Starting phenix.real_space_refine on Fri Aug 22 18:03:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k7s_36940/08_2025/8k7s_36940.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k7s_36940/08_2025/8k7s_36940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k7s_36940/08_2025/8k7s_36940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k7s_36940/08_2025/8k7s_36940.map" model { file = "/net/cci-nas-00/data/ceres_data/8k7s_36940/08_2025/8k7s_36940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k7s_36940/08_2025/8k7s_36940.cif" } resolution = 3.51 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= 0.001 sd= 0.057 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 27 5.16 5 C 4202 2.51 5 N 1083 2.21 5 O 1333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6645 Number of models: 1 Model: "" Number of chains: 9 Chain: "F" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2519 Classifications: {'peptide': 316} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 295} Chain: "A" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1372 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain: "E" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2523 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 296} Chain: "x" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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 Chain: "y" 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: "z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.81, per 1000 atoms: 0.27 Number of scatterers: 6645 At special positions: 0 Unit cell: (78.02, 101.26, 126.16, 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 27 16.00 O 1333 8.00 N 1083 7.00 C 4202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS F 108 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 121 " - pdb=" SG CYS F 180 " distance=2.03 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 226 " - pdb=" SG CYS F 285 " distance=2.03 Simple disulfide: pdb=" SG CYS F 330 " - pdb=" SG CYS F 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 93 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 180 " distance=2.03 Simple disulfide: pdb=" SG CYS E 226 " - pdb=" SG CYS E 285 " distance=2.03 Simple disulfide: pdb=" SG CYS E 330 " - pdb=" SG CYS E 392 " 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 ALPHA1-3 " BMA x 3 " - " MAN x 4 " " BMA z 3 " - " MAN z 4 " ALPHA1-6 " BMA x 3 " - " MAN x 5 " " BMA z 3 " - " MAN z 5 " BETA1-4 " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG A 301 " - " ASN A 160 " " NAG A 302 " - " ASN A 46 " " NAG A 303 " - " ASN A 191 " " NAG E 501 " - " ASN E 238 " " NAG F 501 " - " ASN F 238 " " NAG x 1 " - " ASN F 261 " " NAG y 1 " - " ASN A 67 " " NAG z 1 " - " ASN E 261 " Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 365.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1532 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 17 sheets defined 7.5% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 212 through 218 Processing helix chain 'F' and resid 273 through 280 removed outlier: 3.733A pdb=" N TRP F 277 " --> pdb=" O VAL F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 386 removed outlier: 3.542A pdb=" N GLN F 386 " --> pdb=" O THR F 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'E' and resid 169 through 173 Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 352 through 356 Processing sheet with id=AA1, first strand: chain 'F' and resid 150 through 154 removed outlier: 6.746A pdb=" N SER F 160 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER F 163 " --> pdb=" O CYS F 121 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLN F 118 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER F 106 " --> pdb=" O GLN F 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR F 124 " --> pdb=" O THR F 100 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N HIS F 105 " --> pdb=" O HIS E 105 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N HIS E 105 " --> pdb=" O HIS F 105 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N CYS E 162 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU E 151 " --> pdb=" O CYS E 162 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LYS E 164 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N THR E 149 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASN E 166 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA E 147 " --> pdb=" O ASN E 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 132 through 136 Processing sheet with id=AA3, first strand: chain 'F' and resid 205 through 209 removed outlier: 3.976A pdb=" N ASP F 230 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR F 264 " --> pdb=" O ASP F 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 238 through 242 Processing sheet with id=AA5, first strand: chain 'F' and resid 311 through 315 removed outlier: 3.837A pdb=" N THR F 329 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 349 through 350 Processing sheet with id=AA7, first strand: chain 'A' and resid 31 through 34 Processing sheet with