Starting phenix.real_space_refine on Tue Mar 3 19:50:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7la4_23245/03_2026/7la4_23245.cif Found real_map, /net/cci-nas-00/data/ceres_data/7la4_23245/03_2026/7la4_23245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7la4_23245/03_2026/7la4_23245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7la4_23245/03_2026/7la4_23245.map" model { file = "/net/cci-nas-00/data/ceres_data/7la4_23245/03_2026/7la4_23245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7la4_23245/03_2026/7la4_23245.cif" } resolution = 3.3 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= 0.003 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 Mg 1 5.21 5 S 33 5.16 5 C 5213 2.51 5 N 1386 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8281 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "A" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3467 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 27, 'TRANS': 424} Chain: "B" Number of atoms: 2940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2940 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 357} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" 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: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 1.70, per 1000 atoms: 0.21 Number of scatterers: 8281 At special positions: 0 Unit cell: (102, 110, 100, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 33 16.00 Mg 1 11.99 O 1642 8.00 N 1386 7.00 C 5213 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.02 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " 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 " MAN D 3 " - " MAN D 4 " ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG E 2 " - " MAN E 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1105 " - " ASN A 15 " " NAG C 1 " - " ASN B 99 " " NAG D 1 " - " ASN B 320 " " NAG E 1 " - " ASN B 371 " Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 269.7 milliseconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1912 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 19 sheets defined 11.6% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.940A pdb=" N SER H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.955A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.605A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.575A pdb=" N TYR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.058A pdb=" N GLU B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.760A pdb=" N ARG B 202 " --> pdb=" O GLN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 232 removed outlier: 3.889A pdb=" N ALA B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.794A pdb=" N LEU B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 302 removed outlier: 3.865A pdb=" N LYS B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 removed outlier: 3.775A pdb=" N ASN B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.916A pdb=" N VAL B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'H' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 14 removed outlier: 3.733A pdb=" N GLN L 89 " --> pdb=" O ASN L 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.551A pdb=" N THR A 9 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 23 through 27 Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 77 removed outlier: 3.502A pdb=" N PHE A 87 " --> pdb=" O HIS A 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA9, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.738A pdb=" N GLU A 120 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AB2, first strand: chain 'A' and resid 241 through 242 removed outlier: 3.569A pdb=" N GLU A 252 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 256 through 257 removed outlier: 6.323A pdb=" N VAL A 267 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG A 279 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE A 269 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 293 through 295 removed outlier: 3.535A pdb=" N VAL A 308 " --> pdb=" O TYR A 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AB6, first strand: chain 'A' and resid 360 through 362 removed outlier: 3.691A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB8, first strand: chain 'B' and resid 97 through 102 removed outlier: 3.784A pdb=" N LYS B 98 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 401 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 97 through 102 removed