Starting phenix.real_space_refine on Thu Sep 18 00:55:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dia_46902/09_2025/9dia_46902.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dia_46902/09_2025/9dia_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dia_46902/09_2025/9dia_46902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dia_46902/09_2025/9dia_46902.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dia_46902/09_2025/9dia_46902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dia_46902/09_2025/9dia_46902.map" } 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-2.0-5805/lib/python3.9/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, 17 Unusual residues: {' CA': 3, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 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, 58 Unusual residues: {' MN': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.68, per 1000 atoms: 0.29 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: 1.15 Conformation dependent library (CDL) restraints added in 596.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.34 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: 2.87 Time building geometry restraints manager: 1.64 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 1.850 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: 2.980 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: 0.100 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.850 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 aren 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 covalent geometry : bond 0.00332 ( 7049) covalent geometry : angle 0.54441 ( 9588) SS BOND : bond 0.00135 ( 5) SS BOND : angle 0.58353 ( 10) hydrogen bonds : bond 0.20918 ( 219) hydrogen bonds : angle 8.73122 ( 576) link_ALPHA1-3 : bond 0.00916 ( 1) link_ALPHA1-3 : angle 1.21123 ( 3) link_BETA1-4 : bond 0.00622 ( 6) link_BETA1-4 : angle 2.00944 ( 18) link_BETA1-6 : bond 0.00427 ( 1) link_BETA1-6 : angle 1.38704 ( 3) link_NAG-ASN : bond 0.00201 ( 10) link_NAG-ASN : angle 1.45380 ( 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 : 0.364 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: 1.1410 time to fit residues: 70.0104 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 : 0.248 ------------------------------------------------------------------------------- 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: 0.2980 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: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.100084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.079531 restraints weight = 40709.281| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.06 r_work: 0.3022 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 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 = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7072 Z= 0.125 Angle : 0.551 7.044 9652 Z= 0.276 Chirality : 0.044 0.187 1118 Planarity : 0.004 0.039 1233 Dihedral : 9.703 88.398 1325 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.99 % Allowed : 6.06 % Favored : 92.95 % 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 aren not related in a simple way. whole: -0.38 (0.29), residues: 877 helix: 0.72 (0.46), residues: 136 sheet: 0.16 (0.33), residues: 266 loop : -0.75 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 184 TYR 0.008 0.001 TYR B 325 PHE 0.010 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 covalent geometry : bond 0.00285 ( 7049) covalent geometry : angle 0.53719 ( 9588) SS BOND : bond 0.00161 ( 5) SS BOND : angle 0.60797 ( 10) hydrogen bonds : bond 0.04276 ( 219) hydrogen bonds : angle 6.52499 ( 576) link_ALPHA1-3 : bond 0.01108 ( 1) link_ALPHA1-3 : angle 2.05907 ( 3) link_BETA1-4 : bond 0.00648 ( 6) link_BETA1-4 : angle 2.17522 ( 18) link_BETA1-6 : bond 0.00482 ( 1) link_BETA1-6 : angle 1.45921 ( 3) link_NAG-ASN : bond 0.00258 ( 10) link_NAG-ASN : angle 1.42384 ( 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 51 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8139 (tp30) REVERT: A 317 ARG cc_start: 0.8297 (mtp-110) cc_final: 0.7934 (mtm110) REVERT: B 129 MET cc_start: 0.8564 (ttm) cc_final: 0.8331 (ttt) REVERT: B 383 ASN cc_start: 0.8737 (m110) cc_final: 