id=AA8, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA9, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AB1, first strand: chain 'A' and resid 121 through 122 removed outlier: 3.657A pdb=" N VAL A 122 " --> pdb=" O THR A 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 150 through 157 removed outlier: 6.617A pdb=" N TYR A 145 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR A 154 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A 143 " --> pdb=" O TYR A 154 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR A 156 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR A 141 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A 143 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR A 177 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR A 145 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR A 175 " --> pdb=" O TYR A 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 133 through 137 Processing sheet with id=AB4, first strand: chain 'E' and resid 205 through 209 removed outlier: 3.626A pdb=" N THR E 225 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP E 230 " --> pdb=" O THR E 264 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR E 264 " --> pdb=" O ASP E 230 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 238 through 244 removed outlier: 4.132A pdb=" N GLY E 282 " --> pdb=" O GLU E 244 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 311 through 315 removed outlier: 4.005A pdb=" N THR E 329 " --> pdb=" O PHE E 315 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE E 371 " --> pdb=" O ASN E 334 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 311 through 315 removed outlier: 4.005A pdb=" N THR E 329 " --> pdb=" O PHE E 315 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE E 371 " --> pdb=" O ASN E 334 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU E 362 " --> pdb=" O PHE E 372 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 340 through 344 236 hydrogen bonds defined for protein. 561 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: 1.15 Time building geometry restraints manager: 0.72 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: 2078 1.34 - 1.46: 1588 1.46 - 1.58: 3113 1.58 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 6811 Sorted by residual: bond pdb=" CB PRO E 197 " pdb=" CG PRO E 197 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" CG PRO E 197 " pdb=" CD PRO E 197 " ideal model delta sigma weight residual 1.503 1.538 -0.035 3.40e-02 8.65e+02 1.03e+00 bond pdb=" CB PRO E 201 " pdb=" CG PRO E 201 " ideal model delta sigma weight residual 1.492 1.543 -0.051 5.00e-02 4.00e+02 1.02e+00 bond pdb=" N ASP E 198 " pdb=" CA ASP E 198 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.87e-01 bond pdb=" CB PRO E 222 " pdb=" CG PRO E 222 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 7.18e-01 ... (remaining 6806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 9152 1.92 - 3.85: 119 3.85 - 5.77: 9 5.77 - 7.70: 1 7.70 - 9.62: 2 Bond angle restraints: 9283 Sorted by residual: angle pdb=" C2 NAG A 303 " pdb=" N2 NAG A 303 " pdb=" C7 NAG A 303 " ideal model delta sigma weight residual 124.56 134.18 -9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C GLU F 244 " pdb=" CA GLU F 244 " pdb=" CB GLU F 244 " ideal model delta sigma weight residual 110.42 116.18 -5.76 1.99e+00 2.53e-01 8.37e+00 angle pdb=" C PRO E 197 " pdb=" N ASP E 198 " pdb=" CA ASP E 198 " ideal model delta sigma weight residual 121.54 126.86 -5.32 1.91e+00 2.74e-01 7.77e+00 angle pdb=" C HIS F 114 " pdb=" N SER F 115 " pdb=" CA SER F 115 " ideal model delta sigma weight residual 120.82 124.75 -3.93 1.50e+00 4.44e-01 6.88e+00 angle pdb=" C ASP F 288 " pdb=" N HIS F 289 " pdb=" CA HIS F 289 " ideal model delta sigma weight residual 122.15 130.25 -8.10 3.47e+00 8.31e-02 5.45e+00 ... (remaining 9278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.19: 3953 11.19 - 22.37: 271 22.37 - 33.55: 79 33.55 - 44.74: 15 44.74 - 55.92: 10 Dihedral angle restraints: 4328 sinusoidal: 1971 harmonic: 2357 Sorted by residual: dihedral pdb=" CA TRP F 254 " pdb=" C TRP F 254 " pdb=" N TYR F 255 " pdb=" CA TYR F 255 " ideal model delta harmonic sigma weight residual -180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA CYS F 196 " pdb=" C CYS F 196 " pdb=" N PRO F 197 " pdb=" CA PRO F 197 " ideal model delta harmonic sigma weight residual 180.00 -163.65 -16.35 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA GLU E 321 " pdb=" C GLU E 321 " pdb=" N SER E 322 " pdb=" CA SER E 322 " ideal model delta harmonic sigma weight residual -180.00 -164.62 -15.38 0 5.00e+00 4.00e-02 9.46e+00 ... (remaining 4325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 872 0.047 - 0.093: 145 0.093 - 0.139: 78 0.139 - 0.186: 0 0.186 - 0.232: 2 Chirality restraints: 1097 Sorted by residual: chirality pdb=" C2 NAG A 303 " pdb=" C1 NAG A 303 " pdb=" C3 NAG A 303 " pdb=" N2 NAG A 303 " both_signs ideal model delta sigma weight residual False -2.49 -2.26 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO E 197 " pdb=" N PRO E 197 " pdb=" C PRO E 197 " pdb=" CB PRO E 197 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" C1 