Starting phenix.real_space_refine on Thu Jul 2 11:10:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g3e_50996/07_2026/9g3e_50996.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g3e_50996/07_2026/9g3e_50996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g3e_50996/07_2026/9g3e_50996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g3e_50996/07_2026/9g3e_50996.map" model { file = "/net/cci-nas-00/data/ceres_data/9g3e_50996/07_2026/9g3e_50996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g3e_50996/07_2026/9g3e_50996.cif" } resolution = 3.14 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= 0.010 sd= 0.142 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 28 5.16 5 C 5479 2.51 5 N 1328 2.21 5 O 1418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8255 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3200 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 14, 'TRANS': 378} Chain: "B" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3200 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 14, 'TRANS': 378} Chain: "C" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 878 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "D" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 887 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 1.56, per 1000 atoms: 0.19 Number of scatterers: 8255 At special positions: 0 Unit cell: (76.65, 85.848, 119.574, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 2 15.00 O 1418 8.00 N 1328 7.00 C 5479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 102 " 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: 0.70 Conformation dependent library (CDL) restraints added in 391.6 milliseconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1882 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 6 sheets defined 70.1% alpha, 11.7% 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 8 through 29 Processing helix chain 'A' and resid 30 through 40 removed outlier: 3.691A pdb=" N TRP A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.709A pdb=" N ARG A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 53' Processing helix chain 'A' and resid 54 through 79 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 88 through 125 removed outlier: 4.041A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.942A pdb=" N SER A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 177 removed outlier: 3.974A pdb=" N PHE A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 186 through 227 removed outlier: 4.697A pdb=" N THR A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET A 196 " --> pdb=" O GLN A 192 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 261 removed outlier: 4.414A pdb=" N LEU A 258 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 286 removed outlier: 4.002A pdb=" N LYS A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 337 removed outlier: 3.713A pdb=" N ALA A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET A 317 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A 319 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 337 " --> pdb=" O PHE A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 348 through 394 removed outlier: 3.651A pdb=" N ILE A 370 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 378 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 29 Processing helix chain 'B' and resid 30 through 40 removed outlier: 3.671A pdb=" N TRP B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 removed outlier: 3.801A pdb=" N ARG B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 52 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP B 53 " --> pdb=" O ALA B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 53' Processing helix chain 'B' and resid 54 through 79 removed outlier: 3.557A pdb=" N ILE B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 79 " --> pdb=" O TRP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 125 removed outlier: 4.093A pdb=" N LEU B 89 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 90 " --> pdb=" O TRP B 86 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Proline residue: B 114 - end of helix removed outlier: 3.942A pdb=" N SER B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 177 removed outlier: 4.104A pdb=" N PHE B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 