Starting phenix.real_space_refine on Thu Jul 2 01:56:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qb9_13882/07_2026/7qb9_13882.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qb9_13882/07_2026/7qb9_13882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qb9_13882/07_2026/7qb9_13882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qb9_13882/07_2026/7qb9_13882.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7qb9_13882/07_2026/7qb9_13882.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qb9_13882/07_2026/7qb9_13882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qb9_13882/07_2026/7qb9_13882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qb9_13882/07_2026/7qb9_13882.map" } resolution = 3.1 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= 0.003 sd= 0.119 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 21 5.16 5 C 3732 2.51 5 N 732 2.21 5 O 934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s 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: 5419 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2295 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 290} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2298 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 290} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 413 Unusual residues: {'NAG': 2, 'Y01': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 413 Unusual residues: {'NAG': 2, 'Y01': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.25, per 1000 atoms: 0.23 Number of scatterers: 5419 At special positions: 0 Unit cell: (81.2736, 83.8134, 100.745, 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 21 16.00 O 934 8.00 N 732 7.00 C 3732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 25 " " NAG A 502 " - " ASN A 32 " " NAG B 501 " - " ASN B 25 " " NAG B 502 " - " ASN B 32 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 193.8 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1136 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 75.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 9 through 14 removed outlier: 3.506A pdb=" N PHE A 12 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 14 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 73 removed outlier: 3.638A pdb=" N SER A 47 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 103 removed outlier: 3.856A pdb=" N LEU A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.600A pdb=" N ILE A 120 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 154 removed outlier: 3.806A pdb=" N THR A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 195 removed outlier: 4.070A pdb=" N THR A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 236 removed outlier: 3.705A pdb=" N PHE A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.745A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 272 Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.653A pdb=" N THR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 297 Proline residue: A 290 - end of helix removed outlier: 3.714A pdb=" N MET A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 14 removed outlier: 3.505A pdb=" N PHE B 12 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 14 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 73 removed outlier: 3.637A pdb=" N SER B 47 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET B 54 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 103 removed outlier: 3.857A pdb=" N LEU B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE B 89 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.601A pdb=" N ILE B 120 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 154 removed outlier: 3.806A pdb=" N THR B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN B 132 " --> pdb=" O TYR B 128 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 136 " --> pdb=" O ASN B 132 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 153 " --> pdb=" O GLN B 149 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 195 removed outlier: 4.069A pdb=" N THR B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B 173 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 236 removed outlier: 3.668A pdb=" N PHE B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 256 through 266 removed outlier: 3.746A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 272 Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.653A pdb=" N THR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 297 Proline residue: B 290 - end of helix removed outlier: 3.714A pdb=" N MET B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 28 removed outlier: 6.507A pdb=" N SER A 28 " --> pdb=" O ASN A 32 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 28 removed outlier: 6.507A pdb=" N SER B 28 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 852 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: 0.92 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 749 1.31 - 1.44: 1357 1.44 - 1.56: 3413 1.56 - 1.68: 22 1.68 - 1.81: 38 Bond restraints: 5579 Sorted by residual: bond