0.8459 (m110) outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 1.2660 time to fit residues: 65.4644 Evaluate side-chains 43 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.099507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.079055 restraints weight = 37095.932| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.95 r_work: 0.3021 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7072 Z= 0.145 Angle : 0.538 7.163 9652 Z= 0.266 Chirality : 0.044 0.158 1118 Planarity : 0.004 0.093 1233 Dihedral : 9.037 83.955 1325 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.55 % Allowed : 6.77 % Favored : 91.68 % 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 aren not related in a simple way. whole: -0.43 (0.28), residues: 877 helix: 0.94 (0.47), residues: 125 sheet: 0.09 (0.33), residues: 259 loop : -0.80 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 220 TYR 0.013 0.001 TYR A 261 PHE 0.010 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 covalent geometry : bond 0.00341 ( 7049) covalent geometry : angle 0.52283 ( 9588) SS BOND : bond 0.00196 ( 5) SS BOND : angle 0.58862 ( 10) hydrogen bonds : bond 0.03856 ( 219) hydrogen bonds : angle 5.91881 ( 576) link_ALPHA1-3 : bond 0.01147 ( 1) link_ALPHA1-3 : angle 1.38863 ( 3) link_BETA1-4 : bond 0.00624 ( 6) link_BETA1-4 : angle 2.29020 ( 18) link_BETA1-6 : bond 0.00543 ( 1) link_BETA1-6 : angle 1.33168 ( 3) link_NAG-ASN : bond 0.00339 ( 10) link_NAG-ASN : angle 1.51002 ( 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: 9 poor density : 41 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8349 (tp30) REVERT: A 220 ARG cc_start: 0.8824 (mtm-85) cc_final: 0.8618 (mtp85) outliers start: 9 outliers final: 7 residues processed: 45 average time/residue: 1.1940 time to fit residues: 56.9212 Evaluate side-chains 47 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 224 ASN 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: 0.9980 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3447 r_free = 0.3447 target = 0.098603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078182 restraints weight = 36276.727| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.92 r_work: 0.3011 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- 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 = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1175 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= 0.162 Angle : 0.548 7.286 9652 Z= 0.269 Chirality : 0.044 0.158 1118 Planarity : 0.004 0.063 1233 Dihedral : 8.487 79.197 1325 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % 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 aren not related in a simple way. whole: -0.51 (0.28), residues: 877 helix: 0.94 (0.48), residues: 125 sheet: -0.03 (0.33), residues: 259 loop : -0.83 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 220 TYR 0.012 0.001 TYR A 208 PHE 0.012 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 covalent geometry : bond 0.00388 ( 7049) covalent geometry : angle 0.53120 ( 9588) SS BOND : bond 0.00217 ( 5) SS BOND : angle 0.62210 ( 10) hydrogen bonds : bond 0.03394 ( 219) hydrogen bonds : angle 5.61192 ( 576) link_ALPHA1-3 : bond 0.01241 ( 1) link_ALPHA1-3 : angle 1.48864 ( 3) link_BETA1-4 : bond 0.00598 ( 6) link_BETA1-4 : angle 2.33368 ( 18) link_BETA1-6 : bond 0.00380 ( 1) link_BETA1-6 : angle 1.43674 ( 3) link_NAG-ASN : bond 0.00354 ( 10) link_NAG-ASN : angle 1.56923 ( 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 50 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8345 (tp30) REVERT: A 220 ARG cc_start: 0.8839 (mtm-85) cc_final: 0.8630 (mtp85) outliers start: 9 outliers final: 6 residues processed: 46 average time/residue: 1.2543 time to fit residues: 61.0190 Evaluate side-chains 46 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 224 ASN 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: 0.9980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.098901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.078423 restraints weight = 39911.575| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.02 r_work: 0.3011 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7072 Z= 0.133 Angle : 0.530 7.149 9652 