177 " --> pdb=" O TYR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 186 through 227 removed outlier: 4.815A pdb=" N THR B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET B 196 " --> pdb=" O GLN B 192 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 241 through 263 removed outlier: 3.608A pdb=" N VAL B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 284 removed outlier: 4.358A pdb=" N GLY B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 292 removed outlier: 3.728A pdb=" N ARG B 292 " --> pdb=" O ASP B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 337 removed outlier: 3.974A pdb=" N ASN B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 345 Processing helix chain 'B' and resid 348 through 394 removed outlier: 3.658A pdb=" N GLU B 378 " --> pdb=" O THR B 374 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 97 removed outlier: 3.633A pdb=" N THR D 97 " --> pdb=" O PRO D 94 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 11 through 14 Processing sheet with id=AA2, first strand: chain 'C' and resid 17 through 19 removed outlier: 6.489A pdb=" N VAL C 18 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET C 40 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA C 56 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP C 42 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 19 removed outlier: 6.489A pdb=" N VAL C 18 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 11 through 14 Processing sheet with id=AA5, first strand: chain 'D' and resid 17 through 18 removed outlier: 6.445A pdb=" N MET D 40 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA D 56 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP D 42 " --> pdb=" O VAL D 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 17 through 18 600 hydrogen bonds defined for protein. 1758 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: 1.01 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1311 1.32 - 1.44: 2564 1.44 - 1.56: 4572 1.56 - 1.69: 4 1.69 - 1.81: 50 Bond restraints: 8501 Sorted by residual: bond pdb=" CG LEU B 379 " pdb=" CD1 LEU B 379 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.04e+00 bond pdb=" C VAL A 140 " pdb=" O VAL A 140 " ideal model delta sigma weight residual 1.237 1.246 -0.009 1.13e-02 7.83e+03 7.02e-01 bond pdb=" C VAL B 140 " pdb=" O VAL B 140 " ideal model delta sigma weight residual 1.237 1.246 -0.009 1.13e-02 7.83e+03 6.28e-01 bond pdb=" CA THR D 97 " pdb=" CB THR D 97 " ideal model delta sigma weight residual 1.529 1.540 -0.011 1.43e-02 4.89e+03 6.10e-01 bond pdb=" CA ARG D 78 " pdb=" C ARG D 78 " ideal model delta sigma weight residual 1.522 1.532 -0.009 1.20e-02 6.94e+03 5.89e-01 ... (remaining 8496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 11233 1.33 - 2.65: 263 2.65 - 3.98: 50 3.98 - 5.30: 16 5.30 - 6.63: 6 Bond angle restraints: 11568 Sorted by residual: angle pdb=" N VAL B 284 " pdb=" CA VAL B 284 " pdb=" C VAL B 284 " ideal model delta sigma weight residual 110.09 105.25 4.84 1.50e+00 4.44e-01 1.04e+01 angle pdb=" N ALA D 98 " pdb=" CA ALA D 98 " pdb=" C ALA D 98 " ideal model delta sigma weight residual 107.73 112.85 -5.12 1.61e+00 3.86e-01 1.01e+01 angle pdb=" N ASP D 96 " pdb=" CA ASP D 96 " pdb=" C ASP D 96 " ideal model delta sigma weight residual 112.93 110.07 2.86 1.12e+00 7.97e-01 6.54e+00 angle pdb=" N TYR B 285 " pdb=" CA TYR B 285 " pdb=" C TYR B 285 " ideal model delta sigma weight residual 113.31 108.20 5.11 2.04e+00 2.40e-01 6.27e+00 angle pdb=" N ASP D 79 " pdb=" CA ASP D 79 " pdb=" C ASP D 79 " ideal model delta sigma weight residual 110.44 107.74 2.70 1.20e+00 6.94e-01 5.07e+00 ... (remaining 11563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4147 17.93 - 35.87: 525 35.87 - 53.80: 124 53.80 - 71.74: 17 71.74 - 89.67: 7 Dihedral angle restraints: 4820 sinusoidal: 1865 harmonic: 2955 Sorted by residual: dihedral pdb=" CA LEU B 283 " pdb=" C LEU B 283 " pdb=" N VAL B 284 " pdb=" CA VAL B 284 " ideal model delta harmonic sigma weight residual 180.00 161.63 18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LYS A 8 " pdb=" C LYS A 8 " pdb=" N PRO A 9 " pdb=" CA PRO A 9 " ideal model delta harmonic sigma weight residual -180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA LYS B 8 " pdb=" C LYS B 8 " pdb=" N