Starting phenix.real_space_refine on Thu Oct 22 23:45:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21nz_67857/10_2026/21nz_67857.cif Found real_map, /net/cci-nas-00/data/ceres_data/21nz_67857/10_2026/21nz_67857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21nz_67857/10_2026/21nz_67857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21nz_67857/10_2026/21nz_67857.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21nz_67857/10_2026/21nz_67857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21nz_67857/10_2026/21nz_67857.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.052 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 26 5.16 5 C 4207 2.51 5 N 1157 2.21 5 O 1298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6688 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1374 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2549 Classifications: {'peptide': 313} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 294} Chain: "C" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2564 Classifications: {'peptide': 315} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 295} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.49, per 1000 atoms: 0.22 Number of scatterers: 6688 At special positions: 0 Unit cell: (77.9, 99.75, 127.3, 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 26 16.00 O 1298 8.00 N 1157 7.00 C 4207 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 200 " - pdb=" SG CYS C 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 396 " distance=2.04 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 184 " distance=2.03 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 396 " distance=2.04 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 BETA1-4 " NAG C 503 " - " NAG C 504 " " NAG C 504 " - " BMA C 505 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG B 501 " - " ASN B 240 " " NAG B 502 " - " ASN B 170 " " NAG C 501 " - " ASN C 170 " " NAG C 502 " - " ASN C 240 " " NAG C 503 " - " ASN C 265 " " NAG D 1 " - " ASN A 179 " " NAG E 1 " - " ASN A 62 " " NAG F 1 " - " ASN B 265 " Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 336.1 milliseconds 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1540 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 19 sheets defined 9.1% alpha, 48.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 216 through 222 Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 385 through 391 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.516A pdb=" N GLY C 284 " --> pdb=" O ASP C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 385 through 391 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.627A pdb=" N LEU A 101 " --> pdb=" O GLY A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 112 Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 152 removed outlier: 6.659A pdb=" N TYR A 140 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR A 149 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A 138 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N HIS A 151 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE A 136 " --> pdb=" O HIS A 151 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LYS A 137 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE A 174 " --> pdb=" O LYS A 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 152 removed outlier: 6.659A pdb=" N TYR A 140 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR A 149 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A 138 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N HIS A 151 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE A 136 " --> pdb=" O HIS A 151 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LYS A 137 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE A 174 " --> pdb=" O LYS A 137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 109 removed outlier: 3.548A pdb=" N SER B 167 " --> pdb=" O CYS B 125 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 165 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA