4693 Evaluate side-chains 137 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 204 PHE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 77 optimal weight: 0.0070 chunk 65 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS B 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106555 restraints weight = 7492.773| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.56 r_work: 0.3039 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6678 Z= 0.124 Angle : 0.486 7.420 9115 Z= 0.247 Chirality : 0.036 0.143 1100 Planarity : 0.003 0.029 1097 Dihedral : 3.580 18.142 915 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.92 % Allowed : 24.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG R 66 TYR 0.013 0.001 TYR R 313 PHE 0.009 0.001 PHE R 253 TRP 0.011 0.001 TRP R 230 HIS 0.001 0.000 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6675) covalent geometry : angle 0.48538 ( 9109) SS BOND : bond 0.00539 ( 3) SS BOND : angle 0.87128 ( 6) hydrogen bonds : bond 0.03889 ( 504) hydrogen bonds : angle 3.39734 ( 1500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1702.84 seconds wall clock time: 29 minutes 48.71 seconds (1788.71 seconds total)