outlier: 3.784A pdb=" N LYS B 98 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 401 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 194 through 197 removed outlier: 4.655A pdb=" N LEU B 196 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE B 151 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL B 112 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLY B 152 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 114 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLY B 154 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR B 116 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE B 156 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET B 118 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 247 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 250 " --> pdb=" O ALA B 309 " (cutoff:3.500A) 182 hydrogen bonds defined for protein. 432 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2701 1.34 - 1.46: 1858 1.46 - 1.58: 3847 1.58 - 1.70: 0 1.70 - 1.82: 49 Bond restraints: 8455 Sorted by residual: bond pdb=" N ILE H 72 " pdb=" CA ILE H 72 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.07e-02 8.73e+03 1.03e+01 bond pdb=" N TYR H 100 " pdb=" CA TYR H 100 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.59e+00 bond pdb=" N ILE L 106 " pdb=" CA ILE L 106 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.23e+00 bond pdb=" N ARG L 24 " pdb=" CA ARG L 24 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.23e-02 6.61e+03 7.35e+00 bond pdb=" N ILE L 29 " pdb=" CA ILE L 29 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.08e+00 ... (remaining 8450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 10666 1.49 - 2.98: 677 2.98 - 4.46: 108 4.46 - 5.95: 23 5.95 - 7.44: 12 Bond angle restraints: 11486 Sorted by residual: angle pdb=" N PHE H 104 " pdb=" CA PHE H 104 " pdb=" C PHE H 104 " ideal model delta sigma weight residual 111.71 105.39 6.32 1.34e+00 5.57e-01 2.23e+01 angle pdb=" N ASN L 31 " pdb=" CA ASN L 31 " pdb=" C ASN L 31 " ideal model delta sigma weight residual 112.30 106.45 5.85 1.36e+00 5.41e-01 1.85e+01 angle pdb=" N VAL B 314 " pdb=" CA VAL B 314 " pdb=" C VAL B 314 " ideal model delta sigma weight residual 113.20 109.15 4.05 9.60e-01 1.09e+00 1.78e+01 angle pdb=" N MET H 81 " pdb=" CA MET H 81 " pdb=" C MET H 81 " ideal model delta sigma weight residual 114.64 108.32 6.32 1.52e+00 4.33e-01 1.73e+01 angle pdb=" CA ARG H 84 " pdb=" C ARG H 84 " pdb=" O ARG H 84 " ideal model delta sigma weight residual 121.60 116.89 4.71 1.21e+00 6.83e-01 1.52e+01 ... (remaining 11481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.14: 4827 24.14 - 48.28: 262 48.28 - 72.41: 47 72.41 - 96.55: 20 96.55 - 120.69: 4 Dihedral angle restraints: 5160 sinusoidal: 2151 harmonic: 3009 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 45.51 47.49 1 1.00e+01 1.00e-02 3.11e+01 dihedral pdb=" CA ASN B 377 " pdb=" C ASN B 377 " pdb=" N GLU B 378 " pdb=" CA GLU B 378 " ideal model delta harmonic sigma weight residual -180.00 -152.33 -27.67 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA THR H 28 " pdb=" C THR H 28 " pdb=" N PHE H 29 " pdb=" CA PHE H 29 " ideal model delta harmonic sigma weight residual -180.00 -155.47 -24.53 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 5157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1242 0.113 - 0.225: 44 0.225 - 0.338: 5 0.338 - 0.450: 0 0.450 - 0.563: 1 Chirality restraints: 1292 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN B 99 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.93e+00 chirality pdb=" CA TYR H 106 " pdb=" N TYR H 106 " pdb=" C TYR H 106 " pdb=" CB TYR H 106 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA LEU A 84 " pdb=" N LEU A 84 " pdb=" C LEU A 84 " pdb=" CB LEU A 84 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 1289 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 288 " -0.026 2.00e-02 2.50e+03 1.85e-02 6.81e+00 pdb=" CG TYR A 288 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 288 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 288 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 288 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 288 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 288 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 288 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 99 " -0.024 2.00e-02 2.50e+03 2.24e-02 6.25e+00 pdb=" CG ASN B 99 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 