Starting phenix.real_space_refine on Fri Jul 3 07:01:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dia_46902/07_2026/9dia_46902.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dia_46902/07_2026/9dia_46902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dia_46902/07_2026/9dia_46902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dia_46902/07_2026/9dia_46902.map" model { file = "/net/cci-nas-00/data/ceres_data/9dia_46902/07_2026/9dia_46902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dia_46902/07_2026/9dia_46902.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 Mn 2 7.51 5 S 23 5.16 5 C 4362 2.51 5 N 1125 2.21 5 O 1388 1.98 5 H 5806 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12709 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6515 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 449, 6486 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 31, 'TRANS': 417} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 449, 6486 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 31, 'TRANS': 417} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 6547 Chain: "B" Number of atoms: 5502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5502 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 15, 'TRANS': 355} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 57 Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 445 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 61} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "D" 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: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 14 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 56 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.17, per 1000 atoms: 0.25 Number of scatterers: 12709 At special positions: 0 Unit cell: (72.93, 92.004, 104.346, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 2 24.99 Ca 3 19.99 S 23 16.00 O 1388 8.00 N 1125 7.00 C 4362 6.00 H 5806 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 281 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " BMA E 3 " - " NAG E 5 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " BETA1-6 " NAG F 1 " - " FUC F 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1002 " - " ASN A 256 " " NAG B 801 " - " ASN B 249 " " NAG B 802 " - " ASN B 386 " " NAG B 803 " - " ASN B 397 " " NAG B 804 " - " ASN B 192 " " NAG D 1 " - " ASN A 266 " " NAG E 1 " - " ASN A 275 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN A 43 " " NAG H 1 " - " ASN B 343 " Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 536.8 milliseconds 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1582 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 14 sheets defined 17.7% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 80 through 86 Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.599A pdb=" N TRP A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 203 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.778A pdb=" N GLU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 154 removed outlier: 3.631A pdb=" N MET B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 Processing helix chain 'B' and resid 208 through 218 removed outlier: 3.792A pdb=" N PHE B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 242 removed outlier: 4.312A pdb=" N GLY B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 removed outlier: 3.639A pdb=" N LYS B 269 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 270 " --> pdb=" O ASP B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 310 Processing helix chain 'B' and resid 321 through 332 removed outlier: 3.656A pdb=" N TYR B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 388 through 392 Processing helix chain 'C' and resid 13 through 15 No H-bonds generated for 'chain 'C' and resid 13 through 15' Processing helix chain 'C' and resid 16 through 26 removed outlier: 3.889A pdb=" N GLU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 58 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 3.887A pdb=" N SER A 120 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 108 removed outlier: 3.755A pdb=" N THR A 134 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.927A pdb=" N SER A 169 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 238 removed outlier: 6.417A pdb=" N VAL A 262 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASN A 275 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A 264 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 