pdb=" C7 NAG B 501 " pdb=" N2 NAG B 501 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C7 NAG A 501 " pdb=" N2 NAG A 501 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C7 NAG A 502 " pdb=" N2 NAG A 502 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C7 NAG B 502 " pdb=" N2 NAG B 502 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C1 NAG B 502 " pdb=" O5 NAG B 502 " ideal model delta sigma weight residual 1.406 1.510 -0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 5574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 7140 1.80 - 3.61: 472 3.61 - 5.41: 85 5.41 - 7.21: 16 7.21 - 9.02: 4 Bond angle restraints: 7717 Sorted by residual: angle pdb=" N PHE B 204 " pdb=" CA PHE B 204 " pdb=" C PHE B 204 " ideal model delta sigma weight residual 111.54 106.03 5.51 1.36e+00 5.41e-01 1.64e+01 angle pdb=" N PHE A 204 " pdb=" CA PHE A 204 " pdb=" C PHE A 204 " ideal model delta sigma weight residual 111.54 106.24 5.30 1.36e+00 5.41e-01 1.52e+01 angle pdb=" N PHE B 235 " pdb=" CA PHE B 235 " pdb=" C PHE B 235 " ideal model delta sigma weight residual 111.28 107.10 4.18 1.09e+00 8.42e-01 1.47e+01 angle pdb=" N TYR B 106 " pdb=" CA TYR B 106 " pdb=" C TYR B 106 " ideal model delta sigma weight residual 113.23 108.60 4.63 1.24e+00 6.50e-01 1.39e+01 angle pdb=" N PHE A 235 " pdb=" CA PHE A 235 " pdb=" C PHE A 235 " ideal model delta sigma weight residual 111.28 107.23 4.05 1.09e+00 8.42e-01 1.38e+01 ... (remaining 7712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 2721 15.26 - 30.52: 234 30.52 - 45.78: 63 45.78 - 61.03: 19 61.03 - 76.29: 4 Dihedral angle restraints: 3041 sinusoidal: 1283 harmonic: 1758 Sorted by residual: dihedral pdb=" CA ILE A 263 " pdb=" C ILE A 263 " pdb=" N LEU A 264 " pdb=" CA LEU A 264 " ideal model delta harmonic sigma weight residual 180.00 160.44 19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ILE B 263 " pdb=" C ILE B 263 " pdb=" N LEU B 264 " pdb=" CA LEU B 264 " ideal model delta harmonic sigma weight residual 180.00 160.48 19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" N ASN A 25 " pdb=" C ASN A 25 " pdb=" CA ASN A 25 " pdb=" CB ASN A 25 " ideal model delta harmonic sigma weight residual 122.80 114.48 8.32 0 2.50e+00 1.60e-01 1.11e+01 ... (remaining 3038 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 883 0.079 - 0.157: 98 0.157 - 0.236: 12 0.236 - 0.314: 5 0.314 - 0.393: 2 Chirality restraints: 1000 Sorted by residual: chirality pdb=" CBC Y01 A 513 " pdb=" CAR Y01 A 513 " pdb=" CAV Y01 A 513 " pdb=" OAW Y01 A 513 " both_signs ideal model delta sigma weight residual False -2.54 -2.15 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CBC Y01 A 509 " pdb=" CAR Y01 A 509 " pdb=" CAV Y01 A 509 " pdb=" OAW Y01 A 509 " both_signs ideal model delta sigma weight residual False -2.54 -2.19 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA ASN A 25 " pdb=" N ASN A 25 " pdb=" C ASN A 25 " pdb=" CB ASN A 25 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 997 not shown) Planarity restraints: 820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 269 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO A 270 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 269 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO B 270 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 247 " -0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C LEU B 247 " 0.068 2.00e-02 2.50e+03 pdb=" O LEU B 247 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU B 248 " -0.023 2.00e-02 2.50e+03 ... (remaining 817 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1313 2.81 - 3.33: 4887 3.33 - 3.86: 7972 3.86 - 4.38: 9176 4.38 - 4.90: 16024 Nonbonded interactions: 39372 Sorted by model distance: nonbonded pdb=" O ILE B 175 " pdb=" OG1 THR B 179 " model vdw 2.291 3.040 nonbonded pdb=" O ILE A 175 " pdb=" OG1 THR A 179 " model vdw 2.291 3.040 nonbonded pdb=" O ALA B 61 " pdb=" OG1 THR B 65 " model vdw 2.317 3.040 nonbonded pdb=" O ALA A 61 " pdb=" OG1 THR A 65 " model vdw 2.317 3.040 nonbonded pdb=" O ASN A 46 " pdb=" OG1 THR A 50 " model vdw 2.340 3.040 ... (remaining 39367 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 5 through 249 or (resid 250 and (name N or name CA or name \ C or name O or name CB )) or resid 251 through 513)) } 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.550 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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: 9.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 : 0.008 0.128 5583 Z= 0.430 Angle : 1.018 9.016 7729 Z= 0.546 Chirality : 0.056 0.393 1000 Planarity : 0.010 0.108 816 Dihedral : 13.205 76.292 1905 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: -2.92 (0.29), residues: 594 helix: -1.69 (0.22), residues: 416 sheet: None (None), residues: 0 loop : -2.11 (0.37), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 58 TYR 0.025 0.002 TYR B 266 PHE 0.042 0.003 PHE A 262 TRP 0.012 0.002 TRP B 70 HIS 0.004 0.002 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00811 / 0.43 ( 5579) covalent geometry : angle 1.01256 / 0.54 ( 7717) hydrogen bonds : bond 0.13577 / 8.86 ( 290) hydrogen bonds : angle 5.42656 / 3.78 ( 852) link_NAG-ASN : bond 0.01418 / 0.62 ( 4) link_NAG-ASN : angle 2.92721 / 2.