Starting phenix.real_space_refine on Wed Mar 4 13:37:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z0l_14427/03_2026/7z0l_14427_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z0l_14427/03_2026/7z0l_14427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z0l_14427/03_2026/7z0l_14427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z0l_14427/03_2026/7z0l_14427.map" model { file = "/net/cci-nas-00/data/ceres_data/7z0l_14427/03_2026/7z0l_14427_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z0l_14427/03_2026/7z0l_14427_trim.cif" } resolution = 4.0 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 4478 2.51 5 N 1180 2.21 5 O 1349 1.98 5 H 6713 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13752 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4557 Classifications: {'peptide': 292} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 274} Chain: "B" Number of atoms: 5946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5946 Classifications: {'peptide': 370} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 342} Chain breaks: 5 Chain: "C" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3081 Classifications: {'peptide': 194} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 172} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.43, per 1000 atoms: 0.18 Number of scatterers: 13752 At special positions: 0 Unit cell: (87.98, 95.4, 144.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 1349 8.00 N 1180 7.00 C 4478 6.00 H 6713 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 401 " - " ASN A 157 " " NAG A 402 " - " ASN A 225 " " NAG E 1 " - " ASN A 43 " " NAG F 1 " - " ASN A 61 " " NAG H 1 " - " ASN B 307 " " NAG I 1 " - " ASN C 46 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 390.1 milliseconds 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1628 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 16 sheets defined 20.9% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.541A pdb=" N GLY A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.893A pdb=" N MET A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 290 Processing helix chain 'B' and resid 311 through 318 Processing helix chain 'B' and resid 319 through 332 Processing helix chain 'B' and resid 333 through 344 removed outlier: 3.587A pdb=" N GLN B 344 " --> pdb=" O GLY B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 377 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 399 removed outlier: 3.995A pdb=" N GLU B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 446 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.427A pdb=" N THR A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 39 removed outlier: 6.708A pdb=" N CYS A 103 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY A 117 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU A 101 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR A 119 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL A 99 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 181 removed outlier: 6.659A pdb=" N LEU A 143 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N CYS A 134 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN A 145 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 132 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LYS A 219 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL A 136 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 168 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 230 removed outlier: 4.105A pdb=" N LEU A 226 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER A 241 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL A 228 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS A 239 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 268 through 269 Processing sheet with id=AA8, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.995A pdb=" N ARG B 31 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB1, first strand: chain 'B' and resid 142 through 148 removed outlier: 4.839A pdb=" N HIS B 148 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLY B 133 " --> pdb=" O HIS B 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 181 removed outlier: 6.068A pdb=" N TYR B 163 " --> pdb=" O PRO B 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 35 through 38 removed outlier: 4.542A pdb=" N LEU C 45 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C 87 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 74 through 77 Processing sheet with id=AB5, first strand: chain 'C' and resid 74 through 77 Processing sheet with id=AB6, first strand: chain 'C' and resid 127 through 