289 through 292 Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 312 Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 359 removed outlier: 5.690A pdb=" N ASP A 368 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 400 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 69 Processing sheet with id=AB2, first strand: chain 'B' and resid 109 through 116 removed outlier: 3.593A pdb=" N GLN B 405 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 199 through 206 removed outlier: 6.637A pdb=" N VAL B 202 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N SER B 166 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N SER B 204 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N PHE B 164 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP B 124 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL B 255 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR B 126 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N SER B 257 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 128 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG B 252 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE B 314 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU B 254 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA B 316 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE B 256 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N ALA B 336 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR B 313 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLY B 338 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE B 315 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 283 through 284 Processing sheet with id=AB5, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.622A pdb=" N LYS C 29 " --> pdb=" O LYS C 40 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 576 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: 2.90 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5808 1.03 - 1.23: 22 1.23 - 1.42: 2954 1.42 - 1.62: 4040 1.62 - 1.81: 33 Bond restraints: 12857 Sorted by residual: bond pdb=" C1 MAN E 4 " pdb=" C2 MAN E 4 " ideal model delta sigma weight residual 1.526 1.566 -0.040 2.00e-02 2.50e+03 4.05e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C1 NAG E 5 " pdb=" O5 NAG E 5 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" N PHE A 1 " pdb=" CA PHE A 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.58e+00 bond pdb=" C1 MAN E 4 " pdb=" O5 MAN E 4 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.49e+00 ... (remaining 12852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 21939 1.25 - 2.51: 782 2.51 - 3.76: 62 3.76 - 5.01: 18 5.01 - 6.27: 7 Bond angle restraints: 22808 Sorted by residual: angle pdb=" C MET A 281 " pdb=" N ALA A 282 " pdb=" CA ALA A 282 " ideal model delta sigma weight residual 121.54 125.89 -4.35 1.91e+00 2.74e-01 5.18e+00 angle pdb=" N SER A 283 " pdb=" CA SER A 283 " pdb=" C SER A 283 " ideal model delta sigma weight residual 109.15 106.08 3.07 1.44e+00 4.82e-01 4.54e+00 angle pdb=" C3 MAN E 4 " pdb=" C2 MAN E 4 " pdb=" O2 MAN E 4 " ideal model delta sigma weight residual 111.77 105.50 6.27 3.00e+00 1.11e-01 4.37e+00 angle pdb=" C3 BMA E 3 " pdb=" C2 BMA E 3 " pdb=" O2 BMA E 3 " ideal model delta sigma weight residual 112.95 106.69 6.26 3.00e+00 1.11e-01 4.36e+00 angle pdb=" N ASP A 269 " pdb=" CA ASP A 269 " pdb=" C ASP A 269 " ideal model delta sigma weight residual 110.80 106.50 4.30 2.13e+00 2.20e-01 4.07e+00 ... (remaining 22803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.66: 6009 21.66 - 43.31: 372 43.31 - 64.97: 109 64.97 - 86.62: 17 86.62 - 108.28: 7 Dihedral angle restraints: 6514 sinusoidal: 3587 harmonic: 2927 Sorted by residual: dihedral pdb=" CB CYS A 151 " pdb=" SG CYS A 151 " pdb=" SG CYS A 164 " pdb=" CB CYS A 164 " ideal model delta sinusoidal sigma weight residual 93.00 35.42 57.58 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" CA TYR B 133 " pdb=" C TYR B 133 " pdb=" N SER B 134 " pdb=" CA SER B 134 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA SER A 283 " pdb=" C SER A 283 " pdb=" N TYR A 284 " pdb=" CA TYR A 284 " ideal model delta harmonic sigma weight residual -180.00 -161.17 -18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 6511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 916 0.051 - 0.103: 138 0.103 - 0.154: 62 0.154 - 0.206: 0 0.206 - 0.257: 2 Chirality restraints: 1118 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 43 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C1 