Z= 0.260 Chirality : 0.044 0.150 1118 Planarity : 0.004 0.053 1233 Dihedral : 8.174 75.372 1325 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.55 % Allowed : 7.90 % Favored : 90.55 % 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 aren not related in a simple way. whole: -0.52 (0.28), residues: 877 helix: 0.99 (0.48), residues: 125 sheet: -0.04 (0.33), residues: 259 loop : -0.85 (0.28), 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 0.009 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 covalent geometry : bond 0.00317 ( 7049) covalent geometry : angle 0.51417 ( 9588) SS BOND : bond 0.00191 ( 5) SS BOND : angle 0.53594 ( 10) hydrogen bonds : bond 0.03244 ( 219) hydrogen bonds : angle 5.48029 ( 576) link_ALPHA1-3 : bond 0.01225 ( 1) link_ALPHA1-3 : angle 1.51055 ( 3) link_BETA1-4 : bond 0.00613 ( 6) link_BETA1-4 : angle 2.29764 ( 18) link_BETA1-6 : bond 0.00438 ( 1) link_BETA1-6 : angle 1.32191 ( 3) link_NAG-ASN : bond 0.00286 ( 10) link_NAG-ASN : angle 1.48663 ( 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 48 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8356 (tp30) REVERT: A 317 ARG cc_start: 0.8236 (mtp-110) cc_final: 0.7903 (mtm110) outliers start: 9 outliers final: 6 residues processed: 44 average time/residue: 1.1403 time to fit residues: 53.0778 Evaluate side-chains 45 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 224 ASN 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: 1.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 3 optimal weight: 0.0870 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3459 r_free = 0.3459 target = 0.099663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.077642 restraints weight = 43878.244| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.29 r_work: 0.2997 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- 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 = 0.38 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 = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7072 Z= 0.133 Angle : 0.529 6.901 9652 Z= 0.258 Chirality : 0.044 0.148 1118 Planarity : 0.005 0.103 1233 Dihedral : 7.805 69.817 1325 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.55 % Allowed : 8.32 % Favored : 90.13 % 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 aren not related in a simple way. whole: -0.52 (0.28), residues: 877 helix: 1.04 (0.48), residues: 125 sheet: -0.08 (0.32), residues: 259 loop : -0.83 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 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 covalent geometry : bond 0.00318 ( 7049) covalent geometry : angle 0.51262 ( 9588) SS BOND : bond 0.00186 ( 5) SS BOND : angle 0.54874 ( 10) hydrogen bonds : bond 0.03084 ( 219) hydrogen bonds : angle 5.28569 ( 576) link_ALPHA1-3 : bond 0.01267 ( 1) link_ALPHA1-3 : angle 1.53584 ( 3) link_BETA1-4 : bond 0.00589 ( 6) link_BETA1-4 : angle 2.31875 ( 18) link_BETA1-6 : bond 0.00449 ( 1) link_BETA1-6 : angle 1.38006 ( 3) link_NAG-ASN : bond 0.00276 ( 10) link_NAG-ASN : angle 1.48536 ( 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 50 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8202 (tp30) REVERT: A 220 ARG cc_start: 0.8693 (mtm-85) cc_final: 0.8463 (mtp85) REVERT: A 317 ARG cc_start: 0.8139 (mtp-110) cc_final: 0.7837 (mtm110) outliers start: 9 outliers final: 5 residues processed: 45 average time/residue: 1.3339 time to fit residues: 63.1327 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 : 0.380 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.098923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.078497 restraints weight = 38331.662| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.98 r_work: 0.3013 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- 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 = 0.40 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7072 Z= 0.138 Angle : 0.531 6.879 9652 Z= 0.259 Chirality : 0.044 0.147 1118 Planarity : 0.004 0.078 1233 Dihedral : 7.499 63.763 1325 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % 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 aren not related in a simple way. whole: -0.53 (0.28), residues: 877 helix: 1.11 (0.48), residues: 