PRO B 9 " pdb=" CA PRO B 9 " ideal model delta harmonic sigma weight residual -180.00 -162.88 -17.12 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 4817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 793 0.030 - 0.060: 315 0.060 - 0.090: 101 0.090 - 0.120: 46 0.120 - 0.149: 10 Chirality restraints: 1265 Sorted by residual: chirality pdb=" CA VAL B 284 " pdb=" N VAL B 284 " pdb=" C VAL B 284 " pdb=" CB VAL B 284 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE B 239 " pdb=" N ILE B 239 " pdb=" C ILE B 239 " pdb=" CB ILE B 239 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA MET A 214 " pdb=" N MET A 214 " pdb=" C MET A 214 " pdb=" CB MET A 214 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 1262 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 6 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO B 7 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 79 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C ASP D 79 " -0.026 2.00e-02 2.50e+03 pdb=" O ASP D 79 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN D 80 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 190 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" C ARG A 190 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG A 190 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL A 191 " -0.008 2.00e-02 2.50e+03 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1436 2.76 - 3.30: 7691 3.30 - 3.83: 14139 3.83 - 4.37: 15917 4.37 - 4.90: 28845 Nonbonded interactions: 68028 Sorted by model distance: nonbonded pdb=" N GLU D 95 " pdb=" OE1 GLU D 95 " model vdw 2.226 3.120 nonbonded pdb=" O TRP A 83 " pdb=" OG SER A 87 " model vdw 2.229 3.040 nonbonded pdb=" O VAL D 35 " pdb=" NH2 ARG D 78 " model vdw 2.237 3.120 nonbonded pdb=" OE2 GLU B 276 " pdb=" OH TYR B 309 " model vdw 2.259 3.040 nonbonded pdb=" O ARG A 51 " pdb=" OG SER A 54 " model vdw 2.270 3.040 ... (remaining 68023 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' } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 8 through 121) } 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: 1.000 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.840 Find NCS groups from input model: 0.120 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.003 0.034 8503 Z= 0.140 Angle : 0.529 6.629 11572 Z= 0.298 Chirality : 0.039 0.149 1265 Planarity : 0.004 0.039 1424 Dihedral : 16.467 89.671 2932 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 21.89 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.26), residues: 1007 helix: 1.80 (0.19), residues: 666 sheet: -0.54 (0.50), residues: 105 loop : -1.51 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.018 0.001 TYR B 162 PHE 0.013 0.001 PHE A 60 TRP 0.009 0.001 TRP B 53 HIS 0.002 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 8501) covalent geometry : angle 0.52915 / 0.30 (11568) SS BOND : bond 0.00017 / 0.01 ( 2) SS BOND : angle 0.71146 / 0.43 ( 4) hydrogen bonds : bond 0.10464 / 7.07 ( 591) hydrogen bonds : angle 5.11510 / 3.80 ( 1758) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.251 Fit side-chains REVERT: A 214 MET cc_start: 0.8427 (mtt) cc_final: 0.8222 (mtt) REVERT: B 214 MET cc_start: 0.8574 (mtt) cc_final: 0.8151 (mtt) REVERT: D 79 ASP cc_start: 0.6665 (t70) cc_final: 0.6361 (t0) REVERT: D 91 SER cc_start: 0.8253 (m) cc_final: 0.7959 (t) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.0916 time to fit residues: 11.5530 Evaluate side-chains 88 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.0000 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 GLN ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.155410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.114315 restraints weight = 8893.155| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.91 r_work: 0.3102 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8503 Z= 0.127 Angle : 0.468 6.609 11572 Z= 0.249 Chirality : 0.039 0.143 1265 Planarity : 0.004 0.041 1424 Dihedral : 6.271 59.188 1175 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.78 % Allowed : 22.13 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.26), residues: 1007 helix: 1.93 (0.19), residues: 686 sheet: -0.27 (0.51), residues: 103 loop : -1.33 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 78 TYR 0.017 0.001 TYR A 162 PHE 0.012 