NAG A 303 " pdb=" ND2 ASN A 191 " pdb=" C2 NAG A 303 " pdb=" O5 NAG A 303 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1094 not shown) Planarity restraints: 1165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 196 " 0.078 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO E 197 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO E 197 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO E 197 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 155 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.86e+00 pdb=" C GLU E 155 " 0.024 2.00e-02 2.50e+03 pdb=" O GLU E 155 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY E 156 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS E 289 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO E 290 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 290 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 290 " -0.019 5.00e-02 4.00e+02 ... (remaining 1162 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1254 2.79 - 3.32: 5928 3.32 - 3.85: 10462 3.85 - 4.37: 11974 4.37 - 4.90: 20724 Nonbonded interactions: 50342 Sorted by model distance: nonbonded pdb=" OD1 ASN F 261 " pdb=" OG1 THR F 263 " model vdw 2.263 3.040 nonbonded pdb=" O ASP A 87 " pdb=" OH TYR A 91 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASN E 261 " pdb=" OG1 THR E 263 " model vdw 2.311 3.040 nonbonded pdb=" OG SER E 354 " pdb=" OE1 GLN E 355 " model vdw 2.314 3.040 nonbonded pdb=" OE1 GLU F 321 " pdb=" NE2 GLN E 333 " model vdw 2.345 3.120 ... (remaining 50337 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 'E' and (resid 98 through 413 or resid 501)) selection = chain 'F' } ncs_group { reference = chain 'x' selection = chain 'z' } 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 group one per residue 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.410 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 6839 Z= 0.093 Angle : 0.535 9.619 9357 Z= 0.269 Chirality : 0.043 0.232 1097 Planarity : 0.005 0.119 1157 Dihedral : 8.555 55.925 2766 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.43 % Favored : 92.19 % Rotamer: Outliers : 0.95 % Allowed : 4.06 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.32), residues: 794 helix: -0.31 (0.94), residues: 36 sheet: 1.24 (0.30), residues: 360 loop : -0.84 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 195 TYR 0.008 0.001 TYR F 255 PHE 0.010 0.001 PHE E 292 TRP 0.005 0.001 TRP F 254 HIS 0.003 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 6811) covalent geometry : angle 0.52790 ( 9283) SS BOND : bond 0.00261 ( 10) SS BOND : angle 0.82668 ( 20) hydrogen bonds : bond 0.11242 ( 222) hydrogen bonds : angle 5.35487 ( 561) link_ALPHA1-3 : bond 0.00648 ( 2) link_ALPHA1-3 : angle 1.32711 ( 6) link_ALPHA1-6 : bond 0.00748 ( 2) link_ALPHA1-6 : angle 1.37275 ( 6) link_BETA1-4 : bond 0.00459 ( 6) link_BETA1-4 : angle 1.33029 ( 18) link_NAG-ASN : bond 0.00213 ( 8) link_NAG-ASN : angle 1.02960 ( 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 234 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 227 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6410 (m) cc_final: 0.6069 (p) REVERT: F 298 ARG cc_start: 0.6192 (ttm-80) cc_final: 0.5978 (ttm170) REVERT: F 358 THR cc_start: 0.8496 (m) cc_final: 0.8198 (m) REVERT: F 365 ASN cc_start: 0.6597 (m-40) cc_final: 0.6154 (t0) REVERT: A 67 ASN cc_start: 0.7046 (m-40) cc_final: 0.6718 (m-40) REVERT: A 177 THR cc_start: 0.8722 (m) cc_final: 0.8385 (m) REVERT: E 166 ASN cc_start: 0.6322 (m-40) cc_final: 0.6090 (m-40) REVERT: E 205 ILE cc_start: 0.7586 (mt) cc_final: 0.7213 (mt) REVERT: E 376 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7668 (ttt-90) outliers start: 7 outliers final: 3 residues processed: 234 average time/residue: 0.0918 time to fit residues: 27.6515 Evaluate side-chains 118 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain E residue 108 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.202421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.174419 restraints weight = 8706.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.173742 restraints weight = 6655.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.174414 restraints weight = 5854.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.174726 restraints weight = 5660.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.175250 restraints weight = 5048.033| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 6839 Z= 0.150 Angle : 0.702 10.298 9357 Z= 0.337 Chirality : 0.047 0.204 1097 Planarity : 0.006 0.125 1157 Dihedral : 5.402 54.378 1215 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.05 % Favored : 92.44 % Rotamer: Outliers : 3.25 % Allowed : 12.31 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.32), residues: 794 helix: -0.94 (0.81), residues: 42 sheet: 1.07 (0.29), residues: 357 loop : -0.89 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 307 TYR 0.013 0.002 TYR F 281 PHE 0.024 0.002 PHE E 372 TRP 0.032 0.002 TRP A 64 HIS 0.013 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6811) covalent geometry : angle 0.67398 ( 9283) SS BOND : bond 0.00509 ( 10) SS BOND : angle 2.59923 ( 20) hydrogen bonds : bond 0.02883 ( 222) hydrogen bonds : angle 4.96180 ( 561) link_ALPHA1-3 : bond 0.00367 ( 2) link_ALPHA1-3 : angle 1.57705 ( 6) link_ALPHA1-6 : bond 0.00737 ( 2) link_ALPHA1-6 : angle 1.36764 ( 6) link_BETA1-4 : bond 0.00250 ( 6) link_BETA1-4 : angle 1.49570 ( 18) link_NAG-ASN : bond 0.00444 ( 8) link_NAG-ASN : angle 2.79061 ( 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 149 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6360 (m) cc_final: 0.6070 (p) REVERT: F 194 ARG cc_start: 0.6968 (ptt-90) cc_final: 0.6560 (ptm-80) REVERT: F 292 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.6506 (t80) REVERT: F 327 THR cc_start: 0.8671 (p) cc_final: 0.8306 (t) REVERT: E 198 ASP cc_start: 0.6192 (p0) cc_final: 0.5887 (p0) REVERT: E 205 ILE cc_start: 0.7721 (mt) cc_final: 0.7329 (mt) REVERT: E 307 ARG cc_start: 0.8378 (mtt-85) cc_final: 0.8094 (mtt90) REVERT: E 376 ARG cc_start: 0.8453 (ttp80) cc_final: 0.7809 (ttt-90) outliers start: 24 outliers final: 16 residues processed: 143 average time/residue: 0.0819 time to fit residues: 15.8657 Evaluate side-chains 111 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 223 LYS Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 ASN ** E 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.181557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147839 restraints weight = 8607.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.147021 restraints weight = 6953.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148498 restraints weight = 6751.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.149003 restraints weight = 5769.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.149172 restraints weight = 5113.852| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 6839 Z= 0.297 Angle : 0.864 11.509 9357 Z= 0.426 Chirality : 0.054 0.376 1097 Planarity : 0.007 0.111 1157 Dihedral : 7.044 52.894 1215 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.94 % Favored : 90.55 % Rotamer: Outliers : 7.71 % Allowed : 12.18 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.31), residues: 794 helix: -2.15 (0.68), residues: 47 sheet: 0.67 (0.28), residues: 361 loop : -1.17 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 131 TYR 0.021 0.003 TYR F 313 PHE 0.033 0.005 PHE F 113 TRP 0.022 0.003 TRP E 241 HIS 0.012 0.002 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00714 ( 6811) covalent geometry : angle 0.83764 ( 9283) SS BOND : bond 0.00647 ( 10) SS BOND : angle 2.64760 ( 20) hydrogen bonds : bond 0.03811 ( 222) hydrogen bonds : angle 6.00525 ( 561) link_ALPHA1-3 : bond 0.00343 ( 2) link_ALPHA1-3 : angle 1.89137 ( 6) link_ALPHA1-6 : bond 0.00608 ( 2) link_ALPHA1-6 : angle 1.89806 ( 6) link_BETA1-4 : bond 0.00199 ( 6) link_BETA1-4 : angle 2.24224 ( 18) link_NAG-ASN : bond 0.00335 ( 8) link_NAG-ASN : angle 2.90266 ( 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 156 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 99 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6484 (m) cc_final: 0.6155 (p) REVERT: F 195 ARG cc_start: 0.6995 (mtp180) cc_final: 0.6540 (ttp-170) REVERT: F 292 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.7279 (t80) REVERT: F 298 ARG cc_start: 0.6481 (ttm-80) cc_final: 0.6187 (ttm-80) REVERT: F 365 ASN cc_start: 0.7095 (m-40) cc_final: 0.6624 (t0) REVERT: A 32 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7814 (p) REVERT: A 50 THR cc_start: 0.7693 (OUTLIER) cc_final: 0.7439 (m) REVERT: A 52 ASN cc_start: 0.7869 (OUTLIER) cc_final: 0.6392 (p0) REVERT: A 96 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: A 115 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6959 (pt) REVERT: E 205 ILE cc_start: 0.7865 (mt) cc_final: 0.7505 (mt) REVERT: E 296 ILE cc_start: 0.6270 (OUTLIER) cc_final: 0.5479 (tp) REVERT: E 299 SER cc_start: 0.8160 (OUTLIER) cc_final: 0.7959 (m) REVERT: E 353 ASN cc_start: 0.6911 (OUTLIER) cc_final: 0.6604 (t0) REVERT: E 376 ARG cc_start: 0.8503 (ttp80) cc_final: 0.7758 (ttt-90) outliers start: 57 outliers final: 31 residues processed: 146 average time/residue: 0.0832 time to fit residues: 16.3196 Evaluate side-chains 124 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 84 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 0.2980 chunk 74 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 30 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 111 ASN A 95 HIS ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 GLN ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.186401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.153353 restraints weight = 8650.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.153673 restraints weight = 6314.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.154640 restraints weight = 5855.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.155266 restraints weight = 5037.