124 sheet: -0.09 (0.32), residues: 259 loop : -0.86 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 220 TYR 0.012 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 covalent geometry : bond 0.00329 ( 7049) covalent geometry : angle 0.51432 ( 9588) SS BOND : bond 0.00189 ( 5) SS BOND : angle 0.55774 ( 10) hydrogen bonds : bond 0.03068 ( 219) hydrogen bonds : angle 5.20531 ( 576) link_ALPHA1-3 : bond 0.01175 ( 1) link_ALPHA1-3 : angle 1.41413 ( 3) link_BETA1-4 : bond 0.00604 ( 6) link_BETA1-4 : angle 2.33804 ( 18) link_BETA1-6 : bond 0.00417 ( 1) link_BETA1-6 : angle 1.35947 ( 3) link_NAG-ASN : bond 0.00297 ( 10) link_NAG-ASN : angle 1.51171 ( 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: 8 poor density : 41 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8340 (tp30) REVERT: A 220 ARG cc_start: 0.8853 (mtm-85) cc_final: 0.8598 (mtp85) REVERT: A 312 ARG cc_start: 0.8565 (ptp-110) cc_final: 0.8012 (ttm110) outliers start: 8 outliers final: 5 residues processed: 45 average time/residue: 1.2962 time to fit residues: 61.5401 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 : 0.346 ------------------------------------------------------------------------------- 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: 0.8980 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.099004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.077787 restraints weight = 36087.721| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.00 r_work: 0.3003 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7072 Z= 0.161 Angle : 0.545 6.924 9652 Z= 0.266 Chirality : 0.044 0.164 1118 Planarity : 0.004 0.078 1233 Dihedral : 7.269 57.439 1325 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.13 % Allowed : 9.03 % 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 aren not related in a simple way. whole: -0.57 (0.28), residues: 877 helix: 1.07 (0.48), residues: 124 sheet: -0.12 (0.32), residues: 259 loop : -0.88 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 220 TYR 0.014 0.001 TYR A 205 PHE 0.011 0.001 PHE A 172 TRP 0.006 0.001 TRP C 60 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 7049) covalent geometry : angle 0.52762 ( 9588) SS BOND : bond 0.00214 ( 5) SS BOND : angle 0.58626 ( 10) hydrogen bonds : bond 0.03134 ( 219) hydrogen bonds : angle 5.20213 ( 576) link_ALPHA1-3 : bond 0.01184 ( 1) link_ALPHA1-3 : angle 1.29789 ( 3) link_BETA1-4 : bond 0.00617 ( 6) link_BETA1-4 : angle 2.39350 ( 18) link_BETA1-6 : bond 0.00394 ( 1) link_BETA1-6 : angle 1.41655 ( 3) link_NAG-ASN : bond 0.00343 ( 10) link_NAG-ASN : angle 1.59062 ( 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 48 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8326 (tp30) REVERT: A 312 ARG cc_start: 0.8557 (ptp-110) cc_final: 0.8028 (ttm110) REVERT: A 317 ARG cc_start: 0.8142 (mtp-110) cc_final: 0.7827 (mtm110) outliers start: 6 outliers final: 4 residues processed: 45 average time/residue: 1.3141 time to fit residues: 62.2677 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 : 0.336 ------------------------------------------------------------------------------- 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: 0.6980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.099210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.077442 restraints weight = 42155.253| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.23 r_work: 0.2990 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7072 Z= 0.146 Angle : 0.535 6.915 9652 Z= 0.262 Chirality : 0.044 0.176 1118 Planarity : 0.004 0.073 1233 Dihedral : 6.926 55.996 1323 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.13 % Allowed : 9.03 % 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 aren not related in a simple way. whole: -0.56 (0.29), residues: 877 helix: 1.10 (0.48), residues: 124 sheet: -0.11 (0.32), residues: 259 loop : -0.88 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 220 TYR 0.008 0.001 TYR B 325 PHE 0.009 0.001 PHE A 172 TRP 0.006 0.001 TRP C 60 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7049) covalent geometry : angle 0.51873 ( 9588) SS BOND : bond 0.00195 ( 5) SS BOND : angle 0.57487 ( 10) hydrogen bonds : bond 0.03054 ( 219) hydrogen bonds : angle 