0.001 PHE A 60 TRP 0.008 0.001 TRP A 53 HIS 0.003 0.001 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 8501) covalent geometry : angle 0.46781 / 0.25 (11568) SS BOND : bond 0.00109 / 0.06 ( 2) SS BOND : angle 0.94252 / 0.57 ( 4) hydrogen bonds : bond 0.05008 / 3.31 ( 591) hydrogen bonds : angle 4.02779 / 3.00 ( 1758) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.289 Fit side-chains REVERT: A 180 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7301 (mm-40) REVERT: A 214 MET cc_start: 0.8283 (mtt) cc_final: 0.7954 (mtt) REVERT: B 83 TRP cc_start: 0.8641 (m100) cc_final: 0.8288 (m100) REVERT: B 214 MET cc_start: 0.8224 (mtt) cc_final: 0.7876 (mtt) REVERT: B 253 MET cc_start: 0.6563 (ppp) cc_final: 0.6300 (ppp) REVERT: C 89 MET cc_start: 0.7931 (mpp) cc_final: 0.7669 (mpp) outliers start: 15 outliers final: 8 residues processed: 95 average time/residue: 0.0970 time to fit residues: 12.5972 Evaluate side-chains 91 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain D residue 26 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.154509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.113166 restraints weight = 8864.501| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.91 r_work: 0.3086 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8503 Z= 0.136 Angle : 0.467 6.613 11572 Z= 0.247 Chirality : 0.039 0.147 1265 Planarity : 0.004 0.040 1424 Dihedral : 6.244 58.939 1175 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.25 % Allowed : 22.25 % Favored : 75.50 % 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 are not related in a simple way. whole: 1.60 (0.26), residues: 1007 helix: 1.97 (0.19), residues: 686 sheet: -0.09 (0.52), residues: 103 loop : -1.32 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 385 TYR 0.018 0.001 TYR A 162 PHE 0.012 0.001 PHE A 60 TRP 0.007 0.001 TRP A 53 HIS 0.003 0.001 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 8501) covalent geometry : angle 0.46717 / 0.25 (11568) SS BOND : bond 0.00012 / 0.01 ( 2) SS BOND : angle 0.68986 / 0.40 ( 4) hydrogen bonds : bond 0.05043 / 3.33 ( 591) hydrogen bonds : angle 3.93942 / 2.94 ( 1758) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.224 Fit side-chains REVERT: A 180 GLN cc_start: 0.7554 (mm-40) cc_final: 0.7291 (mm-40) REVERT: A 214 MET cc_start: 0.8234 (mtt) cc_final: 0.7993 (mtt) REVERT: B 214 MET cc_start: 0.8230 (mtt) cc_final: 0.8008 (mtt) REVERT: B 253 MET cc_start: 0.6529 (ppp) cc_final: 0.6234 (ppp) REVERT: C 89 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7718 (mpp) outliers start: 19 outliers final: 12 residues processed: 101 average time/residue: 0.0804 time to fit residues: 11.2413 Evaluate side-chains 96 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 89 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 0.0980 chunk 84 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.154292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.112988 restraints weight = 8989.597| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.94 r_work: 0.3101 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8503 Z= 0.122 Angle : 0.454 6.596 11572 Z= 0.238 Chirality : 0.038 0.149 1265 Planarity : 0.004 0.038 1424 Dihedral : 6.208 58.667 1175 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.49 % Allowed : 21.89 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.26), residues: 1007 helix: 2.09 (0.19), residues: 686 sheet: -0.05 (0.53), residues: 103 loop : -1.27 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 78 TYR 0.017 0.001 TYR A 162 PHE 0.012 0.001 PHE A 60 TRP 0.007 0.001 TRP A 53 HIS 0.003 0.001 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 8501) covalent geometry : angle 0.45394 / 0.24 (11568) SS BOND : bond 0.00134 / 0.07 ( 2) SS BOND : angle 0.65738 / 0.39 ( 4) hydrogen bonds : bond 0.04826 / 3.19 ( 591) hydrogen bonds : angle 3.84630 / 2.87 ( 1758) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.247 Fit side-chains REVERT: A 180 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7248 (mm-40) REVERT: B 173 TYR cc_start: 0.7536 (t80) cc_final: 0.7171 (t80) REVERT: B 181 LEU cc_start: 0.7846 (mt) cc_final: 0.7497 (mt) REVERT: B 253 MET cc_start: 0.6463 (ppp) cc_final: 0.6124 (ppp) REVERT: C 89 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7665 (mpp) REVERT: D 79 