B 163 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 168 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN B 152 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 213 removed outlier: 3.806A pdb=" N ASP B 234 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR B 268 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 247 Processing sheet with id=AB1, first strand: chain 'B' and resid 315 through 319 removed outlier: 3.704A pdb=" N THR B 333 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N PHE B 375 " --> pdb=" O ASN B 338 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 315 through 319 removed outlier: 3.704A pdb=" N THR B 333 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N PHE B 375 " --> pdb=" O ASN B 338 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 376 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 345 through 350 Processing sheet with id=AB4, first strand: chain 'C' and resid 104 through 109 removed outlier: 4.560A pdb=" N ALA C 163 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS C 157 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR C 166 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU C 155 " --> pdb=" O TYR C 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB6, first strand: chain 'C' and resid 209 through 213 removed outlier: 3.661A pdb=" N ASP C 234 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N THR C 268 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 242 through 246 removed outlier: 3.504A pdb=" N THR C 242 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 315 through 319 removed outlier: 3.797A pdb=" N THR C 333 " --> pdb=" O PHE C 319 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE C 375 " --> pdb=" O ASN C 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 315 through 319 removed outlier: 3.797A pdb=" N THR C 333 " --> pdb=" O PHE C 319 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE C 375 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG C 374 " --> pdb=" O TYR C 368 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 345 through 350 279 hydrogen bonds defined for protein. 705 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: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2150 1.34 - 1.46: 1478 1.46 - 1.58: 3190 1.58 - 1.70: 0 1.70 - 1.82: 31 Bond restraints: 6849 Sorted by residual: bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 BMA C 505 " pdb=" C2 BMA C 505 " ideal model delta sigma weight residual 1.519 1.547 -0.028 2.00e-02 2.50e+03 2.00e+00 bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.83e+00 ... (remaining 6844 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 9098 1.96 - 3.92: 166 3.92 - 5.88: 25 5.88 - 7.84: 5 7.84 - 9.80: 2 Bond angle restraints: 9296 Sorted by residual: angle pdb=" N THR C 149 " pdb=" CA THR C 149 " pdb=" C THR C 149 " ideal model delta sigma weight residual 112.68 103.88 8.80 1.33e+00 5.65e-01 4.37e+01 angle pdb=" N GLU C 148 " pdb=" CA GLU C 148 " pdb=" C GLU C 148 " ideal model delta sigma weight residual 108.63 98.83 9.80 1.60e+00 3.91e-01 3.75e+01 angle pdb=" C GLU C 148 " pdb=" CA GLU C 148 " pdb=" CB GLU C 148 " ideal model delta sigma weight residual 110.88 116.87 -5.99 1.60e+00 3.91e-01 1.40e+01 angle pdb=" N LYS A 63 " pdb=" CA LYS A 63 " pdb=" C LYS A 63 " ideal model delta sigma weight residual 108.58 101.96 6.62 1.82e+00 3.02e-01 1.32e+01 angle pdb=" C PRO A 52 " pdb=" N GLU A 53 " pdb=" CA GLU A 53 " ideal model delta sigma weight residual 122.61 127.86 -5.25 1.56e+00 4.11e-01 1.13e+01 ... (remaining 9291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 4018 21.90 - 43.80: 272 43.80 - 65.70: 27 65.70 - 87.61: 31 87.61 - 109.51: 13 Dihedral angle restraints: 4361 sinusoidal: 1999 harmonic: 2362 Sorted by residual: dihedral pdb=" CA ASP A 30 " pdb=" C ASP A 30 " pdb=" N PRO A 31 " pdb=" CA PRO A 31 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" O4 BMA C 505 " pdb=" C4 BMA C 505 " pdb=" C5 BMA C 505 " pdb=" O5 BMA C 505 " ideal model delta sinusoidal sigma weight residual 288.71 179.20 109.51 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.72 108.99 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 4358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 880 0.054 - 0.109: 143 0.109 - 0.163: 44 0.163 - 0.217: 2 0.217 - 0.271: 4 Chirality restraints: 1073 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 62 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C5 BMA C 505 " pdb=" C4 BMA C 505 " pdb=" C6 BMA C 505 " pdb=" O5 BMA C 505 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1070 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " 0.308 2.00e-02 2.50e+03 2.63e-01 8.62e+02 pdb=" C7 NAG C 502 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " -0.459 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 30 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 31 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 225 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO B 226 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 226 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 226 " -0.016 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1189 2.78 - 3.31: 5547 3.31 - 3.84: 10071 3.84 - 4.37: 12015 4.37 - 4.90: 21870 Nonbonded interactions: 50692 Sorted by model distance: nonbonded pdb=" NH2 ARG C 380 " pdb=" OE1 GLU C 382 " model vdw 2.255 3.120 nonbonded pdb=" NE1 TRP A 59 " pdb=" O ASP A 70 " model vdw 2.261 3.120 nonbonded pdb=" OE2 GLU B 238 " pdb=" OG SER B 260 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP A 106 " pdb=" N TRP A 107 " model vdw 2.301 3.120 nonbonded pdb=" NH2 ARG B 199 " pdb=" O CYS C 200 " model vdw 2.314 3.120 ... (remaining 50687 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 'B' and resid 103 through 501) selection = (chain 'C' and (resid 103 through 415 or resid 504)) } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.370 Find NCS groups from input model: 0.110 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:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 0.032 6873 Z= 0.163 Angle : 0.672 9.798 9359 Z= 0.346 Chirality : 0.049 0.271 1073 Planarity : 0.009 0.263 1167 Dihedral : 16.873 109.507 2794 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.29 (0.30), residues: 794 helix: -0.47 (0.64), residues: 58 sheet: 1.15 (0.28), residues: 350 loop : -1.51 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 87 TYR 0.013 0.001 TYR C 147 PHE 0.011 0.001 PHE C 339 TRP 0.010 0.001 TRP C 194 HIS 0.006 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 6849) covalent geometry : angle 0.65363 / 0.34 ( 9296) SS BOND : bond 0.00284 / 0.20 ( 9) SS BOND : angle 0.53951 / 0.32 ( 18) hydrogen bonds : bond 0.24496 / 15.98 ( 244) hydrogen bonds : angle 8.29429 / 5.79 ( 705) link_BETA1-4 : bond 0.00559 / 0.35 ( 7) link_BETA1-4 : angle 1.93301 / 1.10 ( 21) link_NAG-ASN : bond 0.00424 / 0.30 ( 8) link_NAG-ASN : angle 2.68957 / 1.39 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.279 Fit side-chains REVERT: B 338 ASN cc_start: 0.8083 (t0) cc_final: 0.7646 (t0) REVERT: C 251 LYS cc_start: 0.7182 (mttt) cc_final: 0.6851 (ttmm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.5047 time to fit residues: 41.5418 Evaluate side-chains 61 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 350 GLN ** 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 = 0.3738 r_free = 0.3738 target = 0.155962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118099 restraints weight = 7517.507| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.60 r_work: 0.3045 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 6873 Z= 0.226 Angle : 0.731 8.274 9359 Z= 0.368 Chirality : 0.051 0.193 1073 Planarity : 0.005 0.056 1167 Dihedral : 11.145 69.684 1178 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.22 % Allowed : 6.63 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.44 (0.29), residues: 794 helix: -0.83 (0.60), residues: 59 sheet: 1.10 (0.27), residues: 