5.15944 ( 576) link_ALPHA1-3 : bond 0.01118 ( 1) link_ALPHA1-3 : angle 1.37997 ( 3) link_BETA1-4 : bond 0.00625 ( 6) link_BETA1-4 : angle 2.38363 ( 18) link_BETA1-6 : bond 0.00415 ( 1) link_BETA1-6 : angle 1.35756 ( 3) link_NAG-ASN : bond 0.00302 ( 10) link_NAG-ASN : angle 1.53686 ( 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 49 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8175 (tp30) REVERT: A 312 ARG cc_start: 0.8503 (ptp-110) cc_final: 0.8008 (ttm110) outliers start: 6 outliers final: 5 residues processed: 46 average time/residue: 1.3817 time to fit residues: 66.9092 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 : 0.368 ------------------------------------------------------------------------------- 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: 2.9990 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.099198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.077655 restraints weight = 39660.789| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.14 r_work: 0.2997 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 7072 Z= 0.193 Angle : 0.923 59.130 9652 Z= 0.547 Chirality : 0.046 0.452 1118 Planarity : 0.004 0.077 1233 Dihedral : 6.928 55.982 1323 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.99 % Allowed : 9.45 % Favored : 89.56 % Cbeta Deviations : 0.13 % 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 aren not related in a simple way. whole: -0.56 (0.29), residues: 877 helix: 1.10 (0.48), residues: 124 sheet: -0.11 (0.32), residues: 259 loop : -0.88 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 220 TYR 0.008 0.001 TYR B 325 PHE 0.009 0.001 PHE A 172 TRP 0.006 0.001 TRP C 60 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 7049) covalent geometry : angle 0.91557 ( 9588) SS BOND : bond 0.00190 ( 5) SS BOND : angle 0.56376 ( 10) hydrogen bonds : bond 0.03044 ( 219) hydrogen bonds : angle 5.15951 ( 576) link_ALPHA1-3 : bond 0.01126 ( 1) link_ALPHA1-3 : angle 1.37732 ( 3) link_BETA1-4 : bond 0.00622 ( 6) link_BETA1-4 : angle 2.38595 ( 18) link_BETA1-6 : bond 0.00424 ( 1) link_BETA1-6 : angle 1.36701 ( 3) link_NAG-ASN : bond 0.00297 ( 10) link_NAG-ASN : angle 1.53855 ( 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 : 0.354 Fit side-chains revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8160 (tp30) REVERT: A 312 ARG cc_start: 0.8501 (ptp-110) cc_final: 0.8007 (ttm110) outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 1.2720 time to fit residues: 56.5903 Evaluate side-chains 44 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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: 0.8980 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.099198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.077334 restraints weight = 43658.965| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.28 r_work: 0.2988 rms_B_bonded: 3.19 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 = 0.42 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 7072 Z= 0.192 Angle : 0.923 59.200 9652 Z= 0.547 Chirality : 0.046 0.443 1118 Planarity : 0.004 0.077 1233 Dihedral : 6.928 55.982 1323 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.99 % Allowed : 9.45 % Favored : 89.56 % Cbeta Deviations : 0.13 % 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 aren not related in a simple way. whole: -0.56 (0.29), residues: 877 helix: 1.10 (0.48), residues: 124 sheet: -0.11 (0.32), residues: 259 loop : -0.88 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 220 TYR 0.008 0.001 TYR B 325 PHE 0.009 0.001 PHE A 172 TRP 0.006 0.001 TRP C 60 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 7049) covalent geometry : angle 0.91561 ( 9588) SS BOND : bond 0.00191 ( 5) SS BOND : angle 0.56366 ( 10) hydrogen bonds : bond 0.03044 ( 219) hydrogen bonds : angle 5.15953 ( 576) link_ALPHA1-3 : bond 0.01127 ( 1) link_ALPHA1-3 : angle 1.37780 ( 3) link_BETA1-4 : bond 0.00621 ( 6) link_BETA1-4 : angle 2.38564 ( 18) link_BETA1-6 : bond 0.00423 ( 1) link_BETA1-6 : angle 1.36636 ( 3) link_NAG-ASN : bond 0.00297 ( 10) link_NAG-ASN : angle 1.53852 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3958.18 seconds wall clock time: 67 minutes 50.99 seconds (4070.99 seconds total)