NAG B 801 " pdb=" ND2 ASN B 249 " pdb=" C2 NAG B 801 " pdb=" O5 NAG B 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 1115 not shown) Planarity restraints: 2013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 121 " -0.011 2.00e-02 2.50e+03 1.16e-02 5.34e+00 pdb=" CG TRP A 121 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 121 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 121 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 121 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 121 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 121 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 121 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 121 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 121 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP A 121 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP A 121 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP A 121 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 121 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 121 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 121 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 285 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C ASN B 285 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN B 285 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN B 286 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 91 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO A 92 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " -0.022 5.00e-02 4.00e+02 ... (remaining 2010 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 116 2.05 - 2.68: 17977 2.68 - 3.32: 34703 3.32 - 3.96: 46754 3.96 - 4.60: 72665 Nonbonded interactions: 172215 Sorted by model distance: nonbonded pdb="HD21 ASN B 224 " pdb=" H LEU B 225 " model vdw 1.408 2.100 nonbonded pdb=" HG SER B 134 " pdb="MN MN B 805 " model vdw 1.571 2.590 nonbonded pdb=" OE1 GLU A 124 " pdb=" H GLU A 124 " model vdw 1.612 2.450 nonbonded pdb=" ND2 ASN B 224 " pdb=" H LEU B 225 " model vdw 1.628 2.600 nonbonded pdb=" OE1 GLU A 81 " pdb=" H GLU A 81 " model vdw 1.635 2.450 ... (remaining 172210 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 'D' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'H' and resid 1) } 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=0.14 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.200 Find NCS groups from input model: 0.070 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7072 Z= 0.156 Angle : 0.557 6.268 9652 Z= 0.252 Chirality : 0.045 0.257 1118 Planarity : 0.003 0.040 1233 Dihedral : 15.044 108.279 2796 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.42 % Allowed : 0.56 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.29), residues: 877 helix: 1.02 (0.49), residues: 129 sheet: 0.16 (0.33), residues: 265 loop : -0.77 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 155 TYR 0.007 0.001 TYR A 205 PHE 0.008 0.001 PHE A 172 TRP 0.037 0.002 TRP A 121 HIS 0.002 0.000 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 ( 7049) covalent geometry : angle 0.54441 / 0.25 ( 9588) SS BOND : bond 0.00135 / 0.08 ( 5) SS BOND : angle 0.58353 / 0.36 ( 10) hydrogen bonds : bond 0.20918 / 14.78 ( 219) hydrogen bonds : angle 8.73122 / 6.11 ( 576) link_ALPHA1-3 : bond 0.00916 / 0.48 ( 1) link_ALPHA1-3 : angle 1.21123 / 0.87 ( 3) link_BETA1-4 : bond 0.00622 / 0.36 ( 6) link_BETA1-4 : angle 2.00944 / 1.23 ( 18) link_BETA1-6 : bond 0.00427 / 0.22 ( 1) link_BETA1-6 : angle 1.38704 / 1.05 ( 3) link_NAG-ASN : bond 0.00201 / 0.10 ( 10) link_NAG-ASN : angle 1.45380 / 1.01 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7826 (tp30) REVERT: B 383 ASN cc_start: 0.8507 (m110) cc_final: 0.8287 (m110) outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 1.0385 time to fit residues: 63.9821 Evaluate side-chains 43 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 343 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.101068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.079019 restraints weight = 40167.758| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.18 r_work: 0.3022 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (11 function evaluations) r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7072 Z= 0.133 Angle : 0.557 6.907 9652 Z= 0.279 Chirality : 0.044 0.191 1118 Planarity : 0.004 0.039 1233 Dihedral : 9.751 88.785 1325 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.13 % Allowed : 5.78 