ASP cc_start: 0.7042 (t70) cc_final: 0.6189 (t0) outliers start: 21 outliers final: 15 residues processed: 102 average time/residue: 0.0890 time to fit residues: 12.5587 Evaluate side-chains 101 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.156317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115172 restraints weight = 8897.856| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.91 r_work: 0.3110 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8503 Z= 0.118 Angle : 0.454 6.592 11572 Z= 0.237 Chirality : 0.038 0.148 1265 Planarity : 0.003 0.038 1424 Dihedral : 6.146 58.986 1175 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.37 % Allowed : 22.49 % Favored : 75.15 % 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 are not related in a simple way. whole: 1.80 (0.26), residues: 1007 helix: 2.12 (0.19), residues: 688 sheet: 0.09 (0.53), residues: 103 loop : -1.36 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 78 TYR 0.017 0.001 TYR A 162 PHE 0.012 0.001 PHE A 60 TRP 0.007 0.001 TRP A 53 HIS 0.003 0.001 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 8501) covalent geometry : angle 0.45380 / 0.24 (11568) SS BOND : bond 0.00146 / 0.07 ( 2) SS BOND : angle 0.63078 / 0.37 ( 4) hydrogen bonds : bond 0.04732 / 3.13 ( 591) hydrogen bonds : angle 3.80314 / 2.84 ( 1758) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.189 Fit side-chains REVERT: A 180 GLN cc_start: 0.7527 (mm-40) cc_final: 0.7112 (mm-40) REVERT: A 214 MET cc_start: 0.8253 (mtt) cc_final: 0.7911 (mtt) REVERT: B 173 TYR cc_start: 0.7555 (t80) cc_final: 0.7201 (t80) REVERT: B 181 LEU cc_start: 0.7861 (mt) cc_final: 0.7531 (mt) REVERT: B 214 MET cc_start: 0.8264 (mtt) cc_final: 0.7896 (mtt) REVERT: B 253 MET cc_start: 0.6455 (ppp) cc_final: 0.6099 (ppp) REVERT: C 89 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7649 (mpp) REVERT: D 79 ASP cc_start: 0.7082 (t70) cc_final: 0.6223 (t0) outliers start: 20 outliers final: 17 residues processed: 101 average time/residue: 0.0746 time to fit residues: 10.7023 Evaluate side-chains 101 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 95 optimal weight: 0.0000 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 79 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.157633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.116553 restraints weight = 8793.346| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.90 r_work: 0.3125 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8503 Z= 0.112 Angle : 0.448 6.679 11572 Z= 0.233 Chirality : 0.038 0.149 1265 Planarity : 0.003 0.037 1424 Dihedral : 6.093 59.941 1175 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.25 % Allowed : 23.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.26), residues: 1007 helix: 2.23 (0.19), residues: 686 sheet: 0.21 (0.52), residues: 102 loop : -1.22 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 78 TYR 0.016 0.001 TYR A 162 PHE 0.011 0.001 PHE A 60 TRP 0.007 0.001 TRP B 53 HIS 0.002 0.001 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 8501) covalent geometry : angle 0.44750 / 0.23 (11568) SS BOND : bond 0.00142 / 0.07 ( 2) SS BOND : angle 0.55231 / 0.33 ( 4) hydrogen bonds : bond 0.04583 / 3.03 ( 591) hydrogen bonds : angle 3.74858 / 2.79 ( 1758) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.301 Fit side-chains REVERT: A 180 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7044 (mm-40) REVERT: A 214 MET cc_start: 0.8183 (mtt) cc_final: 0.7911 (mtt) REVERT: A 393 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6787 (tt) REVERT: B 173 TYR cc_start: 0.7556 (t80) cc_final: 0.7223 (t80) REVERT: B 181 LEU cc_start: 0.7834 (mt) cc_final: 0.7521 (mt) REVERT: B 214 MET cc_start: 0.8162 (mtt) cc_final: 0.7860 (mtt) REVERT: B 253 MET cc_start: 0.6534 (ppp) cc_final: 0.6168 (ppp) REVERT: C 89 MET cc_start: 0.8037 (mpp) cc_final: 0.7694 (mpp) REVERT: D 79 ASP cc_start: 0.7071 (t70) cc_final: 0.6217 (t0) outliers start: 19 outliers final: 16 residues processed: 101 average time/residue: 0.0747 time to fit residues: 10.6402 Evaluate side-chains 100 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.151994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.109998 restraints weight = 9041.599| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.94 r_work: 0.3034 