135 removed outlier: 6.844A pdb=" N PHE C 129 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA C 147 " --> pdb=" O PHE C 129 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLN C 131 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN C 145 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU C 140 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 172 through 179 removed outlier: 4.396A pdb=" N PHE C 161 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N CYS C 159 " --> pdb=" O PRO C 176 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU C 178 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU C 157 " --> pdb=" O LEU C 178 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 807 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: 3.24 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 6692 1.03 - 1.23: 28 1.23 - 1.42: 3032 1.42 - 1.62: 4150 1.62 - 1.82: 43 Bond restraints: 13945 Sorted by residual: bond pdb=" CB ASN A 131 " pdb=" CG ASN A 131 " ideal model delta sigma weight residual 1.516 1.419 0.097 2.50e-02 1.60e+03 1.50e+01 bond pdb=" CE1 HIS A 57 " pdb=" NE2 HIS A 57 " ideal model delta sigma weight residual 1.321 1.354 -0.033 1.00e-02 1.00e+04 1.09e+01 bond pdb=" CD2 HIS A 57 " pdb=" HD2 HIS A 57 " ideal model delta sigma weight residual 0.930 0.994 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" CG HIS A 57 " pdb=" ND1 HIS A 57 " ideal model delta sigma weight residual 1.378 1.409 -0.031 1.10e-02 8.26e+03 7.85e+00 bond pdb=" C1 NAG A 401 " pdb=" O5 NAG A 401 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.66e+00 ... (remaining 13940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 23706 1.62 - 3.25: 1271 3.25 - 4.87: 111 4.87 - 6.50: 20 6.50 - 8.12: 5 Bond angle restraints: 25113 Sorted by residual: angle pdb=" N ASN A 131 " pdb=" CA ASN A 131 " pdb=" CB ASN A 131 " ideal model delta sigma weight residual 112.63 104.51 8.12 1.61e+00 3.86e-01 2.55e+01 angle pdb=" CA TRP B 356 " pdb=" CB TRP B 356 " pdb=" CG TRP B 356 " ideal model delta sigma weight residual 113.60 120.83 -7.23 1.90e+00 2.77e-01 1.45e+01 angle pdb=" N VAL B 308 " pdb=" CA VAL B 308 " pdb=" C VAL B 308 " ideal model delta sigma weight residual 109.34 116.87 -7.53 2.08e+00 2.31e-01 1.31e+01 angle pdb=" CA ARG C 89 " pdb=" CB ARG C 89 " pdb=" CG ARG C 89 " ideal model delta sigma weight residual 114.10 120.49 -6.39 2.00e+00 2.50e-01 1.02e+01 angle pdb=" N GLN B 280 " pdb=" CA GLN B 280 " pdb=" C GLN B 280 " ideal model delta sigma weight residual 111.02 114.78 -3.76 1.22e+00 6.72e-01 9.49e+00 ... (remaining 25108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.19: 6341 23.19 - 46.37: 296 46.37 - 69.55: 155 69.55 - 92.74: 12 92.74 - 115.92: 17 Dihedral angle restraints: 6821 sinusoidal: 3814 harmonic: 3007 Sorted by residual: dihedral pdb=" CA LEU C 157 " pdb=" C LEU C 157 " pdb=" N ILE C 158 " pdb=" CA ILE C 158 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA PHE B 175 " pdb=" C PHE B 175 " pdb=" N ARG B 176 " pdb=" CA ARG B 176 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA LYS A 175 " pdb=" C LYS A 175 " pdb=" N HIS A 176 " pdb=" CA HIS A 176 " ideal model delta harmonic sigma weight residual 180.00 -152.49 -27.51 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 6818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1075 0.124 - 0.247: 36 0.247 - 0.370: 0 0.370 - 0.494: 0 0.494 - 0.617: 2 Chirality restraints: 1113 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 307 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.51e+00 chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 157 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.35e+00 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 3.59e+00 ... (remaining 1110 not shown) Planarity restraints: 2034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 359 " -0.499 9.50e-02 1.11e+02 1.69e-01 4.83e+01 pdb=" NE ARG B 359 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG B 359 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 359 " 0.059 2.00e-02 2.50e+03 pdb=" NH2 ARG B 359 " 0.040 2.00e-02 2.50e+03 pdb="HH11 ARG B 359 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 359 " -0.040 2.00e-02 2.50e+03 pdb="HH21 ARG B 359 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 359 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 262 " 0.182 9.50e-02 1.11e+02 6.59e-02 1.87e+01 pdb=" NE ARG B 262 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 262 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 262 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 262 " -0.053 2.00e-02 2.50e+03 pdb="HH11 ARG B 