356 loop : -1.67 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 311 TYR 0.019 0.002 TYR C 166 PHE 0.022 0.002 PHE B 339 TRP 0.009 0.002 TRP B 194 HIS 0.005 0.002 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.23 ( 6849) covalent geometry : angle 0.70740 / 0.36 ( 9296) SS BOND : bond 0.00712 / 0.50 ( 9) SS BOND : angle 1.15802 / 0.68 ( 18) hydrogen bonds : bond 0.04579 / 3.07 ( 244) hydrogen bonds : angle 5.69899 / 3.98 ( 705) link_BETA1-4 : bond 0.00492 / 0.32 ( 7) link_BETA1-4 : angle 2.86809 / 1.69 ( 21) link_NAG-ASN : bond 0.00406 / 0.28 ( 8) link_NAG-ASN : angle 2.47579 / 1.32 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.467 Fit side-chains REVERT: B 219 ASP cc_start: 0.7059 (m-30) cc_final: 0.6752 (m-30) REVERT: B 338 ASN cc_start: 0.8572 (t0) cc_final: 0.8008 (t0) outliers start: 9 outliers final: 5 residues processed: 77 average time/residue: 0.4871 time to fit residues: 39.8455 Evaluate side-chains 63 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 277 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [5, 50, 48, 35, 42, 24, 64, 30, 72, 75, 4] chunk 5 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 64 optimal weight: 0.0670 chunk 30 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.160237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.123190 restraints weight = 7437.930| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.57 r_work: 0.3127 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6873 Z= 0.116 Angle : 0.601 7.545 9359 Z= 0.303 Chirality : 0.047 0.194 1073 Planarity : 0.004 0.034 1167 Dihedral : 8.737 58.650 1178 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.35 % Allowed : 9.34 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.17 (0.29), residues: 794 helix: -0.60 (0.62), residues: 58 sheet: 1.32 (0.27), residues: 354 loop : -1.52 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 198 TYR 0.011 0.001 TYR C 166 PHE 0.013 0.002 PHE C 376 TRP 0.007 0.001 TRP B 139 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 6849) covalent geometry : angle 0.57949 / 0.30 ( 9296) SS BOND : bond 0.00390 / 0.28 ( 9) SS BOND : angle 0.64632 / 0.35 ( 18) hydrogen bonds : bond 0.03527 / 2.37 ( 244) hydrogen bonds : angle 5.14647 / 3.59 ( 705) link_BETA1-4 : bond 0.00533 / 0.35 ( 7) link_BETA1-4 : angle 2.60762 / 1.55 ( 21) link_NAG-ASN : bond 0.00427 / 0.29 ( 8) link_NAG-ASN : angle 2.12053 / 1.19 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8728 (tt0) cc_final: 0.8262 (tp40) REVERT: A 177 ARG cc_start: 0.7853 (mmm-85) cc_final: 0.7555 (mpt-90) REVERT: B 199 ARG cc_start: 0.8641 (ttt-90) cc_final: 0.8362 (ttt-90) REVERT: B 219 ASP cc_start: 0.7071 (m-30) cc_final: 0.6768 (m-30) REVERT: B 338 ASN cc_start: 0.8413 (t0) cc_final: 0.7858 (t0) REVERT: C 251 LYS cc_start: 0.7058 (mttt) cc_final: 0.6649 (ttmm) outliers start: 10 outliers final: 6 residues processed: 73 average time/residue: 0.4528 time to fit residues: 35.1718 Evaluate side-chains 68 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 244 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [50, 7, 70, 74, 3, 21, 65, 61, 39, 37, 15] chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 3 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.157437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.120050 restraints weight = 7590.121| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.60 r_work: 0.3182 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6873 Z= 0.153 Angle : 0.623 6.920 9359 Z= 0.313 Chirality : 0.047 0.196 1073 Planarity : 0.004 0.036 1167 Dihedral : 7.639 55.964 1178 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.89 % Allowed : 10.42 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.11 (0.29), residues: 794 helix: -0.51 (0.62), residues: 59 sheet: 1.37 (0.27), residues: 355 loop : -1.51 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 198 TYR 0.016 0.002 TYR C 166 PHE 0.016 0.002 PHE B 339 TRP 0.009 0.001 TRP B 388 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 