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.155426 restraints weight = 4802.653| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 6839 Z= 0.131 Angle : 0.684 11.352 9357 Z= 0.334 Chirality : 0.047 0.245 1097 Planarity : 0.006 0.117 1157 Dihedral : 6.034 53.355 1213 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.44 % Favored : 91.06 % Rotamer: Outliers : 3.52 % Allowed : 17.32 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.31), residues: 794 helix: -1.33 (0.74), residues: 40 sheet: 0.66 (0.28), residues: 369 loop : -1.25 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 40 TYR 0.014 0.001 TYR E 217 PHE 0.029 0.002 PHE E 372 TRP 0.028 0.002 TRP A 64 HIS 0.010 0.002 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6811) covalent geometry : angle 0.66865 ( 9283) SS BOND : bond 0.00238 ( 10) SS BOND : angle 1.44572 ( 20) hydrogen bonds : bond 0.02903 ( 222) hydrogen bonds : angle 5.45083 ( 561) link_ALPHA1-3 : bond 0.00379 ( 2) link_ALPHA1-3 : angle 1.27383 ( 6) link_ALPHA1-6 : bond 0.00841 ( 2) link_ALPHA1-6 : angle 1.57139 ( 6) link_BETA1-4 : bond 0.00248 ( 6) link_BETA1-4 : angle 1.75589 ( 18) link_NAG-ASN : bond 0.00215 ( 8) link_NAG-ASN : angle 2.07057 ( 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 122 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6289 (m) cc_final: 0.6028 (p) REVERT: F 194 ARG cc_start: 0.7428 (ptt-90) cc_final: 0.6917 (ptt90) REVERT: F 298 ARG cc_start: 0.6399 (ttm-80) cc_final: 0.6068 (ttm-80) REVERT: F 321 GLU cc_start: 0.5891 (OUTLIER) cc_final: 0.5022 (pm20) REVERT: F 327 THR cc_start: 0.8802 (p) cc_final: 0.8425 (t) REVERT: F 355 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7253 (mp10) REVERT: A 52 ASN cc_start: 0.7615 (OUTLIER) cc_final: 0.6103 (p0) REVERT: E 205 ILE cc_start: 0.7771 (mt) cc_final: 0.7435 (mt) REVERT: E 376 ARG cc_start: 0.8448 (ttp80) cc_final: 0.7774 (ttt-90) outliers start: 26 outliers final: 15 residues processed: 118 average time/residue: 0.0885 time to fit residues: 14.0350 Evaluate side-chains 97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 13 optimal weight: 0.0050 chunk 7 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 overall best weight: 0.4292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.187424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.152769 restraints weight = 8713.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.155623 restraints weight = 6224.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.157463 restraints weight = 4987.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.158630 restraints weight = 4301.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.159223 restraints weight = 3919.180| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6839 Z= 0.123 Angle : 0.655 11.437 9357 Z= 0.317 Chirality : 0.046 0.214 1097 Planarity : 0.006 0.118 1157 Dihedral : 5.608 54.128 1213 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.93 % Favored : 91.56 % Rotamer: Outliers : 4.47 % Allowed : 17.86 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.31), residues: 794 helix: -1.39 (0.72), residues: 41 sheet: 0.63 (0.28), residues: 368 loop : -1.16 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 307 TYR 0.021 0.001 TYR F 255 PHE 0.029 0.002 PHE E 372 TRP 0.032 0.001 TRP A 64 HIS 0.009 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6811) covalent geometry : angle 0.64079 ( 9283) SS BOND : bond 0.00275 ( 10) SS BOND : angle 1.55621 ( 20) hydrogen bonds : bond 0.02768 ( 222) hydrogen bonds : angle 5.22513 ( 561) link_ALPHA1-3 : bond 0.00541 ( 2) link_ALPHA1-3 : angle 1.34622 ( 6) link_ALPHA1-6 : bond 0.00809 ( 2) link_ALPHA1-6 : angle 1.53605 ( 6) link_BETA1-4 : bond 0.00373 ( 6) link_BETA1-4 : angle 1.81090 ( 18) link_NAG-ASN : bond 0.00203 ( 8) link_NAG-ASN : angle 1.76818 ( 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 123 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: F 100 THR cc_start: 0.6428 (m) cc_final: 0.6187 (p) REVERT: F 194 ARG cc_start: 0.7367 (ptt-90) cc_final: 0.6842 (ptt90) REVERT: F 298 ARG cc_start: 0.6349 (ttm-80) cc_final: 0.5973 (ttm170) REVERT: F 321 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.5105 (pm20) REVERT: F 327 THR cc_start: 0.8835 (p) cc_final: 0.8452 (t) REVERT: F 355 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: F 365 ASN cc_start: 0.6918 (m-40) cc_final: 0.6468 (t0) REVERT: A 32 VAL cc_start: 0.7935 (OUTLIER) cc_final: 0.7588 (m) REVERT: A 67 ASN cc_start: 0.7215 (m-40) cc_final: 0.6749 (m-40) REVERT: E 137 MET cc_start: 0.5795 (ttp) cc_final: 0.5462 (ttp) REVERT: E 173 MET cc_start: 0.7941 (mmm) cc_final: 0.7580 (mmm) REVERT: E 205 ILE cc_start: 0.7726 (mt) cc_final: 0.7397 (mt) REVERT: E 299 SER cc_start: 0.8254 (OUTLIER) cc_final: 0.8031 (m) REVERT: E 307 ARG cc_start: 0.8803 (mmt90) cc_final: 0.8542 (mmt90) REVERT: E 331 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7724 (tt) REVERT: E 376 ARG cc_start: 0.8452 (ttp80) cc_final: 0.7737 (ttt-90) outliers start: 33 outliers final: 20 residues processed: 119 average time/residue: 0.0907 time to fit residues: 14.1694 Evaluate side-chains 106 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 339 ASP Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 356 HIS Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 51 optimal weight: 0.4980 chunk 53 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 63 optimal weight: 0.0770 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 284 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.184504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.152270 restraints weight = 8723.