262 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG B 262 " -0.010 2.00e-02 2.50e+03 pdb="HH21 ARG B 262 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 262 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 436 " 0.340 9.50e-02 1.11e+02 1.14e-01 1.68e+01 pdb=" NE ARG B 436 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 436 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 436 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG B 436 " -0.006 2.00e-02 2.50e+03 pdb="HH11 ARG B 436 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 436 " 0.021 2.00e-02 2.50e+03 pdb="HH21 ARG B 436 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 436 " 0.008 2.00e-02 2.50e+03 ... (remaining 2031 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 283 2.06 - 2.70: 20884 2.70 - 3.33: 39568 3.33 - 3.97: 49580 3.97 - 4.60: 77201 Nonbonded interactions: 187516 Sorted by model distance: nonbonded pdb=" H ALA B 203 " pdb=" OG SER B 213 " model vdw 1.426 2.450 nonbonded pdb=" O ALA B 203 " pdb=" H SER B 213 " model vdw 1.480 2.450 nonbonded pdb=" O PHE B 326 " pdb=" HG1 THR B 330 " model vdw 1.537 2.450 nonbonded pdb="HE22 GLN B 204 " pdb=" OD1 ASP B 208 " model vdw 1.556 2.450 nonbonded pdb=" O VAL B 201 " pdb=" H SER B 216 " model vdw 1.585 2.450 ... (remaining 187511 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' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.770 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: 0.070 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.620 Find NCS groups from input model: 0.060 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:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5111 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 : 0.005 0.097 7243 Z= 0.261 Angle : 0.967 9.410 9892 Z= 0.533 Chirality : 0.062 0.617 1113 Planarity : 0.013 0.191 1245 Dihedral : 15.673 115.924 2852 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.65 % Allowed : 4.78 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.28), residues: 840 helix: -2.00 (0.36), residues: 137 sheet: 0.36 (0.28), residues: 298 loop : -0.37 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.004 ARG C 72 TYR 0.042 0.005 TYR B 282 PHE 0.022 0.003 PHE B 159 TRP 0.029 0.005 TRP C 84 HIS 0.039 0.004 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 7232) covalent geometry : angle 0.94669 ( 9859) hydrogen bonds : bond 0.17927 ( 282) hydrogen bonds : angle 8.72577 ( 807) link_BETA1-4 : bond 0.00705 ( 5) link_BETA1-4 : angle 2.68907 ( 15) link_NAG-ASN : bond 0.00990 ( 6) link_NAG-ASN : angle 4.09558 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 210 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.7198 (t80) cc_final: 0.6910 (t80) REVERT: A 144 CYS cc_start: 0.9303 (m) cc_final: 0.8840 (m) REVERT: B 31 ARG cc_start: 0.7405 (tpm-80) cc_final: 0.6046 (mmm160) REVERT: B 93 VAL cc_start: 0.6175 (t) cc_final: 0.5938 (t) REVERT: B 264 GLU cc_start: 0.8546 (mm-30) cc_final: 0.7395 (mm-30) REVERT: B 430 LEU cc_start: 0.8845 (tp) cc_final: 0.8567 (tp) REVERT: B 440 ASP cc_start: 0.8176 (m-30) cc_final: 0.7707 (m-30) REVERT: C 60 VAL cc_start: 0.7699 (t) cc_final: 0.7321 (p) outliers start: 5 outliers final: 1 residues processed: 213 average time/residue: 0.2219 time to fit residues: 59.0535 Evaluate side-chains 162 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5039 r_free = 0.5039 target = 0.224469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.178478 restraints weight = 39134.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.189529 restraints weight = 15843.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.196480 restraints weight = 8560.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.200845 restraints weight = 5542.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.203423 restraints weight = 4072.107| |-----------------------------------------------------------------------------| r_work (final): 0.4825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5110 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7243 Z= 0.179 Angle : 0.748 12.773 9892 Z= 0.376 Chirality : 0.045 0.223 1113 Planarity : 0.007 0.059 1245 Dihedral : 12.322 84.657 1181 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.94 % Allowed : 10.98 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.28), residues: 840 helix: 0.12 (0.39), residues: 138 sheet: 0.26 (0.28), residues: 290 loop : 0.27 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 262 TYR 0.015 0.002 TYR A 30 PHE 0.018 0.002 PHE B 61 TRP 0.023 0.002 TRP B 356 HIS 0.007 0.002 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 