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.124 Fit side-chains REVERT: A 218 MET cc_start: 0.8242 (tpt) cc_final: 0.7568 (tpt) REVERT: B 180 MET cc_start: 0.7601 (tpt) cc_final: 0.7273 (tpp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0635 time to fit residues: 4.1033 Evaluate side-chains 42 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.179104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125369 restraints weight = 5619.679| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.26 r_work: 0.3287 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 0.027 5583 Z= 0.131 Angle : 0.546 5.640 7729 Z= 0.274 Chirality : 0.038 0.204 1000 Planarity : 0.005 0.066 816 Dihedral : 9.139 59.599 924 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.97 % Allowed : 6.41 % Favored : 92.62 % 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: -0.51 (0.32), residues: 594 helix: 0.33 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -1.82 (0.39), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 58 TYR 0.019 0.001 TYR B 266 PHE 0.024 0.002 PHE B 244 TRP 0.010 0.001 TRP B 70 HIS 0.004 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 5579) covalent geometry : angle 0.53848 / 0.27 ( 7717) hydrogen bonds : bond 0.06057 / 3.83 ( 290) hydrogen bonds : angle 3.99924 / 2.81 ( 852) link_NAG-ASN : bond 0.00738 / 0.37 ( 4) link_NAG-ASN : angle 2.39217 / 1.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.166 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 50 average time/residue: 0.0522 time to fit residues: 3.7762 Evaluate side-chains 42 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain B residue 190 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.174527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.120503 restraints weight = 5649.791| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.26 r_work: 0.3183 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5583 Z= 0.143 Angle : 0.541 5.715 7729 Z= 0.263 Chirality : 0.038 0.196 1000 Planarity : 0.004 0.054 816 Dihedral : 8.988 59.712 924 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.94 % Allowed : 7.77 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.61 (0.35), residues: 594 helix: 1.27 (0.27), residues: 408 sheet: None (None), residues: 0 loop : -1.54 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 58 TYR 0.020 0.001 TYR A 266 PHE 0.017 0.002 PHE B 55 TRP 0.010 0.001 TRP A 70 HIS 0.004 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 5579) covalent geometry : angle 0.53634 / 0.26 ( 7717) hydrogen bonds : bond 0.06256 / 3.96 ( 290) hydrogen bonds : angle 3.76841 / 2.66 ( 852) link_NAG-ASN : bond 0.00510 / 0.26 ( 4) link_NAG-ASN : angle 1.91378 / 1.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 244 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6053 (m-80) outliers start: 10 outliers final: 6 residues processed: 57 average time/residue: 0.0454 time to fit residues: 3.6999 Evaluate side-chains 51 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 244 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 48 optimal weight: 0.0370 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.177513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122396 restraints weight = 5674.171| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.37 r_work: 0.3218 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5583 Z= 0.108 Angle : 0.476 4.978 7729 Z= 0.232 Chirality : 0.036 0.183 1000 Planarity : 0.004 0.049 816 Dihedral : 8.649 58.767 924 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.94 % Allowed : 10.10 % Favored : 87.96 % 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: 1.22 (0.36), residues: 594 helix: 1.69 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -1.33 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 58 TYR 0.017 0.001 TYR A 266 PHE 0.013 0.001 PHE B 244 TRP 0.006 0.001 TRP A 70 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 5579) covalent geometry : angle 0.46771 / 0.23 ( 7717) hydrogen bonds : bond 0.05125 / 3.25 ( 290) hydrogen bonds : angle 3.50583 / 2.46 ( 852) link_NAG-ASN : bond 0.00550 / 0.27 ( 4) link_NAG-ASN : angle 2.23696 / 1.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: B 228 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.7031 (tt) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.0449 time to fit residues: 3.4323 Evaluate side-chains 51 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.171251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116530 restraints weight = 5752.360| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.33 r_work: 0.3139 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5583 Z= 0.155 Angle : 0.559 5.170 7729 Z= 0.266 Chirality : 0.039 0.183 1000 Planarity : 0.004 0.047 816 Dihedral : 8.943 59.615 924 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.52 % Allowed : 9.90 % Favored : 87.57 % 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: 1.14 (0.35), residues: 594 helix: 1.62 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -1.36 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 58 TYR 0.016 0.001 TYR B 266 PHE 0.018 0.002 PHE B 55 TRP 0.004 0.001 TRP B 295 HIS 0.004 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 5579) covalent geometry : angle 0.55181 / 0.26 ( 7717) hydrogen bonds : bond 0.06633 / 4.20 ( 290) hydrogen bonds : angle 3.71580 / 2.61 ( 852) link_NAG-ASN : bond 0.00723 / 0.35 ( 4) link_NAG-ASN : angle 2.38438 / 1.