6849) covalent geometry : angle 0.60102 / 0.31 ( 9296) SS BOND : bond 0.00476 / 0.33 ( 9) SS BOND : angle 0.81526 / 0.45 ( 18) hydrogen bonds : bond 0.03555 / 2.40 ( 244) hydrogen bonds : angle 4.93266 / 3.44 ( 705) link_BETA1-4 : bond 0.00540 / 0.36 ( 7) link_BETA1-4 : angle 2.75402 / 1.63 ( 21) link_NAG-ASN : bond 0.00469 / 0.32 ( 8) link_NAG-ASN : angle 2.11237 / 1.19 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8771 (tt0) cc_final: 0.8353 (tp40) REVERT: A 177 ARG cc_start: 0.7925 (mmm-85) cc_final: 0.7567 (mpt-90) REVERT: B 153 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7765 (t0) REVERT: B 199 ARG cc_start: 0.8670 (ttt-90) cc_final: 0.8340 (ttt-90) REVERT: B 219 ASP cc_start: 0.7119 (m-30) cc_final: 0.6815 (m-30) REVERT: B 338 ASN cc_start: 0.8494 (t0) cc_final: 0.7889 (t0) REVERT: C 279 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6316 (mmtm) outliers start: 14 outliers final: 8 residues processed: 70 average time/residue: 0.4644 time to fit residues: 34.5839 Evaluate side-chains 69 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 279 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [74, 42, 68, 9, 35, 29, 65, 7, 4, 22, 8] chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 9 optimal weight: 0.0060 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.158276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.120960 restraints weight = 7628.859| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.59 r_work: 0.3177 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6873 Z= 0.164 Angle : 0.627 7.234 9359 Z= 0.316 Chirality : 0.048 0.197 1073 Planarity : 0.004 0.037 1167 Dihedral : 7.391 53.969 1178 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.03 % Allowed : 11.23 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.19 (0.29), residues: 794 helix: -0.65 (0.61), residues: 59 sheet: 1.33 (0.27), residues: 356 loop : -1.58 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 198 TYR 0.016 0.002 TYR C 166 PHE 0.017 0.002 PHE B 339 TRP 0.007 0.001 TRP B 388 HIS 0.005 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 ( 6849) covalent geometry : angle 0.60547 / 0.31 ( 9296) SS BOND : bond 0.00483 / 0.34 ( 9) SS BOND : angle 0.79132 / 0.44 ( 18) hydrogen bonds : bond 0.03555 / 2.42 ( 244) hydrogen bonds : angle 4.90981 / 3.42 ( 705) link_BETA1-4 : bond 0.00512 / 0.35 ( 7) link_BETA1-4 : angle 2.73767 / 1.60 ( 21) link_NAG-ASN : bond 0.00446 / 0.31 ( 8) link_NAG-ASN : angle 2.07459 / 1.16 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8795 (tt0) cc_final: 0.8319 (tp40) REVERT: A 177 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7682 (mpt-90) REVERT: B 199 ARG cc_start: 0.8643 (ttt-90) cc_final: 0.8352 (ttt-90) REVERT: B 219 ASP cc_start: 0.7212 (m-30) cc_final: 0.6903 (m-30) REVERT: B 338 ASN cc_start: 0.8531 (t0) cc_final: 0.7897 (t0) REVERT: C 251 LYS cc_start: 0.7115 (mttt) cc_final: 0.6724 (ttmm) REVERT: C 279 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6312 (mmtm) outliers start: 15 outliers final: 9 residues processed: 73 average time/residue: 0.4751 time to fit residues: 36.9072 Evaluate side-chains 69 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 279 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [51, 71, 20, 74, 67, 22, 73, 16, 31, 55, 33] chunk 51 optimal weight: 4.9990 chunk 71 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 67 optimal weight: 0.0980 chunk 22 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 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 = 0.3773 r_free = 0.3773 target = 0.159103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.121974 restraints weight = 7607.051| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.59 r_work: 0.3210 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6873 Z= 0.109 Angle : 0.561 5.783 9359 Z= 0.285 Chirality : 0.045 0.186 1073 Planarity : 0.004 0.034 1167 Dihedral : 6.515 47.969 1178 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.62 % Allowed : 11.64 