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8503 Z= 0.198 Angle : 0.510 7.377 11572 Z= 0.269 Chirality : 0.041 0.151 1265 Planarity : 0.004 0.041 1424 Dihedral : 6.266 58.733 1175 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.84 % Allowed : 22.25 % Favored : 74.91 % 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 are not related in a simple way. whole: 1.65 (0.26), residues: 1007 helix: 2.04 (0.19), residues: 674 sheet: -0.02 (0.52), residues: 104 loop : -1.25 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.021 0.001 TYR B 162 PHE 0.012 0.001 PHE A 60 TRP 0.006 0.001 TRP A 75 HIS 0.004 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 ( 8501) covalent geometry : angle 0.50968 / 0.27 (11568) SS BOND : bond 0.00137 / 0.07 ( 2) SS BOND : angle 1.17679 / 0.72 ( 4) hydrogen bonds : bond 0.05573 / 3.67 ( 591) hydrogen bonds : angle 3.96609 / 2.97 ( 1758) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.264 Fit side-chains REVERT: A 180 GLN cc_start: 0.7543 (mm-40) cc_final: 0.7070 (mm-40) REVERT: A 214 MET cc_start: 0.8285 (mtt) cc_final: 0.8011 (mtt) REVERT: A 393 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6745 (tt) REVERT: B 214 MET cc_start: 0.8274 (mtt) cc_final: 0.7974 (mtt) REVERT: B 253 MET cc_start: 0.6598 (ppp) cc_final: 0.6204 (ppp) REVERT: C 89 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7677 (mpp) REVERT: D 79 ASP cc_start: 0.7266 (t70) cc_final: 0.6373 (t0) outliers start: 24 outliers final: 21 residues processed: 103 average time/residue: 0.0963 time to fit residues: 13.5884 Evaluate side-chains 104 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.154810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.113042 restraints weight = 8982.814| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.96 r_work: 0.3076 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8503 Z= 0.130 Angle : 0.460 6.577 11572 Z= 0.243 Chirality : 0.039 0.149 1265 Planarity : 0.004 0.036 1424 Dihedral : 6.269 59.221 1175 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.72 % Allowed : 22.25 % Favored : 75.03 % 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 are not related in a simple way. whole: 1.81 (0.26), residues: 1007 helix: 2.18 (0.19), residues: 676 sheet: 0.21 (0.53), residues: 102 loop : -1.36 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 385 TYR 0.017 0.001 TYR A 162 PHE 0.012 0.001 PHE A 60 TRP 0.006 0.001 TRP B 53 HIS 0.003 0.001 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8501) covalent geometry : angle 0.45959 / 0.24 (11568) SS BOND : bond 0.00112 / 0.05 ( 2) SS BOND : angle 0.82818 / 0.50 ( 4) hydrogen bonds : bond 0.04972 / 3.29 ( 591) hydrogen bonds : angle 3.83470 / 2.86 ( 1758) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.340 Fit side-chains REVERT: A 180 GLN cc_start: 0.7468 (mm-40) cc_final: 0.6998 (mm-40) REVERT: A 214 MET cc_start: 0.8266 (mtt) cc_final: 0.8020 (mtt) REVERT: A 393 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6696 (tt) REVERT: B 214 MET cc_start: 0.8249 (mtt) cc_final: 0.7975 (mtt) REVERT: B 253 MET cc_start: 0.6600 (ppp) cc_final: 0.6206 (ppp) REVERT: C 89 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7701 (mpp) REVERT: D 79 ASP cc_start: 0.7162 (t70) cc_final: 0.6270 (t0) outliers start: 23 outliers final: 19 residues processed: 99 average time/residue: 0.0793 time to fit residues: 11.3133 Evaluate side-chains 102 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9980 chunk 23 optimal weight: 0.0570 chunk 89 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.157007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115274 restraints weight = 8934.795| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.94 r_work: 0.3109 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8503 Z= 0.119 Angle : 0.448 6.605 11572 Z= 0.236 Chirality : 0.038 0.148 1265 Planarity : 0.004 0.039 1424 Dihedral : 6.184 59.694 1175 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.60 % Allowed : 22.49 % Favored : 74.91 % 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 are not related in a simple way. whole: 1.97 (0.26), residues: 1007 helix: 2.29 (0.19), residues: 676 sheet: 0.36 (0.52), residues: 102 loop : -1.31 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 385 TYR 0.017 0.001 TYR A 162 PHE 0.012 0.001 PHE A 60 TRP 