7232) covalent geometry : angle 0.73726 ( 9859) hydrogen bonds : bond 0.06041 ( 282) hydrogen bonds : angle 6.66240 ( 807) link_BETA1-4 : bond 0.00392 ( 5) link_BETA1-4 : angle 1.22186 ( 15) link_NAG-ASN : bond 0.00285 ( 6) link_NAG-ASN : angle 2.86715 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PRO cc_start: 0.3432 (Cg_exo) cc_final: 0.3063 (Cg_endo) REVERT: B 31 ARG cc_start: 0.7565 (tpm-80) cc_final: 0.6188 (mmm160) REVERT: B 35 HIS cc_start: 0.2943 (p-80) cc_final: 0.2549 (p90) REVERT: B 264 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7619 (mm-30) REVERT: B 430 LEU cc_start: 0.8841 (tp) cc_final: 0.8639 (tp) REVERT: B 440 ASP cc_start: 0.8761 (m-30) cc_final: 0.7961 (m-30) REVERT: C 60 VAL cc_start: 0.7404 (t) cc_final: 0.7137 (p) outliers start: 15 outliers final: 11 residues processed: 176 average time/residue: 0.2164 time to fit residues: 48.0978 Evaluate side-chains 165 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 196 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 31 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 366 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5024 r_free = 0.5024 target = 0.223089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.176063 restraints weight = 37305.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.186992 restraints weight = 15025.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.194053 restraints weight = 8172.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.198509 restraints weight = 5300.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.201579 restraints weight = 3900.709| |-----------------------------------------------------------------------------| r_work (final): 0.4811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5139 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7243 Z= 0.168 Angle : 0.696 11.494 9892 Z= 0.342 Chirality : 0.043 0.226 1113 Planarity : 0.006 0.048 1245 Dihedral : 9.843 66.391 1181 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.58 % Allowed : 12.27 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.29), residues: 840 helix: 1.13 (0.39), residues: 138 sheet: 0.03 (0.29), residues: 279 loop : 0.24 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 439 TYR 0.017 0.002 TYR C 209 PHE 0.009 0.002 PHE B 159 TRP 0.020 0.002 TRP B 356 HIS 0.008 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7232) covalent geometry : angle 0.68067 ( 9859) hydrogen bonds : bond 0.05315 ( 282) hydrogen bonds : angle 6.22774 ( 807) link_BETA1-4 : bond 0.00244 ( 5) link_BETA1-4 : angle 1.34711 ( 15) link_NAG-ASN : bond 0.00242 ( 6) link_NAG-ASN : angle 3.25168 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.8380 (t0) cc_final: 0.7848 (m-30) REVERT: B 31 ARG cc_start: 0.7594 (tpm-80) cc_final: 0.6187 (mmm160) REVERT: B 35 HIS cc_start: 0.3039 (p-80) cc_final: 0.2681 (p90) REVERT: B 205 ASP cc_start: -0.4203 (OUTLIER) cc_final: -0.4522 (t70) REVERT: B 260 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 264 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7555 (mm-30) REVERT: B 387 LYS cc_start: 0.4150 (tppt) cc_final: 0.3551 (mppt) REVERT: B 440 ASP cc_start: 0.8734 (m-30) cc_final: 0.8019 (m-30) REVERT: C 55 LEU cc_start: 0.7075 (mt) cc_final: 0.6751 (tp) REVERT: C 60 VAL cc_start: 0.7353 (t) cc_final: 0.7133 (p) outliers start: 20 outliers final: 15 residues processed: 170 average time/residue: 0.2260 time to fit residues: 48.3335 Evaluate side-chains 167 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 186 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.219137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.172966 restraints weight = 37276.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.183252 restraints weight = 15479.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.189991 restraints weight = 8599.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.194397 restraints weight = 5677.