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.02 (0.30), residues: 794 helix: -0.46 (0.62), residues: 58 sheet: 1.47 (0.28), residues: 352 loop : -1.46 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 198 TYR 0.012 0.001 TYR C 166 PHE 0.012 0.001 PHE C 376 TRP 0.006 0.001 TRP B 388 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 6849) covalent geometry : angle 0.54129 / 0.28 ( 9296) SS BOND : bond 0.00335 / 0.24 ( 9) SS BOND : angle 0.58315 / 0.31 ( 18) hydrogen bonds : bond 0.03045 / 2.08 ( 244) hydrogen bonds : angle 4.66383 / 3.25 ( 705) link_BETA1-4 : bond 0.00541 / 0.36 ( 7) link_BETA1-4 : angle 2.43515 / 1.44 ( 21) link_NAG-ASN : bond 0.00457 / 0.32 ( 8) link_NAG-ASN : angle 1.94299 / 1.10 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8677 (tt0) cc_final: 0.8136 (tp40) REVERT: A 177 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7483 (mpt-90) REVERT: B 199 ARG cc_start: 0.8626 (ttt-90) cc_final: 0.8343 (ttt-90) REVERT: B 219 ASP cc_start: 0.7201 (m-30) cc_final: 0.6907 (m-30) REVERT: B 338 ASN cc_start: 0.8388 (t0) cc_final: 0.7790 (t0) REVERT: B 367 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8339 (ttmm) REVERT: C 251 LYS cc_start: 0.7074 (mttt) cc_final: 0.6696 (ttmm) REVERT: C 279 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6308 (mmtm) outliers start: 12 outliers final: 10 residues processed: 74 average time/residue: 0.4558 time to fit residues: 35.9857 Evaluate side-chains 71 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 384 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [62, 50, 65, 55, 45, 32, 52, 14, 2, 1, 15] chunk 62 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 350 GLN ** 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 = 0.3775 r_free = 0.3775 target = 0.159404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122290 restraints weight = 7502.980| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.59 r_work: 0.3133 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6873 Z= 0.136 Angle : 0.590 7.916 9359 Z= 0.297 Chirality : 0.046 0.194 1073 Planarity : 0.004 0.035 1167 Dihedral : 6.490 41.789 1178 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.76 % Allowed : 12.31 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.06 (0.30), residues: 794 helix: -0.49 (0.62), residues: 58 sheet: 1.46 (0.28), residues: 353 loop : -1.52 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 198 TYR 0.015 0.001 TYR C 166 PHE 0.014 0.002 PHE B 339 TRP 0.007 0.001 TRP C 194 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 6849) covalent geometry : angle 0.56954 / 0.29 ( 9296) SS BOND : bond 0.00404 / 0.28 ( 9) SS BOND : angle 0.70019 / 0.38 ( 18) hydrogen bonds : bond 0.03219 / 2.20 ( 244) hydrogen bonds : angle 4.66391 / 3.25 ( 705) link_BETA1-4 : bond 0.00528 / 0.35 ( 7) link_BETA1-4 : angle 2.55975 / 1.50 ( 21) link_NAG-ASN : bond 0.00435 / 0.30 ( 8) link_NAG-ASN : angle 1.97771 / 1.11 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8694 (tt0) cc_final: 0.8273 (tp40) REVERT: A 177 ARG cc_start: 0.7856 (mmm-85) cc_final: 0.7519 (mpt-90) REVERT: B 199 ARG cc_start: 0.8636 (ttt-90) cc_final: 0.8327 (ttt-90) REVERT: B 219 ASP cc_start: 0.7250 (m-30) cc_final: 0.6944 (m-30) REVERT: B 338 ASN cc_start: 0.8465 (t0) cc_final: 0.7826 (t0) REVERT: B 367 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8297 (ttmm) REVERT: C 251 LYS cc_start: 0.7053 (mttt) cc_final: 0.6657 (ttmm) REVERT: C 279 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6311 (mmtm) outliers start: 13 outliers final: 11 residues processed: 71 average time/residue: 0.4783 time to fit residues: 36.1288 Evaluate side-chains 72 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 384 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [16, 40, 45, 67, 48, 76, 60, 58, 69, 17, 51] chunk 16 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 350 GLN ** 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 = 0.3772 r_free = 0.3772 target = 0.159031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.121958 