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.151246 restraints weight = 6792.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.152498 restraints weight = 6184.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152810 restraints weight = 5559.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.153090 restraints weight = 5194.789| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6839 Z= 0.176 Angle : 0.714 11.720 9357 Z= 0.343 Chirality : 0.048 0.256 1097 Planarity : 0.006 0.122 1157 Dihedral : 5.796 53.562 1213 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.06 % Favored : 91.44 % Rotamer: Outliers : 4.19 % Allowed : 18.94 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.30), residues: 794 helix: -1.98 (0.66), residues: 47 sheet: 0.58 (0.28), residues: 367 loop : -1.17 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 131 TYR 0.015 0.002 TYR E 283 PHE 0.029 0.002 PHE E 372 TRP 0.027 0.002 TRP E 254 HIS 0.007 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 6811) covalent geometry : angle 0.69695 ( 9283) SS BOND : bond 0.00554 ( 10) SS BOND : angle 1.97237 ( 20) hydrogen bonds : bond 0.02967 ( 222) hydrogen bonds : angle 5.30050 ( 561) link_ALPHA1-3 : bond 0.00389 ( 2) link_ALPHA1-3 : angle 1.43604 ( 6) link_ALPHA1-6 : bond 0.00715 ( 2) link_ALPHA1-6 : angle 1.60156 ( 6) link_BETA1-4 : bond 0.00283 ( 6) link_BETA1-4 : angle 1.91642 ( 18) link_NAG-ASN : bond 0.00212 ( 8) link_NAG-ASN : angle 1.91248 ( 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 108 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6507 (m) cc_final: 0.6228 (p) REVERT: F 194 ARG cc_start: 0.7503 (ptt-90) cc_final: 0.7073 (ptm-80) REVERT: F 298 ARG cc_start: 0.6435 (ttm-80) cc_final: 0.6064 (ttm-80) REVERT: F 355 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7234 (mp10) REVERT: A 67 ASN cc_start: 0.6788 (m-40) cc_final: 0.6403 (m-40) REVERT: E 137 MET cc_start: 0.5295 (ttp) cc_final: 0.5004 (ttp) REVERT: E 205 ILE cc_start: 0.7878 (mt) cc_final: 0.7577 (mt) REVERT: E 331 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7826 (tt) REVERT: E 376 ARG cc_start: 0.8477 (ttp80) cc_final: 0.7807 (ttt180) outliers start: 31 outliers final: 25 residues processed: 105 average time/residue: 0.0799 time to fit residues: 11.4897 Evaluate side-chains 99 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 339 ASP Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 356 HIS Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 171 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 = 0.4165 r_free = 0.4165 target = 0.185809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.153126 restraints weight = 8662.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.152210 restraints weight = 6978.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.152734 restraints weight = 6270.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.153191 restraints weight = 5817.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.153310 restraints weight = 5425.716| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6839 Z= 0.145 Angle : 0.672 11.312 9357 Z= 0.325 Chirality : 0.047 0.228 1097 Planarity : 0.006 0.117 1157 Dihedral : 5.702 53.804 1213 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.06 % Favored : 91.31 % Rotamer: Outliers : 4.19 % Allowed : 19.35 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.30), residues: 794 helix: -1.46 (0.71), residues: 42 sheet: 0.61 (0.28), residues: 367 loop : -1.30 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 131 TYR 0.015 0.002 TYR E 283 PHE 0.030 0.002 PHE E 372 TRP 0.032 0.002 TRP E 254 HIS 0.007 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6811) covalent geometry : angle 0.65806 ( 9283) SS BOND : bond 0.00409 ( 10) SS BOND : angle 1.38740 ( 20) hydrogen bonds : bond 0.02816 ( 222) hydrogen bonds : angle 5.22610 ( 561) link_ALPHA1-3 : bond 0.00426 ( 2) link_ALPHA1-3 : angle 1.35124 ( 6) link_ALPHA1-6 : bond 0.00646 ( 2) link_ALPHA1-6 : angle 1.53217 ( 6) link_BETA1-4 : bond 0.00246 ( 6) link_BETA1-4 : angle 1.84984 ( 18) link_NAG-ASN : bond 0.00210 ( 8) link_NAG-ASN : angle 1.79116 ( 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 107 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6493 (m) cc_final: 0.6220 (p) REVERT: F 194 ARG cc_start: 0.7490 (ptt-90) cc_final: 0.7084 (ptm-80) REVERT: F 298 ARG cc_start: 0.6355 (ttm-80) cc_final: 0.6032 (ttm-80) REVERT: F 355 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7228 (mp10) REVERT: A 67 ASN cc_start: 0.7251 (m-40) cc_final: 0.6818 (m-40) REVERT: E 137 MET cc_start: 0.5585 (ttp) cc_final: 0.5281 (ttp) REVERT: E 205 ILE cc_start: 0.7751 (mt) cc_final: 0.7203 (mt) REVERT: E 331 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7857 (tt) REVERT: E 376 ARG cc_start: 0.8465 (ttp80) cc_final: 0.7813 (ttt-90) outliers start: 31 outliers final: 27 residues processed: 105 average time/residue: 0.0867 time to fit residues: 12.3224 Evaluate side-chains 97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 339 ASP Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 356 HIS Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 47 optimal weight: 0.2980 chunk 48 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 GLN E 289 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.183916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.151553 restraints weight = 8678.