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.29), residues: 877 helix: 0.68 (0.46), residues: 136 sheet: 0.12 (0.32), residues: 266 loop : -0.80 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 184 TYR 0.008 0.001 TYR B 325 PHE 0.011 0.001 PHE A 172 TRP 0.016 0.001 TRP A 121 HIS 0.002 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 7049) covalent geometry : angle 0.54207 / 0.28 ( 9588) SS BOND : bond 0.00170 / 0.11 ( 5) SS BOND : angle 0.62741 / 0.38 ( 10) hydrogen bonds : bond 0.04258 / 3.01 ( 219) hydrogen bonds : angle 6.55910 / 4.51 ( 576) link_ALPHA1-3 : bond 0.01081 / 0.57 ( 1) link_ALPHA1-3 : angle 2.06751 / 1.22 ( 3) link_BETA1-4 : bond 0.00611 / 0.35 ( 6) link_BETA1-4 : angle 2.20809 / 1.34 ( 18) link_BETA1-6 : bond 0.00423 / 0.22 ( 1) link_BETA1-6 : angle 1.43226 / 1.12 ( 3) link_NAG-ASN : bond 0.00263 / 0.14 ( 10) link_NAG-ASN : angle 1.43136 / 0.92 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8145 (tp30) REVERT: A 317 ARG cc_start: 0.8304 (mtp-110) cc_final: 0.7931 (mtm110) REVERT: B 129 MET cc_start: 0.8566 (ttm) cc_final: 0.8347 (ttt) REVERT: B 383 ASN cc_start: 0.8747 (m110) cc_final: 0.8460 (m110) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 1.0554 time to fit residues: 52.8575 Evaluate side-chains 45 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain C residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.100173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.078302 restraints weight = 37025.756| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.08 r_work: 0.3007 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7072 Z= 0.150 Angle : 0.542 7.128 9652 Z= 0.268 Chirality : 0.044 0.159 1118 Planarity : 0.004 0.085 1233 Dihedral : 9.155 84.940 1325 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.41 % Allowed : 6.63 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.28), residues: 877 helix: 0.67 (0.46), residues: 136 sheet: 0.03 (0.32), residues: 265 loop : -0.86 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 220 TYR 0.012 0.001 TYR A 261 PHE 0.010 0.001 PHE A 172 TRP 0.010 0.001 TRP A 121 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 7049) covalent geometry : angle 0.52599 / 0.27 ( 9588) SS BOND : bond 0.00205 / 0.13 ( 5) SS BOND : angle 0.59333 / 0.36 ( 10) hydrogen bonds : bond 0.03945 / 2.83 ( 219) hydrogen bonds : angle 6.02961 / 4.13 ( 576) link_ALPHA1-3 : bond 0.01188 / 0.63 ( 1) link_ALPHA1-3 : angle 1.50692 / 0.94 ( 3) link_BETA1-4 : bond 0.00606 / 0.36 ( 6) link_BETA1-4 : angle 2.28671 / 1.43 ( 18) link_BETA1-6 : bond 0.00485 / 0.26 ( 1) link_BETA1-6 : angle 1.33190 / 1.04 ( 3) link_NAG-ASN : bond 0.00336 / 0.21 ( 10) link_NAG-ASN : angle 1.50875 / 0.99 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8342 (tp30) REVERT: A 220 ARG cc_start: 0.8832 (mtm-85) cc_final: 0.8611 (mtp85) REVERT: B 129 MET cc_start: 0.8697 (ttm) cc_final: 0.8490 (ttt) outliers start: 8 outliers final: 6 residues processed: 45 average time/residue: 1.0935 time to fit residues: 52.5157 Evaluate side-chains 48 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 GLN B 72 ASN B 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.099312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.077617 restraints weight = 36245.859| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.03 r_work: 0.2999 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7072 Z= 0.173 Angle : 0.555 7.472 9652 Z= 0.273 Chirality : 0.044 0.158 1118 Planarity : 0.004 0.068 1233 Dihedral : 8.593 80.339 1325 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.55 % Allowed : 7.19 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.28), residues: 877 helix: 0.89 (0.47), residues: 125 sheet: -0.03 (0.33), residues: 259 loop : -0.93 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 220 TYR 0.012 0.001 TYR A 208 PHE 0.013 0.001 PHE A 172 TRP 0.009 0.001 TRP A 121 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 ( 7049) covalent geometry : angle 0.53770 / 0.27 ( 9588) SS BOND : bond 0.00227 / 0.14 ( 5) SS BOND : angle 0.64361 / 0.40 ( 10) hydrogen bonds : bond 0.03529 / 2.50 ( 219) hydrogen bonds : angle 5.65656 / 3.86 ( 576) link_ALPHA1-3 : bond 0.01300 / 0.68 ( 1) link_ALPHA1-3 : angle 1.43113 / 0.90 ( 3) link_BETA1-4 : bond 0.00602 / 0.35 ( 6) link_BETA1-4 : angle 2.35554 / 1.48 ( 18) link_BETA1-6 : bond 0.00396 / 0.21 ( 1) link_BETA1-6 : angle 1.43884 / 1.14 ( 3) link_NAG-ASN : bond 0.00388 / 0.25 ( 10) link_NAG-ASN : angle 1.63266 / 1.08 