restraints weight = 7607.245| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.58 r_work: 0.3185 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6873 Z= 0.143 Angle : 0.593 5.836 9359 Z= 0.300 Chirality : 0.047 0.193 1073 Planarity : 0.004 0.035 1167 Dihedral : 6.465 34.203 1178 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.44 % Allowed : 12.18 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.09 (0.29), residues: 794 helix: -0.55 (0.61), residues: 58 sheet: 1.42 (0.28), residues: 356 loop : -1.53 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 198 TYR 0.015 0.001 TYR C 166 PHE 0.015 0.002 PHE B 339 TRP 0.006 0.001 TRP B 388 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 6849) covalent geometry : angle 0.57272 / 0.30 ( 9296) SS BOND : bond 0.00420 / 0.29 ( 9) SS BOND : angle 0.71761 / 0.39 ( 18) hydrogen bonds : bond 0.03294 / 2.25 ( 244) hydrogen bonds : angle 4.68022 / 3.27 ( 705) link_BETA1-4 : bond 0.00509 / 0.34 ( 7) link_BETA1-4 : angle 2.57494 / 1.51 ( 21) link_NAG-ASN : bond 0.00427 / 0.29 ( 8) link_NAG-ASN : angle 1.98184 / 1.11 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ARG cc_start: 0.7883 (mmm-85) cc_final: 0.7542 (mpt-90) REVERT: B 219 ASP cc_start: 0.7301 (m-30) cc_final: 0.6999 (m-30) REVERT: B 222 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6671 (tt0) REVERT: B 338 ASN cc_start: 0.8474 (t0) cc_final: 0.7835 (t0) REVERT: B 367 LYS cc_start: 0.8615 (mtmt) cc_final: 0.8288 (ttmm) REVERT: C 251 LYS cc_start: 0.7045 (mttt) cc_final: 0.6656 (ttmm) REVERT: C 279 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6326 (mmtm) outliers start: 18 outliers final: 13 residues processed: 74 average time/residue: 0.4427 time to fit residues: 34.9402 Evaluate side-chains 73 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 384 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [1, 46, 12, 30, 75, 68, 78, 7, 20, 2, 61] chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 78 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.160803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123742 restraints weight = 7567.470| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.59 r_work: 0.3118 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6873 Z= 0.110 Angle : 0.563 9.119 9359 Z= 0.284 Chirality : 0.045 0.191 1073 Planarity : 0.004 0.034 1167 Dihedral : 5.885 32.339 1178 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.89 % Allowed : 13.26 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.05 (0.30), residues: 794 helix: -0.49 (0.62), residues: 58 sheet: 1.51 (0.28), residues: 353 loop : -1.41 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 198 TYR 0.012 0.001 TYR C 166 PHE 0.012 0.001 PHE C 376 TRP 0.006 0.001 TRP B 388 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6849) covalent geometry : angle 0.54431 / 0.28 ( 9296) SS BOND : bond 0.00323 / 0.23 ( 9) SS BOND : angle 0.59396 / 0.31 ( 18) hydrogen bonds : bond 0.02975 / 2.03 ( 244) hydrogen bonds : angle 4.54064 / 3.17 ( 705) link_BETA1-4 : bond 0.00527 / 0.35 ( 7) link_BETA1-4 : angle 2.36929 / 1.40 ( 21) link_NAG-ASN : bond 0.00435 / 0.30 ( 8) link_NAG-ASN : angle 1.88500 / 1.07 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 85 MET cc_start: 0.7284 (mmp) cc_final: 0.6971 (mmp) REVERT: A 100 GLN cc_start: 0.8697 (tt0) cc_final: 0.8151 (tp40) REVERT: A 177 ARG cc_start: 0.7806 (mmm-85) cc_final: 0.7481 (mpt-90) REVERT: B 199 ARG cc_start: 0.8651 (ttt-90) cc_final: 0.8326 (ttt-90) REVERT: B 219 ASP cc_start: 0.7288 (m-30) cc_final: 0.6975 (m-30) REVERT: B 222 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6637 (tt0) REVERT: B 338 ASN cc_start: 0.8390 (t0) cc_final: 0.7769 (t0) REVERT: B 367 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8250 (ttmm) REVERT: C 251 LYS cc_start: 0.7001 (mttt) cc_final: 0.6672 (ttmm) REVERT: C 279 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6302 (mmtm) outliers start: 14 outliers final: 12 residues processed: 72 average