0.007 0.001 TRP B 53 HIS 0.003 0.001 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 8501) covalent geometry : angle 0.44752 / 0.24 (11568) SS BOND : bond 0.00159 / 0.08 ( 2) SS BOND : angle 0.75183 / 0.44 ( 4) hydrogen bonds : bond 0.04700 / 3.11 ( 591) hydrogen bonds : angle 3.75276 / 2.79 ( 1758) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.226 Fit side-chains REVERT: A 180 GLN cc_start: 0.7415 (mm-40) cc_final: 0.6916 (mm-40) REVERT: A 214 MET cc_start: 0.8145 (mtt) cc_final: 0.7910 (mtt) REVERT: A 393 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6716 (tt) REVERT: B 173 TYR cc_start: 0.7557 (t80) cc_final: 0.7177 (t80) REVERT: B 214 MET cc_start: 0.8114 (mtt) cc_final: 0.7850 (mtt) REVERT: B 253 MET cc_start: 0.6539 (ppp) cc_final: 0.6147 (ppp) REVERT: C 89 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7773 (mpp) REVERT: D 79 ASP cc_start: 0.7148 (t70) cc_final: 0.6262 (t0) outliers start: 22 outliers final: 20 residues processed: 97 average time/residue: 0.0787 time to fit residues: 10.8414 Evaluate side-chains 103 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.146830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111839 restraints weight = 8893.421| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.50 r_work: 0.2965 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8503 Z= 0.193 Angle : 0.505 7.233 11572 Z= 0.267 Chirality : 0.040 0.148 1265 Planarity : 0.004 0.038 1424 Dihedral : 6.307 56.533 1175 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.84 % Allowed : 22.37 % Favored : 74.79 % 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 are not related in a simple way. whole: 1.66 (0.26), residues: 1007 helix: 2.05 (0.19), residues: 676 sheet: 0.14 (0.52), residues: 103 loop : -1.37 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 385 TYR 0.021 0.001 TYR B 162 PHE 0.012 0.001 PHE A 60 TRP 0.006 0.001 TRP A 75 HIS 0.004 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 ( 8501) covalent geometry : angle 0.50473 / 0.27 (11568) SS BOND : bond 0.00133 / 0.07 ( 2) SS BOND : angle 0.91780 / 0.56 ( 4) hydrogen bonds : bond 0.05556 / 3.66 ( 591) hydrogen bonds : angle 3.94904 / 2.95 ( 1758) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.322 Fit side-chains REVERT: A 180 GLN cc_start: 0.7465 (mm-40) cc_final: 0.6984 (mm-40) REVERT: A 214 MET cc_start: 0.8203 (mtt) cc_final: 0.7956 (mtt) REVERT: A 393 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6707 (tt) REVERT: B 214 MET cc_start: 0.8187 (mtt) cc_final: 0.7940 (mtt) REVERT: B 253 MET cc_start: 0.6626 (ppp) cc_final: 0.6222 (ppp) REVERT: C 89 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7626 (mpp) REVERT: D 79 ASP cc_start: 0.7107 (t70) cc_final: 0.6350 (t0) outliers start: 24 outliers final: 22 residues processed: 104 average time/residue: 0.0752 time to fit residues: 11.3640 Evaluate side-chains 108 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 89 MET Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.0870 chunk 22 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.151024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117181 restraints weight = 8855.355| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.54 r_work: 0.3047 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8503 Z= 0.119 Angle : 0.450 6.579 11572 Z= 0.237 Chirality : 0.038 0.147 1265 Planarity : 0.004 0.038 1424 Dihedral : 6.230 59.011 1175 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.57 % Favored : 96.33 % Rotamer: Outliers : 2.49 % Allowed : 23.20 % Favored : 74.32 % 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 are not related in a simple way. whole: 1.95 (0.26), residues: 1007 helix: 2.27 (0.19), residues: 676 sheet: 0.28 (0.52), residues: 102 loop : -1.30 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 385 TYR 0.016 0.001 TYR A 162 PHE 0.011 0.001 PHE A 60 TRP 0.008 0.001 TRP B 53 HIS 0.003 0.001 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 8501) covalent geometry : angle 0.44951 / 0.24 (11568) SS BOND : bond 0.00143 / 0.07 ( 2) SS BOND : angle 0.64771 / 0.39 ( 4) hydrogen bonds : bond 0.04738 / 3.13 ( 591) hydrogen bonds : angle 3.77124 / 2.81 ( 1758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1871.83 seconds wall clock time: 32 minutes 43.88 seconds (1963.88 seconds total)