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.197286 restraints weight = 4213.175| |-----------------------------------------------------------------------------| r_work (final): 0.4773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5246 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7243 Z= 0.199 Angle : 0.702 7.923 9892 Z= 0.351 Chirality : 0.044 0.214 1113 Planarity : 0.006 0.053 1245 Dihedral : 8.677 64.740 1181 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.75 % Allowed : 12.02 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.29), residues: 840 helix: 0.75 (0.39), residues: 138 sheet: -0.28 (0.30), residues: 279 loop : -0.11 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 439 TYR 0.021 0.002 TYR A 30 PHE 0.012 0.002 PHE C 92 TRP 0.015 0.002 TRP B 356 HIS 0.009 0.002 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 7232) covalent geometry : angle 0.69362 ( 9859) hydrogen bonds : bond 0.05029 ( 282) hydrogen bonds : angle 6.22374 ( 807) link_BETA1-4 : bond 0.00231 ( 5) link_BETA1-4 : angle 1.48063 ( 15) link_NAG-ASN : bond 0.00481 ( 6) link_NAG-ASN : angle 2.29389 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 CYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7989 (m) REVERT: B 35 HIS cc_start: 0.2936 (p-80) cc_final: 0.2651 (p90) REVERT: B 204 GLN cc_start: 0.0673 (OUTLIER) cc_final: -0.0531 (tt0) REVERT: B 260 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7908 (tm-30) REVERT: B 264 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7566 (mm-30) REVERT: B 337 MET cc_start: 0.7699 (mtm) cc_final: 0.7116 (ptp) REVERT: B 387 LYS cc_start: 0.4518 (tppt) cc_final: 0.3941 (mppt) REVERT: B 440 ASP cc_start: 0.8779 (m-30) cc_final: 0.8043 (m-30) REVERT: C 55 LEU cc_start: 0.7150 (mt) cc_final: 0.6777 (tp) REVERT: C 60 VAL cc_start: 0.7412 (t) cc_final: 0.7178 (p) outliers start: 29 outliers final: 24 residues processed: 161 average time/residue: 0.2148 time to fit residues: 43.8116 Evaluate side-chains 169 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 196 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.221172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.174201 restraints weight = 37388.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.184768 restraints weight = 15590.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.191651 restraints weight = 8660.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.196121 restraints weight = 5723.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.199144 restraints weight = 4250.736| |-----------------------------------------------------------------------------| r_work (final): 0.4793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5226 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7243 Z= 0.142 Angle : 0.632 7.256 9892 Z= 0.315 Chirality : 0.042 0.183 1113 Planarity : 0.005 0.042 1245 Dihedral : 8.393 63.652 1181 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.97 % Allowed : 13.70 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.29), residues: 840 helix: 1.40 (0.39), residues: 138 sheet: -0.36 (0.30), residues: 279 loop : 0.04 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 262 TYR 0.015 0.002 TYR C 209 PHE 0.016 0.002 PHE B 286 TRP 0.016 0.001 TRP B 356 HIS 0.005 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7232) covalent geometry : angle 0.62343 ( 9859) hydrogen bonds : bond 0.04437 ( 282) hydrogen bonds : angle 5.81230 ( 807) link_BETA1-4 : bond 0.00239 ( 5) link_BETA1-4 : angle 1.22371 ( 15) link_NAG-ASN : bond 0.00121 ( 6) link_NAG-ASN : angle 2.32064 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 CYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8030 (m) REVERT: A 216 ASP cc_start: 0.8292 (t0) cc_final: 0.7728 (m-30) REVERT: B 204 GLN cc_start: 0.0786 (OUTLIER) cc_final: -0.0830 (tt0) REVERT: B 208 ASP cc_start: 0.1374 (OUTLIER) cc_final: 0.0598 (t70) REVERT: B 260 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7893 (tm-30) REVERT: B 264 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7527 (mm-30) REVERT: B 289 SER cc_start: 0.8238 (OUTLIER) cc_final: 0.7855 (t) REVERT: B 387 LYS cc_start: 0.4467 (tppt) cc_final: 0.3961 (mppt) REVERT: C 60 VAL cc_start: 0.7418 (t) cc_final: 0.7199 (p) REVERT: C 96 ASP cc_start: 0.8433 (m-30) cc_final: 0.7837 (m-30) REVERT: C 136 GLU cc_start: 0.9056 (pm20) cc_final: 0.8799 (pm20) outliers start: 23 outliers final: 16 residues processed: 157 average time/residue: 0.2228 time to fit residues: 43.6746 Evaluate side-chains 161 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 187 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.221619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.174749 restraints weight = 37618.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.185421 restraints weight = 15757.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.192177 restraints weight = 8753.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.196807 restraints weight = 5820.