time/residue: 0.4764 time to fit residues: 36.4455 Evaluate side-chains 70 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 384 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [56, 11, 12, 28, 8, 9, 73, 29, 21, 3, 5] chunk 56 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 28 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.160500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.123498 restraints weight = 7521.141| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.58 r_work: 0.3152 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6873 Z= 0.102 Angle : 0.549 8.488 9359 Z= 0.278 Chirality : 0.045 0.185 1073 Planarity : 0.004 0.033 1167 Dihedral : 5.391 29.936 1178 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.89 % Allowed : 13.40 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.15 (0.30), residues: 794 helix: -0.35 (0.63), residues: 58 sheet: 1.56 (0.28), residues: 353 loop : -1.33 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 198 TYR 0.012 0.001 TYR C 166 PHE 0.012 0.001 PHE C 376 TRP 0.014 0.001 TRP C 194 HIS 0.002 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 6849) covalent geometry : angle 0.53076 / 0.27 ( 9296) SS BOND : bond 0.00309 / 0.22 ( 9) SS BOND : angle 0.55249 / 0.29 ( 18) hydrogen bonds : bond 0.02840 / 1.94 ( 244) hydrogen bonds : angle 4.42842 / 3.08 ( 705) link_BETA1-4 : bond 0.00526 / 0.35 ( 7) link_BETA1-4 : angle 2.25420 / 1.34 ( 21) link_NAG-ASN : bond 0.00574 / 0.40 ( 8) link_NAG-ASN : angle 1.90499 / 1.10 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.7332 (mmp) cc_final: 0.7051 (mmp) REVERT: A 100 GLN cc_start: 0.8628 (tt0) cc_final: 0.8220 (tp40) REVERT: A 177 ARG cc_start: 0.7745 (mmm-85) cc_final: 0.7506 (mpt-90) REVERT: B 199 ARG cc_start: 0.8654 (ttt-90) cc_final: 0.8335 (ttt-90) REVERT: B 219 ASP cc_start: 0.7376 (m-30) cc_final: 0.7073 (m-30) REVERT: B 222 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6323 (mm-30) REVERT: B 239 GLU cc_start: 0.7548 (mm-30) cc_final: 0.6922 (mt-10) REVERT: B 338 ASN cc_start: 0.8366 (t0) cc_final: 0.7746 (t0) REVERT: B 367 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8291 (ttmm) REVERT: C 251 LYS cc_start: 0.6993 (mttt) cc_final: 0.6660 (ttmm) REVERT: C 279 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6281 (mmtm) outliers start: 14 outliers final: 11 residues processed: 69 average time/residue: 0.4583 time to fit residues: 33.8926 Evaluate side-chains 69 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 259 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 384 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [38, 45, 16, 48, 22, 72, 75, 54, 42, 34, 56] chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.156626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119446 restraints weight = 7501.147| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.57 r_work: 0.3098 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6873 Z= 0.187 Angle : 0.645 8.548 9359 Z= 0.323 Chirality : 0.048 0.201 1073 Planarity : 0.005 0.041 1167 Dihedral : 6.472 35.691 1178 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.17 % Allowed : 13.26 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.09 (0.29), residues: 794 helix: -0.72 (0.60), residues: 59 sheet: 1.40 (0.28), residues: 356 loop : -1.49 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 198 TYR 0.019 0.002 TYR C 166 PHE 0.019 0.002 PHE B 339 TRP 0.020 0.002 TRP C 194 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 ( 6849) covalent geometry : angle 0.62491 / 0.32 ( 9296) SS BOND : bond 0.00483 / 0.33 ( 9) SS BOND : angle 0.85992 / 0.48 ( 18) hydrogen bonds : bond 0.03537 / 2.41 ( 244) hydrogen bonds : angle 4.71720 / 3.30 ( 705) link_BETA1-4 : bond 0.00474 / 0.33 ( 7) link_BETA1-4 : angle 2.71763 / 1.59 ( 21) link_NAG-ASN : bond 0.00467 / 0.32 ( 8) link_NAG-ASN : angle 2.04234 / 1.15 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1846.49 seconds wall clock time: 32 minutes 17.44 seconds (1937.44 seconds total)