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6915 (OUTLIER) cc_final: 0.6104 (m-80) REVERT: B 228 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7042 (tt) REVERT: B 244 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6154 (m-80) outliers start: 13 outliers final: 10 residues processed: 51 average time/residue: 0.0490 time to fit residues: 3.5241 Evaluate side-chains 57 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 244 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.173059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118561 restraints weight = 5660.191| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.30 r_work: 0.3203 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5583 Z= 0.122 Angle : 0.505 5.154 7729 Z= 0.242 Chirality : 0.038 0.251 1000 Planarity : 0.003 0.045 816 Dihedral : 8.757 58.454 924 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.52 % Allowed : 10.49 % Favored : 86.99 % 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: 1.57 (0.36), residues: 594 helix: 1.96 (0.27), residues: 416 sheet: None (None), residues: 0 loop : -1.23 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 58 TYR 0.014 0.001 TYR A 266 PHE 0.012 0.001 PHE B 244 TRP 0.005 0.001 TRP B 70 HIS 0.004 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 5579) covalent geometry : angle 0.49495 / 0.24 ( 7717) hydrogen bonds : bond 0.05599 / 3.55 ( 290) hydrogen bonds : angle 3.52764 / 2.46 ( 852) link_NAG-ASN : bond 0.00615 / 0.30 ( 4) link_NAG-ASN : angle 2.59615 / 1.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6826 (OUTLIER) cc_final: 0.6114 (m-80) REVERT: B 228 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6923 (tt) REVERT: B 244 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.6144 (m-80) outliers start: 13 outliers final: 7 residues processed: 55 average time/residue: 0.0513 time to fit residues: 4.0105 Evaluate side-chains 55 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 244 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.172863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118256 restraints weight = 5718.019| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.33 r_work: 0.3183 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5583 Z= 0.133 Angle : 0.519 5.220 7729 Z= 0.248 Chirality : 0.038 0.197 1000 Planarity : 0.003 0.044 816 Dihedral : 8.853 57.876 924 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.52 % Allowed : 10.68 % Favored : 86.80 % 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 (0.36), residues: 594 helix: 2.05 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -1.28 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 58 TYR 0.014 0.001 TYR B 266 PHE 0.015 0.001 PHE B 55 TRP 0.004 0.001 TRP B 70 HIS 0.004 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 5579) covalent geometry : angle 0.51145 / 0.25 ( 7717) hydrogen bonds : bond 0.05950 / 3.77 ( 290) hydrogen bonds : angle 3.56287 / 2.49 ( 852) link_NAG-ASN : bond 0.00583 / 0.29 ( 4) link_NAG-ASN : angle 2.32798 / 1.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6879 (OUTLIER) cc_final: 0.6173 (m-80) REVERT: B 228 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6970 (tt) REVERT: B 244 PHE cc_start: 0.6855 (OUTLIER) cc_final: 0.6155 (m-80) outliers start: 13 outliers final: 9 residues processed: 56 average time/residue: 0.0425 time to fit residues: 3.4071 Evaluate side-chains 59 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 244 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 0.0170 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 0.0470 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.173841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.119342 restraints weight = 5626.098| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.31 r_work: 0.3204 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5583 Z= 0.116 Angle : 0.497 5.400 7729 Z= 0.237 Chirality : 0.038 0.209 1000 Planarity : 0.003 0.044 816 Dihedral : 8.735 58.011 924 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.33 % Allowed : 10.87 % Favored : 86.80 % 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: 1.91 (0.36), residues: 594 helix: 2.32 (0.27), residues: 408 sheet: None (None), residues: 0 loop : -1.23 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 58 TYR 0.014 0.001 TYR B 266 PHE 0.012 0.001 PHE B 55 TRP 0.005 0.001 TRP B 70 HIS 0.004 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 5579) covalent geometry : angle 0.48773 / 0.24 ( 7717) hydrogen bonds : bond 0.05441 / 3.45 ( 290) hydrogen bonds : angle 3.47484 / 2.43 ( 852) link_NAG-ASN : bond 0.00638 / 0.31 ( 4) link_NAG-ASN : angle 2.42627 / 1.