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.199675 restraints weight = 4303.342| |-----------------------------------------------------------------------------| r_work (final): 0.4794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5260 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7243 Z= 0.139 Angle : 0.624 7.141 9892 Z= 0.309 Chirality : 0.042 0.180 1113 Planarity : 0.005 0.041 1245 Dihedral : 8.179 63.039 1181 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.10 % Allowed : 13.95 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.29), residues: 840 helix: 1.68 (0.39), residues: 138 sheet: -0.29 (0.29), residues: 290 loop : 0.03 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 81 TYR 0.018 0.002 TYR C 209 PHE 0.017 0.002 PHE B 96 TRP 0.016 0.001 TRP B 356 HIS 0.005 0.001 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7232) covalent geometry : angle 0.61535 ( 9859) hydrogen bonds : bond 0.04271 ( 282) hydrogen bonds : angle 5.74673 ( 807) link_BETA1-4 : bond 0.00242 ( 5) link_BETA1-4 : angle 1.24706 ( 15) link_NAG-ASN : bond 0.00163 ( 6) link_NAG-ASN : angle 2.27739 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 CYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7900 (m) REVERT: A 216 ASP cc_start: 0.8346 (t0) cc_final: 0.7719 (m-30) REVERT: B 204 GLN cc_start: 0.0809 (OUTLIER) cc_final: -0.0780 (tt0) REVERT: B 208 ASP cc_start: 0.1423 (OUTLIER) cc_final: 0.0647 (t70) REVERT: B 260 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 264 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7475 (mm-30) REVERT: B 387 LYS cc_start: 0.4410 (tppt) cc_final: 0.3955 (mppt) REVERT: C 60 VAL cc_start: 0.7431 (t) cc_final: 0.7218 (p) REVERT: C 96 ASP cc_start: 0.8391 (m-30) cc_final: 0.7843 (m-30) REVERT: C 136 GLU cc_start: 0.9030 (pm20) cc_final: 0.8810 (pm20) outliers start: 24 outliers final: 20 residues processed: 149 average time/residue: 0.2295 time to fit residues: 42.5515 Evaluate side-chains 161 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 187 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 21 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.214810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.167684 restraints weight = 40091.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.177718 restraints weight = 16806.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.184147 restraints weight = 9412.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.188473 restraints weight = 6323.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.191115 restraints weight = 4760.368| |-----------------------------------------------------------------------------| r_work (final): 0.4664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5405 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7243 Z= 0.253 Angle : 0.748 7.940 9892 Z= 0.383 Chirality : 0.044 0.172 1113 Planarity : 0.006 0.061 1245 Dihedral : 8.843 65.783 1181 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.13 % Allowed : 14.73 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.29), residues: 840 helix: 1.10 (0.41), residues: 138 sheet: -0.74 (0.29), residues: 303 loop : -0.14 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 202 TYR 0.022 0.003 TYR C 209 PHE 0.024 0.002 PHE C 92 TRP 0.022 0.002 TRP C 214 HIS 0.010 0.002 HIS C 63 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 7232) covalent geometry : angle 0.73741 ( 9859) hydrogen bonds : bond 0.05178 ( 282) hydrogen bonds : angle 6.17705 ( 807) link_BETA1-4 : bond 0.00357 ( 5) link_BETA1-4 : angle 1.84465 ( 15) link_NAG-ASN : bond 0.00532 ( 6) link_NAG-ASN : angle 2.56841 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 CYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7965 (m) REVERT: B 204 GLN cc_start: 0.1274 (OUTLIER) cc_final: 0.0323 (tt0) REVERT: B 208 ASP cc_start: 0.1616 (OUTLIER) cc_final: 0.1108 (t70) REVERT: B 264 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7366 (mm-30) REVERT: B 289 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.7967 (t) REVERT: B 387 LYS cc_start: 0.4707 (tppt) cc_final: 0.4257 (mppt) REVERT: C 60 VAL cc_start: 0.7371 (t) cc_final: 0.7100 (p) REVERT: C 206 GLU cc_start: 0.8179 (tp30) cc_final: 0.7824 (tp30) outliers start: 32 outliers final: 26 residues processed: 151 average time/residue: 0.2369 time to fit residues: 44.6574 Evaluate side-chains 156 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 187 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 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 = 0.4963 r_free = 0.4963 target = 0.217016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.169623 restraints weight = 40346.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.179605 restraints weight = 17204.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.186020 restraints weight = 9745.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.190393 restraints weight = 6592.