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 51 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8353 (tp30) REVERT: A 220 ARG cc_start: 0.8847 (mtm-85) cc_final: 0.8630 (mtp85) REVERT: A 317 ARG cc_start: 0.8217 (mtp-110) cc_final: 0.7884 (mtm110) REVERT: B 129 MET cc_start: 0.8679 (ttm) cc_final: 0.8476 (ttt) outliers start: 9 outliers final: 5 residues processed: 46 average time/residue: 1.1801 time to fit residues: 57.5148 Evaluate side-chains 46 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 ASN B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.099266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.077201 restraints weight = 39813.234| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.17 r_work: 0.2988 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7072 Z= 0.167 Angle : 0.548 7.453 9652 Z= 0.269 Chirality : 0.044 0.151 1118 Planarity : 0.004 0.053 1233 Dihedral : 8.311 76.837 1325 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.41 % Allowed : 8.32 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.28), residues: 877 helix: 0.91 (0.48), residues: 125 sheet: -0.01 (0.33), residues: 257 loop : -0.97 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 220 TYR 0.013 0.001 TYR A 208 PHE 0.011 0.001 PHE A 172 TRP 0.007 0.001 TRP A 121 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 7049) covalent geometry : angle 0.53121 / 0.27 ( 9588) SS BOND : bond 0.00225 / 0.14 ( 5) SS BOND : angle 0.57312 / 0.35 ( 10) hydrogen bonds : bond 0.03430 / 2.41 ( 219) hydrogen bonds : angle 5.51576 / 3.77 ( 576) link_ALPHA1-3 : bond 0.01262 / 0.66 ( 1) link_ALPHA1-3 : angle 1.41728 / 0.90 ( 3) link_BETA1-4 : bond 0.00629 / 0.37 ( 6) link_BETA1-4 : angle 2.33793 / 1.46 ( 18) link_BETA1-6 : bond 0.00408 / 0.21 ( 1) link_BETA1-6 : angle 1.39288 / 1.06 ( 3) link_NAG-ASN : bond 0.00362 / 0.23 ( 10) link_NAG-ASN : angle 1.58525 / 1.05 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 51 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8210 (tp30) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 1.1186 time to fit residues: 55.9039 Evaluate side-chains 46 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 2 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 ASN B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.099190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.078186 restraints weight = 43681.164| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.16 r_work: 0.2996 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7072 Z= 0.123 Angle : 0.529 7.211 9652 Z= 0.259 Chirality : 0.043 0.149 1118 Planarity : 0.005 0.093 1233 Dihedral : 7.948 71.673 1325 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.41 % Allowed : 8.60 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.28), residues: 877 helix: 1.01 (0.48), residues: 125 sheet: -0.12 (0.32), residues: 263 loop : -0.93 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 220 TYR 0.011 0.001 TYR A 208 PHE 0.009 0.001 PHE A 172 TRP 0.006 0.001 TRP A 157 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 7049) covalent geometry : angle 0.51313 / 0.26 ( 9588) SS BOND : bond 0.00178 / 0.12 ( 5) SS BOND : angle 0.54051 / 0.32 ( 10) hydrogen bonds : bond 0.03126 / 2.18 ( 219) hydrogen bonds : angle 5.32746 / 3.65 ( 576) link_ALPHA1-3 : bond 0.01220 / 0.64 ( 1) link_ALPHA1-3 : angle 1.56666 / 0.98 ( 3) link_BETA1-4 : bond 0.00597 / 0.36 ( 6) link_BETA1-4 : angle 2.32183 / 1.43 ( 18) link_BETA1-6 : bond 0.00441 / 0.23 ( 1) link_BETA1-6 : angle 1.32471 / 1.01 ( 3) link_NAG-ASN : bond 0.00259 / 0.16 ( 10) link_NAG-ASN : angle 1.47183 / 0.96 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 49 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8210 (tp30) REVERT: A 220 ARG cc_start: 0.8688 (mtm-85) cc_final: 0.8454 (mtp85) REVERT: A 317 ARG cc_start: 0.8110 (mtp-110) cc_final: 0.7807 (mtm110) outliers start: 8 outliers final: 5 residues processed: 45 average time/residue: 1.1022 time to fit residues: 52.8534 Evaluate side-chains 46 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 ASN B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.098748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.078154 restraints weight = 38153.324| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.98 r_work: 0.3007 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7072 Z= 0.149 Angle : 0.537 7.016 9652 Z= 0.263 Chirality : 0.044 0.149 1118 Planarity : 0.004 0.081 1233 Dihedral : 7.706 67.097 1325 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.27 % Allowed : 8.46 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.28), residues: 877 helix: 0.99 (0.48), residues: 125 sheet: -0.07 (0.32), residues: 257 loop : -0.97 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 220 TYR 0.010 0.001 TYR A 208 PHE 0.010 0.001 PHE A 172 TRP 0.006 0.001 TRP A 157 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 7049) covalent geometry : angle 0.52070 / 0.26 ( 9588) SS BOND : bond 0.00197 / 0.12 ( 5) SS BOND : angle 0.57311 / 0.35 ( 10) hydrogen bonds : bond 0.03144 / 2.16 ( 219) hydrogen bonds : angle 5.24002 / 3.60 ( 576) link_ALPHA1-3 : bond 0.01203 / 0.63 ( 1) link_ALPHA1-3 : angle 1.37374 / 0.89 ( 3) link_BETA1-4 : bond 0.00602 / 0.36 ( 6) link_BETA1-4 : angle 2.36051 / 1.47 ( 18) link_BETA1-6 : bond 0.00398 / 0.21 ( 1) link_BETA1-6 : angle 1.40767 / 1.07 ( 3) link_NAG-ASN : bond 0.00329 / 0.21 ( 10) link_NAG-ASN : angle 1.56160 / 1.02 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 49 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8337 (tp30) REVERT: A 220 ARG cc_start: 0.8851 (mtm-85) cc_final: 0.8599 (mtp85) REVERT: A 312 ARG cc_start: 0.8481 (ptp-110) cc_final: 0.8080 (ttm110) REVERT: A 317 ARG cc_start: 0.8120 (mtp-110) cc_final: 0.7804 (mtm110) outliers start: 7 outliers final: 5 residues processed: 46 average time/residue: 1.1775 time to fit residues: 57.4399 Evaluate side-chains 47 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 7 optimal weight: 0.4980 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 ASN B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.100127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.078484 restraints weight = 35967.129| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.05 r_work: 0.3015 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7072 Z= 0.124 Angle : 0.525 6.860 9652 Z= 0.256 Chirality : 0.044 0.151 1118 Planarity : 0.004 0.079 1233 Dihedral : 7.291 58.766 1325 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.13 % Allowed : 8.89 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.28), residues: 877 helix: 1.13 (0.49), residues: 124 sheet: -0.12 (0.32), residues: 262 loop : -0.93 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 220 TYR 0.013 0.001 TYR A 205 PHE 0.009 0.001 PHE A 172 TRP 0.006 0.001 TRP A 157 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 ( 7049) covalent geometry : angle 0.50930 / 0.25 ( 9588) SS BOND : bond 0.00174 / 0.11 ( 5) SS BOND : angle 0.54180 / 0.33 ( 10) hydrogen bonds : bond 0.02973 / 2.03 ( 219) hydrogen bonds : angle 5.13706 / 3.52 ( 576) link_ALPHA1-3 : bond 0.01135 / 0.60 ( 1) link_ALPHA1-3 : angle 1.51836 / 1.00 ( 3) link_BETA1-4 : bond 0.00611 / 0.37 ( 6) link_BETA1-4 : angle 2.34470 / 1.44 ( 18) link_BETA1-6 : bond 0.00442 / 0.23 ( 1) link_BETA1-6 : angle 1.32063 / 0.98 ( 3) link_NAG-ASN : bond 0.00244 / 0.15 ( 10) link_NAG-ASN : angle 1.45787 / 0.94 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 49 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8256 (tp30) REVERT: A 312 ARG cc_start: 0.8476 (ptp-110) cc_final: 0.8120 (ttm110) REVERT: A 317 ARG cc_start: 0.8121 (mtp-110) cc_final: 0.7809 (mtm110) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 1.0676 time to fit residues: 52.0790 Evaluate side-chains 46 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 69 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 ASN B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.100320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.078195 restraints weight = 41988.976| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.28 r_work: 0.3005 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7072 Z= 0.119 Angle : 0.519 6.751 9652 Z= 0.253 Chirality : 0.044 0.173 1118 Planarity : 0.004 0.039 1233 Dihedral : 6.905 55.500 1323 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.13 % Allowed : 9.31 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.29), residues: 877 helix: 1.21 (0.49), residues: 124 sheet: -0.11 (0.32), residues: 262 loop : -0.93 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 220 TYR 0.009 0.001 TYR A 208 PHE 0.008 0.001 PHE A 172 TRP 0.006 0.001 TRP A 157 HIS 0.002 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 7049) covalent geometry : angle 0.50321 / 0.25 ( 9588) SS BOND : bond 0.00166 / 0.11 ( 5) SS BOND : angle 0.56268 / 0.34 ( 10) hydrogen bonds : bond 0.02901 / 1.97 ( 219) hydrogen bonds : angle 5.05397 / 3.47 ( 576) link_ALPHA1-3 : bond 0.01119 / 0.59 ( 1) link_ALPHA1-3 : angle 1.47287 / 0.99 ( 3) link_BETA1-4 : bond 0.00600 / 0.36 ( 6) link_BETA1-4 : angle 2.33534 / 1.44 ( 18) link_BETA1-6 : bond 0.00416 / 0.22 ( 1) link_BETA1-6 : angle 1.31635 / 0.99 ( 3) link_NAG-ASN : bond 0.00238 / 0.15 ( 10) link_NAG-ASN : angle 1.45655 / 0.95 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 48 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8107 (tp30) REVERT: A 312 ARG cc_start: 0.8403 (ptp-110) cc_final: 0.8110 (ttm110) REVERT: A 317 ARG cc_start: 0.8053 (mtp-110) cc_final: 0.7749 (mtm110) REVERT: B 361 GLU cc_start: 0.7599 (pt0) cc_final: 0.7131 (pp20) outliers start: 6 outliers final: 5 residues processed: 45 average time/residue: 1.1726 time to fit residues: 56.0046 Evaluate side-chains 44 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.100199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.078280 restraints weight = 39520.476| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.19 r_work: 0.3011 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 7072 Z= 0.164 Angle : 0.912 59.199 9652 Z= 0.534 Chirality : 0.044 0.175 1118 Planarity : 0.004 0.041 1233 Dihedral : 6.905 55.515 1323 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.99 % Allowed : 9.17 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.29), residues: 877 helix: 1.21 (0.49), residues: 124 sheet: -0.11 (0.32), residues: 262 loop : -0.93 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.010 0.001 TYR A 208 PHE 0.008 0.001 PHE A 172 TRP 0.006 0.001 TRP A 157 HIS 0.002 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 7049) covalent geometry : angle 0.90457 / 0.53 ( 9588) SS BOND : bond 0.00181 / 0.11 ( 5) SS BOND : angle 0.56232 / 0.34 ( 10) hydrogen bonds : bond 0.02919 / 1.98 ( 219) hydrogen bonds : angle 5.05285 / 3.47 ( 576) link_ALPHA1-3 : bond 0.01138 / 0.60 ( 1) link_ALPHA1-3 : angle 1.57403 / 1.06 ( 3) link_BETA1-4 : bond 0.00628 / 0.37 ( 6) link_BETA1-4 : angle 2.35486 / 1.45 ( 18) link_BETA1-6 : bond 0.00325 / 0.17 ( 1) link_BETA1-6 : angle 1.26695 / 0.95 ( 3) link_NAG-ASN : bond 0.00245 / 0.15 ( 10) link_NAG-ASN : angle 1.45474 / 0.94 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1754 Ramachandran restraints generated. 877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 75 is missing expected H atoms. Skipping. Residue LYS 397 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LYS 378 is missing expected H atoms. Skipping. Residue LYS 414 is missing expected H atoms. Skipping. Residue LYS 417 is missing expected H atoms. Skipping. Residue LYS 418 is missing expected H atoms. Skipping. Evaluate side-chains 45 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8107 (tp30) REVERT: A 312 ARG cc_start: 0.8403 (ptp-110) cc_final: 0.8113 (ttm110) REVERT: A 317 ARG cc_start: 0.8055 (mtp-110) cc_final: 0.7752 (mtm110) REVERT: B 361 GLU cc_start: 0.7591 (pt0) cc_final: 0.7129 (pp20) outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 1.2557 time to fit residues: 55.7757 Evaluate side-chains 45 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.100193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.077971 restraints weight = 43557.724| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.32 r_work: 0.2996 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 7072 Z= 0.164 Angle : 0.912 59.199 9652 Z= 0.534 Chirality : 0.044 0.175 1118 Planarity : 0.004 0.041 1233 Dihedral : 6.905 55.515 1323 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.99 % Allowed : 9.31 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.29), residues: 877 helix: 1.21 (0.49), residues: 124 sheet: -0.11 (0.32), residues: 262 loop : -0.93 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.010 0.001 TYR A 208 PHE 0.008 0.001 PHE A 172 TRP 0.006 0.001 TRP A 157 HIS 0.002 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 7049) covalent geometry : angle 0.90457 / 0.53 ( 9588) SS BOND : bond 0.00181 / 0.11 ( 5) SS BOND : angle 0.56232 / 0.34 ( 10) hydrogen bonds : bond 0.02919 / 1.98 ( 219) hydrogen bonds : angle 5.05285 / 3.47 ( 576) link_ALPHA1-3 : bond 0.01138 / 0.60 ( 1) link_ALPHA1-3 : angle 1.57403 / 1.06 ( 3) link_BETA1-4 : bond 0.00628 / 0.37 ( 6) link_BETA1-4 : angle 2.35486 / 1.45 ( 18) link_BETA1-6 : bond 0.00325 / 0.17 ( 1) link_BETA1-6 : angle 1.26695 / 0.95 ( 3) link_NAG-ASN : bond 0.00245 / 0.15 ( 10) link_NAG-ASN : angle 1.45474 / 0.94 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3788.65 seconds wall clock time: 65 minutes 11.73 seconds (3911.73 seconds total)