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.149675 restraints weight = 7155.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.150746 restraints weight = 6491.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.150980 restraints weight = 5893.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152673 restraints weight = 5478.282| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6839 Z= 0.168 Angle : 0.701 12.619 9357 Z= 0.340 Chirality : 0.047 0.250 1097 Planarity : 0.006 0.115 1157 Dihedral : 5.909 53.635 1213 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.94 % Favored : 90.55 % Rotamer: Outliers : 4.33 % Allowed : 19.35 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.30), residues: 794 helix: -1.44 (0.71), residues: 42 sheet: 0.60 (0.28), residues: 362 loop : -1.36 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 131 TYR 0.016 0.002 TYR E 283 PHE 0.029 0.002 PHE E 372 TRP 0.035 0.002 TRP E 254 HIS 0.007 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 6811) covalent geometry : angle 0.68528 ( 9283) SS BOND : bond 0.00266 ( 10) SS BOND : angle 1.82592 ( 20) hydrogen bonds : bond 0.02946 ( 222) hydrogen bonds : angle 5.28969 ( 561) link_ALPHA1-3 : bond 0.00359 ( 2) link_ALPHA1-3 : angle 1.42968 ( 6) link_ALPHA1-6 : bond 0.00532 ( 2) link_ALPHA1-6 : angle 1.56490 ( 6) link_BETA1-4 : bond 0.00211 ( 6) link_BETA1-4 : angle 1.91984 ( 18) link_NAG-ASN : bond 0.00203 ( 8) link_NAG-ASN : angle 1.84428 ( 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 107 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6724 (m) cc_final: 0.6388 (p) REVERT: F 194 ARG cc_start: 0.7159 (ptt-90) cc_final: 0.6589 (ptt90) REVERT: F 298 ARG cc_start: 0.6501 (ttm-80) cc_final: 0.6218 (ttm-80) REVERT: F 327 THR cc_start: 0.8973 (p) cc_final: 0.8634 (t) REVERT: F 355 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7202 (mp10) REVERT: A 67 ASN cc_start: 0.7326 (m-40) cc_final: 0.6844 (m-40) REVERT: E 137 MET cc_start: 0.5577 (ttp) cc_final: 0.5281 (ttp) REVERT: E 198 ASP cc_start: 0.7091 (p0) cc_final: 0.6759 (p0) REVERT: E 205 ILE cc_start: 0.7322 (mt) cc_final: 0.7116 (mt) REVERT: E 376 ARG cc_start: 0.8477 (ttp80) cc_final: 0.7831 (ttt180) outliers start: 32 outliers final: 25 residues processed: 106 average time/residue: 0.0805 time to fit residues: 11.5158 Evaluate side-chains 94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 339 ASP Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 356 HIS Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 166 ASN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.182802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.149416 restraints weight = 8858.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.148131 restraints weight = 7375.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149425 restraints weight = 6627.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.149538 restraints weight = 5823.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.151458 restraints weight = 5495.158| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6839 Z= 0.197 Angle : 0.746 12.747 9357 Z= 0.362 Chirality : 0.049 0.282 1097 Planarity : 0.006 0.113 1157 Dihedral : 6.097 53.247 1213 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.94 % Favored : 90.30 % Rotamer: Outliers : 3.79 % Allowed : 20.03 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.30), residues: 794 helix: -1.37 (0.73), residues: 41 sheet: 0.45 (0.28), residues: 362 loop : -1.46 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 131 TYR 0.018 0.002 TYR E 283 PHE 0.029 0.003 PHE E 372 TRP 0.038 0.002 TRP E 254 HIS 0.007 0.002 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 6811) covalent geometry : angle 0.72901 ( 9283) SS BOND : bond 0.00405 ( 10) SS BOND : angle 1.98838 ( 20) hydrogen bonds : bond 0.03116 ( 222) hydrogen bonds : angle 5.54364 ( 561) link_ALPHA1-3 : bond 0.00285 ( 2) link_ALPHA1-3 : angle 1.48976 ( 6) link_ALPHA1-6 : bond 0.00491 ( 2) link_ALPHA1-6 : angle 1.59943 ( 6) link_BETA1-4 : bond 0.00185 ( 6) link_BETA1-4 : angle 2.02493 ( 18) link_NAG-ASN : bond 0.00261 ( 8) link_NAG-ASN : angle 1.99700 ( 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 101 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6658 (m) cc_final: 0.6423 (p) REVERT: F 298 ARG cc_start: 0.6422 (ttm-80) cc_final: 0.6059 (ttm170) REVERT: F 355 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7231 (mp10) REVERT: A 63 LYS cc_start: 0.7136 (pttm) cc_final: 0.6929 (pttm) REVERT: A 67 ASN