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6867 (OUTLIER) cc_final: 0.6199 (m-80) REVERT: B 228 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6935 (tt) REVERT: B 244 PHE cc_start: 0.6844 (OUTLIER) cc_final: 0.6181 (m-80) outliers start: 12 outliers final: 8 residues processed: 56 average time/residue: 0.0509 time to fit residues: 4.0208 Evaluate side-chains 59 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 244 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 29 optimal weight: 0.0050 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.171008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.116892 restraints weight = 5692.309| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.28 r_work: 0.3150 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5583 Z= 0.140 Angle : 0.537 5.409 7729 Z= 0.254 Chirality : 0.039 0.194 1000 Planarity : 0.003 0.045 816 Dihedral : 9.054 59.265 924 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.14 % Allowed : 11.46 % Favored : 86.41 % 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 (0.36), residues: 594 helix: 2.25 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.30 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 58 TYR 0.015 0.001 TYR A 266 PHE 0.015 0.001 PHE A 55 TRP 0.005 0.001 TRP A 70 HIS 0.004 0.001 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 5579) covalent geometry : angle 0.52785 / 0.25 ( 7717) hydrogen bonds : bond 0.06193 / 3.93 ( 290) hydrogen bonds : angle 3.61332 / 2.53 ( 852) link_NAG-ASN : bond 0.00599 / 0.29 ( 4) link_NAG-ASN : angle 2.58474 / 1.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.6255 (m-80) REVERT: B 228 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6998 (tt) REVERT: B 244 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6237 (m-80) outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 0.0489 time to fit residues: 3.8044 Evaluate side-chains 58 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 244 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 2 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.173772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119830 restraints weight = 5657.793| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.28 r_work: 0.3194 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5583 Z= 0.115 Angle : 0.495 5.455 7729 Z= 0.235 Chirality : 0.037 0.191 1000 Planarity : 0.003 0.044 816 Dihedral : 8.818 58.518 924 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.33 % Allowed : 11.26 % Favored : 86.41 % 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: 2.03 (0.36), residues: 594 helix: 2.35 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -1.19 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 74 TYR 0.014 0.001 TYR B 266 PHE 0.012 0.001 PHE A 171 TRP 0.007 0.001 TRP A 70 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 5579) covalent geometry : angle 0.48488 / 0.23 ( 7717) hydrogen bonds : bond 0.05310 / 3.37 ( 290) hydrogen bonds : angle 3.44977 / 2.40 ( 852) link_NAG-ASN : bond 0.00623 / 0.30 ( 4) link_NAG-ASN : angle 2.59115 / 1.63 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.6910 (OUTLIER) cc_final: 0.6244 (m-80) REVERT: B 228 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6898 (tt) REVERT: B 244 PHE cc_start: 0.6865 (OUTLIER) cc_final: 0.6221 (m-80) outliers start: 12 outliers final: 8 residues processed: 57 average time/residue: 0.0574 time to fit residues: 4.6775 Evaluate side-chains 60 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 244 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 1 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.175556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121724 restraints weight = 5623.981| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.28 r_work: 0.3220 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5583 Z= 0.103 Angle : 0.471 5.516 7729 Z= 0.225 Chirality : 0.036 0.184 1000 Planarity : 0.003 0.044 816 Dihedral : 8.502 58.450 924 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.33 % Allowed : 11.46 % Favored : 86.21 % 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: 2.17 (0.36), residues: 594 helix: 2.46 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -1.14 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 58 TYR 0.014 0.001 TYR A 266 PHE 0.012 0.001 PHE B 171 TRP 0.006 0.001 TRP A 70 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 5579) covalent geometry : angle 0.46010 / 0.22 ( 7717) hydrogen bonds : bond 0.04817 / 3.06 ( 290) hydrogen bonds : angle 3.33222 / 2.32 ( 852) link_NAG-ASN : bond 0.00643 / 0.31 ( 4) link_NAG-ASN : angle 2.59991 / 1.63 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1033.38 seconds wall clock time: 18 minutes 24.75 seconds (1104.75 seconds total)