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.193210 restraints weight = 4971.374| |-----------------------------------------------------------------------------| r_work (final): 0.4699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5379 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7243 Z= 0.180 Angle : 0.681 7.274 9892 Z= 0.343 Chirality : 0.043 0.171 1113 Planarity : 0.006 0.073 1245 Dihedral : 8.672 64.749 1181 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.88 % Allowed : 15.76 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.29), residues: 840 helix: 1.25 (0.40), residues: 138 sheet: -0.66 (0.29), residues: 298 loop : -0.19 (0.34), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 124 TYR 0.018 0.002 TYR C 209 PHE 0.010 0.002 PHE A 91 TRP 0.016 0.002 TRP B 215 HIS 0.008 0.002 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 7232) covalent geometry : angle 0.67248 ( 9859) hydrogen bonds : bond 0.04686 ( 282) hydrogen bonds : angle 5.99993 ( 807) link_BETA1-4 : bond 0.00196 ( 5) link_BETA1-4 : angle 1.43546 ( 15) link_NAG-ASN : bond 0.00262 ( 6) link_NAG-ASN : angle 2.37122 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 CYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7939 (m) REVERT: A 216 ASP cc_start: 0.8281 (t0) cc_final: 0.7736 (m-30) REVERT: B 204 GLN cc_start: 0.1603 (OUTLIER) cc_final: 0.0844 (tt0) REVERT: B 208 ASP cc_start: 0.1715 (OUTLIER) cc_final: 0.1224 (t70) REVERT: B 264 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7433 (mm-30) REVERT: B 289 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.7912 (t) REVERT: B 370 ARG cc_start: 0.8756 (ttt-90) cc_final: 0.8533 (mmm160) REVERT: B 387 LYS cc_start: 0.4697 (tppt) cc_final: 0.4298 (mppt) REVERT: C 136 GLU cc_start: 0.9129 (pm20) cc_final: 0.8867 (pm20) REVERT: C 187 GLU cc_start: 0.7559 (tt0) cc_final: 0.7292 (tt0) REVERT: C 206 GLU cc_start: 0.8176 (tp30) cc_final: 0.7825 (tp30) outliers start: 30 outliers final: 23 residues processed: 150 average time/residue: 0.2259 time to fit residues: 42.7662 Evaluate side-chains 158 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 75 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 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 = 0.4978 r_free = 0.4978 target = 0.218690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.171375 restraints weight = 40051.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.181432 restraints weight = 17113.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.188038 restraints weight = 9679.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.192290 restraints weight = 6489.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.195245 restraints weight = 4913.181| |-----------------------------------------------------------------------------| r_work (final): 0.4723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5340 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7243 Z= 0.143 Angle : 0.646 7.077 9892 Z= 0.321 Chirality : 0.042 0.165 1113 Planarity : 0.005 0.066 1245 Dihedral : 8.373 63.500 1181 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.49 % Allowed : 15.89 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.30), residues: 840 helix: 1.59 (0.40), residues: 137 sheet: -0.54 (0.29), residues: 298 loop : -0.09 (0.34), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 124 TYR 0.030 0.002 TYR C 197 PHE 0.011 0.001 PHE B 334 TRP 0.016 0.002 TRP B 356 HIS 0.007 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7232) covalent geometry : angle 0.63721 ( 9859) hydrogen bonds : bond 0.04329 ( 282) hydrogen bonds : angle 5.74578 ( 807) link_BETA1-4 : bond 0.00277 ( 5) link_BETA1-4 : angle 1.31673 ( 15) link_NAG-ASN : bond 0.00140 ( 6) link_NAG-ASN : angle 2.27804 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 CYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8001 (m) REVERT: A 145 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8907 (mm110) REVERT: A 216 ASP cc_start: 0.8294 (t0) cc_final: 0.7720 (m-30) REVERT: B 39 TYR cc_start: 0.1256 (t80) cc_final: 0.0966 (t80) REVERT: B 204 GLN cc_start: 0.1451 (OUTLIER) cc_final: 0.0698 (tt0) REVERT: B 208 ASP cc_start: 0.1499 (OUTLIER) cc_final: 0.1050 (t70) REVERT: B 264 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7425 (mm-30) REVERT: B 370 ARG cc_start: 0.8748 (ttt-90) cc_final: 0.8509 (mmm160) REVERT: B 387 LYS cc_start: 0.4685 (tppt) cc_final: 0.4313 (mppt) REVERT: C 96 ASP cc_start: 0.8465 (m-30) cc_final: 0.7888 (m-30) REVERT: C 136 GLU cc_start: 0.9094 (pm20) cc_final: 0.8829 (pm20) REVERT: C 187 GLU cc_start: 0.7627 (tt0) cc_final: 0.7367 (tt0) REVERT: C 206 GLU cc_start: 0.8199 (tp30) cc_final: 0.7817 (tp30) outliers start: 27 outliers final: 22 residues processed: 146 average time/residue: 0.2383 time to fit residues: 43.4330 Evaluate side-chains 155 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 67 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 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 = 0.4966 r_free = 0.4966 target = 0.217171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.169910 restraints weight = 39683.