cc_start: 0.7432 (m-40) cc_final: 0.6913 (m-40) REVERT: E 103 LEU cc_start: 0.5763 (tp) cc_final: 0.5536 (tp) REVERT: E 198 ASP cc_start: 0.7116 (p0) cc_final: 0.6764 (p0) REVERT: E 376 ARG cc_start: 0.8483 (ttp80) cc_final: 0.7900 (ttt-90) outliers start: 28 outliers final: 24 residues processed: 99 average time/residue: 0.0816 time to fit residues: 10.7640 Evaluate side-chains 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 339 ASP Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 356 HIS Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 47 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 57 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** 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 = 0.4166 r_free = 0.4166 target = 0.186151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.153512 restraints weight = 8778.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152417 restraints weight = 6996.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.153399 restraints weight = 6090.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.154039 restraints weight = 5659.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.154177 restraints weight = 5123.706| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6839 Z= 0.124 Angle : 0.692 12.111 9357 Z= 0.333 Chirality : 0.047 0.211 1097 Planarity : 0.005 0.110 1157 Dihedral : 5.752 53.782 1213 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.19 % Favored : 91.18 % Rotamer: Outliers : 2.98 % Allowed : 20.70 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.30), residues: 794 helix: -1.32 (0.74), residues: 42 sheet: 0.52 (0.28), residues: 362 loop : -1.35 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 298 TYR 0.016 0.001 TYR F 255 PHE 0.036 0.002 PHE E 372 TRP 0.042 0.002 TRP E 254 HIS 0.006 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6811) covalent geometry : angle 0.67907 ( 9283) SS BOND : bond 0.00274 ( 10) SS BOND : angle 1.43996 ( 20) hydrogen bonds : bond 0.02758 ( 222) hydrogen bonds : angle 5.27349 ( 561) link_ALPHA1-3 : bond 0.00461 ( 2) link_ALPHA1-3 : angle 1.34712 ( 6) link_ALPHA1-6 : bond 0.00684 ( 2) link_ALPHA1-6 : angle 1.46956 ( 6) link_BETA1-4 : bond 0.00338 ( 6) link_BETA1-4 : angle 1.82388 ( 18) link_NAG-ASN : bond 0.00209 ( 8) link_NAG-ASN : angle 1.72800 ( 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 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 100 THR cc_start: 0.6606 (m) cc_final: 0.6344 (p) REVERT: F 194 ARG cc_start: 0.7347 (ptt-90) cc_final: 0.6913 (ptm-80) REVERT: F 298 ARG cc_start: 0.6391 (ttm-80) cc_final: 0.5877 (ttm170) REVERT: F 327 THR cc_start: 0.8810 (p) cc_final: 0.8456 (t) REVERT: F 355 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7230 (mp10) REVERT: A 67 ASN cc_start: 0.7285 (m-40) cc_final: 0.6832 (m-40) REVERT: E 198 ASP cc_start: 0.6981 (p0) cc_final: 0.6631 (p0) REVERT: E 288 ASP cc_start: 0.6757 (t0) cc_final: 0.6462 (t70) REVERT: E 376 ARG cc_start: 0.8434 (ttp80) cc_final: 0.7814 (ttt-90) outliers start: 22 outliers final: 18 residues processed: 91 average time/residue: 0.0710 time to fit residues: 8.7889 Evaluate side-chains 83 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 355 GLN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.0770 chunk 48 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 HIS ** 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 = 0.4142 r_free = 0.4142 target = 0.183472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151240 restraints weight = 8665.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150284 restraints weight = 6699.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.151086 restraints weight = 6181.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.151361 restraints weight = 5770.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151587 restraints weight = 5458.048| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6839 Z= 0.176 Angle : 0.721 12.953 9357 Z= 0.349 Chirality : 0.049 0.258 1097 Planarity : 0.005 0.106 1157 Dihedral : 5.931 53.518 1213 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.82 % Favored : 90.43 % Rotamer: Outliers : 2.98 % Allowed : 20.97 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.30), residues: 794 helix: -1.34 (0.73), residues: 42 sheet: 0.46 (0.27), residues: 370 loop : -1.41 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 131 TYR 0.017 0.002 TYR E 283 PHE 0.032 0.002 PHE E 372 TRP 0.039 0.002 TRP E 254 HIS 0.007 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 6811) covalent geometry : angle 0.70564 ( 9283) SS BOND : bond 0.00371 ( 10) SS BOND : angle 1.66230 ( 20) hydrogen bonds : bond 0.03057 ( 222) hydrogen bonds : angle 5.48590 ( 561) link_ALPHA1-3 : bond 0.00317 ( 2) link_ALPHA1-3 : angle 1.45365 ( 6) link_ALPHA1-6 : bond 0.00378 ( 2) link_ALPHA1-6 : angle 1.60382 ( 6) link_BETA1-4 : bond 0.00249 ( 6) link_BETA1-4 : angle 1.98968 ( 18) link_NAG-ASN : bond 0.00184 ( 8) link_NAG-ASN : angle 1.88725 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1196.34 seconds wall clock time: 21 minutes 23.22 seconds (1283.22 seconds total)