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.179805 restraints weight = 16991.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.186254 restraints weight = 9629.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.190529 restraints weight = 6480.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.193438 restraints weight = 4906.508| |-----------------------------------------------------------------------------| r_work (final): 0.4709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5362 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7243 Z= 0.162 Angle : 0.657 7.140 9892 Z= 0.328 Chirality : 0.042 0.164 1113 Planarity : 0.005 0.065 1245 Dihedral : 8.277 62.274 1181 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.36 % Allowed : 15.89 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.30), residues: 840 helix: 1.66 (0.40), residues: 137 sheet: -0.57 (0.29), residues: 298 loop : -0.11 (0.34), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 124 TYR 0.015 0.002 TYR C 209 PHE 0.011 0.002 PHE B 326 TRP 0.016 0.002 TRP B 356 HIS 0.006 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7232) covalent geometry : angle 0.64800 ( 9859) hydrogen bonds : bond 0.04457 ( 282) hydrogen bonds : angle 5.74223 ( 807) link_BETA1-4 : bond 0.00217 ( 5) link_BETA1-4 : angle 1.37193 ( 15) link_NAG-ASN : bond 0.00227 ( 6) link_NAG-ASN : angle 2.38431 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 CYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8022 (m) REVERT: A 145 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8933 (mm110) REVERT: B 39 TYR cc_start: 0.1290 (t80) cc_final: 0.1014 (t80) REVERT: B 204 GLN cc_start: 0.1457 (OUTLIER) cc_final: 0.0760 (tt0) REVERT: B 208 ASP cc_start: 0.1546 (OUTLIER) cc_final: 0.1106 (t70) REVERT: B 264 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7397 (mm-30) REVERT: B 387 LYS cc_start: 0.4708 (tppt) cc_final: 0.4335 (mppt) REVERT: C 96 ASP cc_start: 0.8491 (m-30) cc_final: 0.7892 (m-30) REVERT: C 136 GLU cc_start: 0.9097 (pm20) cc_final: 0.8828 (pm20) REVERT: C 206 GLU cc_start: 0.8261 (tp30) cc_final: 0.7888 (tp30) outliers start: 26 outliers final: 19 residues processed: 149 average time/residue: 0.2288 time to fit residues: 42.4488 Evaluate side-chains 151 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 chunk 5 optimal weight: 0.0050 chunk 32 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 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 = 0.4996 r_free = 0.4996 target = 0.220257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.172896 restraints weight = 39594.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.183063 restraints weight = 16819.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.189632 restraints weight = 9478.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.194110 restraints weight = 6378.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.197000 restraints weight = 4792.621| |-----------------------------------------------------------------------------| r_work (final): 0.4743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5284 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7243 Z= 0.115 Angle : 0.624 7.124 9892 Z= 0.307 Chirality : 0.043 0.178 1113 Planarity : 0.005 0.054 1245 Dihedral : 7.951 59.894 1181 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.45 % Allowed : 17.05 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.30), residues: 840 helix: 2.00 (0.40), residues: 136 sheet: -0.41 (0.30), residues: 292 loop : -0.07 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 370 TYR 0.022 0.002 TYR A 32 PHE 0.024 0.002 PHE A 290 TRP 0.018 0.001 TRP B 356 HIS 0.009 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7232) covalent geometry : angle 0.61545 ( 9859) hydrogen bonds : bond 0.03991 ( 282) hydrogen bonds : angle 5.46195 ( 807) link_BETA1-4 : bond 0.00287 ( 5) link_BETA1-4 : angle 1.27131 ( 15) link_NAG-ASN : bond 0.00108 ( 6) link_NAG-ASN : angle 2.25535 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2938.21 seconds wall clock time: 50 minutes 37.12 seconds (3037.12 seconds total)