99 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 99 " 0.024 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.013 2.00e-02 2.50e+03 1.44e-02 5.16e+00 pdb=" CG TRP H 47 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " -0.001 2.00e-02 2.50e+03 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 244 2.66 - 3.22: 8204 3.22 - 3.78: 13004 3.78 - 4.34: 18660 4.34 - 4.90: 30829 Nonbonded interactions: 70941 Sorted by model distance: nonbonded pdb=" OE2 GLU B 220 " pdb="MG MG B2001 " model vdw 2.100 2.170 nonbonded pdb=" OD1 ASN A 430 " pdb=" O HOH A1201 " model vdw 2.127 3.040 nonbonded pdb=" OH TYR A 353 " pdb=" OE1 GLU B 297 " model vdw 2.138 3.040 nonbonded pdb=" OG SER A 22 " pdb=" O GLY A 94 " model vdw 2.156 3.040 nonbonded pdb=" OE1 GLN A 197 " pdb=" OG SER A 220 " model vdw 2.159 3.040 ... (remaining 70936 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.390 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 : 0.006 0.046 8473 Z= 0.320 Angle : 0.853 7.438 11532 Z= 0.493 Chirality : 0.056 0.563 1292 Planarity : 0.004 0.043 1485 Dihedral : 16.129 120.689 3224 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.58 % Favored : 89.94 % Rotamer: Outliers : 1.91 % Allowed : 2.70 % Favored : 95.39 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 7.55 % 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: -4.02 (0.24), residues: 1044 helix: -3.78 (0.40), residues: 95 sheet: -2.97 (0.25), residues: 351 loop : -2.26 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 41 TYR 0.044 0.002 TYR A 288 PHE 0.017 0.002 PHE B 370 TRP 0.037 0.003 TRP H 47 HIS 0.010 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00597 ( 8455) covalent geometry : angle 0.84387 (11486) SS BOND : bond 0.00457 ( 8) SS BOND : angle 1.23502 ( 16) hydrogen bonds : bond 0.25976 ( 178) hydrogen bonds : angle 11.85270 ( 432) link_ALPHA1-3 : bond 0.01013 ( 1) link_ALPHA1-3 : angle 1.67376 ( 3) link_ALPHA1-4 : bond 0.01025 ( 2) link_ALPHA1-4 : angle 2.77565 ( 6) link_BETA1-4 : bond 0.00639 ( 3) link_BETA1-4 : angle 1.64593 ( 9) link_NAG-ASN : bond 0.00554 ( 4) link_NAG-ASN : angle 2.90592 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 26 SER cc_start: 0.7798 (p) cc_final: 0.7472 (t) REVERT: A 232 ASP cc_start: 0.8234 (m-30) cc_final: 0.7997 (m-30) outliers start: 17 outliers final: 2 residues processed: 158 average time/residue: 0.1009 time to fit residues: 21.6072 Evaluate side-chains 121 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 72 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.136607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.113746 restraints weight = 11550.729| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.78 r_work: 0.3245 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8473 Z= 0.178 Angle : 0.697 7.627 11532 Z= 0.350 Chirality : 0.049 0.403 1292 Planarity : 0.005 0.047 1485 Dihedral : 10.640 106.524 1355 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.77 % Favored : 90.04 % Rotamer: Outliers : 2.25 % Allowed : 10.45 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -3.77 (0.24), residues: 1044 helix: -3.49 (0.37), residues: 98 sheet: -2.88 (0.24), residues: 368 loop : -1.99 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 41 TYR 0.029 0.002 TYR A 288 PHE 0.014 0.002 PHE B 308 TRP 0.015 0.002 TRP A 235 HIS 0.008 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8455) covalent geometry : angle 0.68355 (11486) SS BOND : bond 0.00426 ( 8) SS BOND : angle 1.01743 ( 16) hydrogen bonds : bond 0.04340 ( 178) hydrogen bonds : angle 8.39587 ( 432) link_ALPHA1-3 : bond 0.02666 ( 1) link_ALPHA1-3 : angle 3.36274 ( 3) link_ALPHA1-4 : bond 0.02110 ( 2) link_ALPHA1-4 : angle 3.73849 ( 6) link_BETA1-4 : bond 0.00513 ( 3) link_BETA1-4 : angle 1.37082 ( 9) link_NAG-ASN : bond 0.00329 ( 4) link_NAG-ASN : angle 2.59748 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8063 (pp) REVERT: A 285 MET cc_start: 0.8955 (mtp) cc_final: 0.8661 (mtm) REVERT: B 400 GLU cc_start: 0.7474 (tt0) cc_final: 0.6887 (tt0) outliers start: 20 outliers final: 8 residues processed: 152 average time/residue: 0.0911 time to fit residues: 19.0890 Evaluate side-chains 130 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 423 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 31 ASN L 38 GLN L 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.132586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105538 restraints weight = 11427.643| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.23 r_work: 0.3158 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8473 Z= 0.258 Angle : 0.726 12.615 11532 Z= 0.359 Chirality : 0.048 0.176 1292 Planarity : 0.004 0.047 1485 Dihedral : 10.219 106.739 1353 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.96 % Favored : 89.85 % Rotamer: Outliers : 2.70 % Allowed : 13.71 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -3.73 (0.24), residues: 1044 helix: -3.38 (0.37), residues: 98 sheet: -2.90 (0.24), residues: 369 loop : -1.94 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 41 TYR 0.035 0.002 TYR A 288 PHE 0.017 0.002 PHE B 308 TRP 0.013 0.002 TRP H 47 HIS 0.009 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00601 ( 8455) covalent geometry : angle 0.70106 (11486) SS BOND : bond 0.00490 ( 8) SS BOND : angle 1.15292 ( 16) hydrogen bonds : bond 0.03919 ( 178) hydrogen bonds : angle 7.91073 ( 432) link_ALPHA1-3 : bond 0.01953 ( 1) link_ALPHA1-3 : angle 2.95087 ( 3) link_ALPHA1-4 : bond 0.02124 ( 2) link_ALPHA1-4 : angle 3.77332 ( 6) link_BETA1-4 : bond 0.00674 ( 3) link_BETA1-4 : angle 1.15294 ( 9) link_NAG-ASN : bond 0.00536 ( 4) link_NAG-ASN : angle 4.96200 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8577 (tm-30) REVERT: H 10 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8095 (mm-30) REVERT: H 23 LYS cc_start: 0.8483 (tppt) cc_final: 0.7910 (tptp) REVERT: A 208 ARG cc_start: 0.8365 (mmt-90) cc_final: 0.8040 (mmt-90) REVERT: A 270 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8087 (pp) REVERT: A 285 MET cc_start: 0.8952 (mtp) cc_final: 0.8692 (mtm) REVERT: B 124 MET cc_start: 0.8494 (tpt) cc_final: 0.7960 (mmt) REVERT: B 390 LYS cc_start: 0.6580 (tmtt) cc_final: 0.6118 (mttm) outliers start: 24 outliers final: 18 residues processed: 142 average time/residue: 0.0919 time to fit residues: 17.9150 Evaluate side-chains 138 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 423 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.134893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107970 restraints weight = 11619.249| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.26 r_work: 0.3175 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8473 Z= 0.206 Angle : 0.719 14.208 11532 Z= 0.350 Chirality : 0.049 0.399 1292 Planarity : 0.004 0.048 1485 Dihedral : 9.962 105.330 1351 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 2.92 % Allowed : 14.94 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -3.61 (0.24), residues: 1044 helix: -3.27 (0.38), residues: 99 sheet: -2.80 (0.25), residues: 365 loop : -1.88 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 41 TYR 0.024 0.002 TYR A 288 PHE 0.014 0.002 PHE B 308 TRP 0.015 0.002 TRP H 107 HIS 0.007 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 8455) covalent geometry : angle 0.68557 (11486) SS BOND : bond 0.00414 ( 8) SS BOND : angle 1.00268 ( 16) hydrogen bonds : bond 0.03479 ( 178) hydrogen bonds : angle 7.68133 ( 432) link_ALPHA1-3 : bond 0.02131 ( 1) link_ALPHA1-3 : angle 3.22827 ( 3) link_ALPHA1-4 : bond 0.02135 ( 2) link_ALPHA1-4 : angle 3.80131 ( 6) link_BETA1-4 : bond 0.00857 ( 3) link_BETA1-4 : angle 1.83960 ( 9) link_NAG-ASN : bond 0.00238 ( 4) link_NAG-ASN : angle 5.70467 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8604 (tm-30) REVERT: H 23 LYS cc_start: 0.8481 (tppt) cc_final: 0.7895 (tptp) REVERT: A 270 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7855 (pp) REVERT: B 390 LYS cc_start: 0.6547 (tmtt) cc_final: 0.6077 (mttm) REVERT: B 400 GLU cc_start: 0.7871 (tt0) cc_final: 0.7531 (mm-30) outliers start: 26 outliers final: 19 residues processed: 140 average time/residue: 0.0982 time to fit residues: 18.5713 Evaluate side-chains 141 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 423 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 0.0770 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.135987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.109063 restraints weight = 11348.865| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.20 r_work: 0.3211 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8473 Z= 0.159 Angle : 0.652 7.976 11532 Z= 0.322 Chirality : 0.045 0.185 1292 Planarity : 0.004 0.047 1485 Dihedral : 11.241 117.083 1351 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 2.92 % Allowed : 17.53 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.44 (0.25), residues: 1044 helix: -2.93 (0.41), residues: 91 sheet: -2.70 (0.25), residues: 372 loop : -1.80 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 41 TYR 0.018 0.001 TYR A 288 PHE 0.014 0.001 PHE B 100 TRP 0.014 0.001 TRP H 47 HIS 0.006 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8455) covalent geometry : angle 0.63934 (11486) SS BOND : bond 0.00306 ( 8) SS BOND : angle 0.78894 ( 16) hydrogen bonds : bond 0.03197 ( 178) hydrogen bonds : angle 7.33355 ( 432) link_ALPHA1-3 : bond 0.02244 ( 1) link_ALPHA1-3 : angle 3.41422 ( 3) link_ALPHA1-4 : bond 0.02102 ( 2) link_ALPHA1-4 : angle 3.78763 ( 6) link_BETA1-4 : bond 0.00657 ( 3) link_BETA1-4 : angle 1.84525 ( 9) link_NAG-ASN : bond 0.00534 ( 4) link_NAG-ASN : angle 1.92115 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8601 (tt0) REVERT: A 208 ARG cc_start: 0.8327 (mmt-90) cc_final: 0.8029 (mmt-90) REVERT: A 270 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7772 (pp) REVERT: B 124 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8046 (mmt) REVERT: B 387 MET cc_start: 0.7249 (ttt) cc_final: 0.6407 (mtm) REVERT: B 390 LYS cc_start: 0.6594 (tmtt) cc_final: 0.6101 (mttm) REVERT: B 400 GLU cc_start: 0.7846 (tt0) cc_final: 0.7478 (mm-30) outliers start: 26 outliers final: 19 residues processed: 148 average time/residue: 0.0844 time to fit residues: 17.1132 Evaluate side-chains 143 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 227 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 81 optimal weight: 0.2980 chunk 92 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 0.0470 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.138146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110832 restraints weight = 11347.557| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.26 r_work: 0.3224 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8473 Z= 0.143 Angle : 0.650 10.062 11532 Z= 0.317 Chirality : 0.046 0.236 1292 Planarity : 0.004 0.049 1485 Dihedral : 10.350 102.934 1351 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 2.81 % Allowed : 17.87 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -3.28 (0.25), residues: 1044 helix: -2.78 (0.42), residues: 91 sheet: -2.56 (0.25), residues: 369 loop : -1.74 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 84 TYR 0.016 0.001 TYR A 288 PHE 0.014 0.001 PHE B 100 TRP 0.013 0.001 TRP H 47 HIS 0.006 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8455) covalent geometry : angle 0.63006 (11486) SS BOND : bond 0.00274 ( 8) SS BOND : angle 0.70185 ( 16) hydrogen bonds : bond 0.03074 ( 178) hydrogen bonds : angle 7.07705 ( 432) link_ALPHA1-3 : bond 0.02381 ( 1) link_ALPHA1-3 : angle 3.62546 ( 3) link_ALPHA1-4 : bond 0.02179 ( 2) link_ALPHA1-4 : angle 3.90250 ( 6) link_BETA1-4 : bond 0.00683 ( 3) link_BETA1-4 : angle 1.47964 ( 9) link_NAG-ASN : bond 0.00299 ( 4) link_NAG-ASN : angle 3.56159 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8574 (tt0) REVERT: H 47 TRP cc_start: 0.8013 (OUTLIER) cc_final: 0.7577 (t60) REVERT: A 208 ARG cc_start: 0.8335 (mmt-90) cc_final: 0.8025 (mmt-90) REVERT: A 259 THR cc_start: 0.9117 (m) cc_final: 0.8613 (p) REVERT: B 124 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8014 (mmt) REVERT: B 390 LYS cc_start: 0.6582 (tmtt) cc_final: 0.6087 (mttm) outliers start: 25 outliers final: 19 residues processed: 151 average time/residue: 0.0873 time to fit residues: 18.4053 Evaluate side-chains 146 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 311 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 74 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.137110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109515 restraints weight = 11466.959| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.27 r_work: 0.3206 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8473 Z= 0.181 Angle : 0.665 8.296 11532 Z= 0.326 Chirality : 0.046 0.226 1292 Planarity : 0.004 0.047 1485 Dihedral : 10.848 116.476 1351 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 3.48 % Allowed : 18.88 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.24 (0.25), residues: 1044 helix: -2.71 (0.42), residues: 91 sheet: -2.55 (0.25), residues: 372 loop : -1.70 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 41 TYR 0.020 0.001 TYR A 288 PHE 0.017 0.002 PHE B 100 TRP 0.015 0.001 TRP H 47 HIS 0.007 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8455) covalent geometry : angle 0.65003 (11486) SS BOND : bond 0.00334 ( 8) SS BOND : angle 0.76659 ( 16) hydrogen bonds : bond 0.03110 ( 178) hydrogen bonds : angle 7.10367 ( 432) link_ALPHA1-3 : bond 0.02305 ( 1) link_ALPHA1-3 : angle 3.56183 ( 3) link_ALPHA1-4 : bond 0.02308 ( 2) link_ALPHA1-4 : angle 4.05523 ( 6) link_BETA1-4 : bond 0.00428 ( 3) link_BETA1-4 : angle 1.37267 ( 9) link_NAG-ASN : bond 0.00684 ( 4) link_NAG-ASN : angle 2.54106 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8548 (tt0) REVERT: H 34 MET cc_start: 0.8591 (tpp) cc_final: 0.8316 (mmm) REVERT: H 47 TRP cc_start: 0.8040 (OUTLIER) cc_final: 0.7586 (t60) REVERT: A 208 ARG cc_start: 0.8358 (mmt-90) cc_final: 0.8040 (mmt-90) REVERT: A 270 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7818 (pp) REVERT: B 124 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8043 (mmt) REVERT: B 149 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8266 (pt) REVERT: B 390 LYS cc_start: 0.6566 (tmtt) cc_final: 0.6075 (mttm) REVERT: B 400 GLU cc_start: 0.7899 (tt0) cc_final: 0.7435 (mm-30) outliers start: 31 outliers final: 20 residues processed: 142 average time/residue: 0.0890 time to fit residues: 17.6963 Evaluate side-chains 146 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 311 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 36 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.137293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.110536 restraints weight = 11423.625| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.15 r_work: 0.3240 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8473 Z= 0.155 Angle : 0.667 14.220 11532 Z= 0.321 Chirality : 0.046 0.375 1292 Planarity : 0.004 0.045 1485 Dihedral : 9.061 100.902 1351 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 3.26 % Allowed : 19.44 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -3.11 (0.25), residues: 1044 helix: -2.60 (0.42), residues: 91 sheet: -2.41 (0.25), residues: 369 loop : -1.65 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 41 TYR 0.017 0.001 TYR A 288 PHE 0.011 0.001 PHE B 308 TRP 0.014 0.001 TRP H 47 HIS 0.006 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8455) covalent geometry : angle 0.63575 (11486) SS BOND : bond 0.00302 ( 8) SS BOND : angle 0.78503 ( 16) hydrogen bonds : bond 0.03015 ( 178) hydrogen bonds : angle 6.95901 ( 432) link_ALPHA1-3 : bond 0.02251 ( 1) link_ALPHA1-3 : angle 3.64210 ( 3) link_ALPHA1-4 : bond 0.02346 ( 2) link_ALPHA1-4 : angle 4.04129 ( 6) link_BETA1-4 : bond 0.01383 ( 3) link_BETA1-4 : angle 1.50562 ( 9) link_NAG-ASN : bond 0.00490 ( 4) link_NAG-ASN : angle 5.21259 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.8529 (tpp) cc_final: 0.8235 (mmm) REVERT: H 47 TRP cc_start: 0.7997 (OUTLIER) cc_final: 0.7599 (t60) REVERT: A 259 THR cc_start: 0.9042 (m) cc_final: 0.8593 (p) REVERT: A 270 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7819 (pp) REVERT: B 124 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8029 (mmt) REVERT: B 149 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8235 (pt) REVERT: B 390 LYS cc_start: 0.6643 (tmtt) cc_final: 0.6169 (mttm) outliers start: 29 outliers final: 21 residues processed: 144 average time/residue: 0.0890 time to fit residues: 17.7245 Evaluate side-chains 146 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 311 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.109120 restraints weight = 11465.185| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.12 r_work: 0.3218 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8473 Z= 0.195 Angle : 0.672 8.960 11532 Z= 0.329 Chirality : 0.046 0.230 1292 Planarity : 0.004 0.045 1485 Dihedral : 10.444 118.730 1351 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 3.71 % Allowed : 19.10 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.11 (0.25), residues: 1044 helix: -2.59 (0.42), residues: 91 sheet: -2.41 (0.26), residues: 364 loop : -1.68 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 41 TYR 0.021 0.002 TYR A 288 PHE 0.013 0.002 PHE B 308 TRP 0.015 0.001 TRP H 47 HIS 0.007 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 8455) covalent geometry : angle 0.65632 (11486) SS BOND : bond 0.00355 ( 8) SS BOND : angle 0.80789 ( 16) hydrogen bonds : bond 0.03073 ( 178) hydrogen bonds : angle 7.02667 ( 432) link_ALPHA1-3 : bond 0.02404 ( 1) link_ALPHA1-3 : angle 3.67879 ( 3) link_ALPHA1-4 : bond 0.02530 ( 2) link_ALPHA1-4 : angle 4.22730 ( 6) link_BETA1-4 : bond 0.00485 ( 3) link_BETA1-4 : angle 1.26778 ( 9) link_NAG-ASN : bond 0.00582 ( 4) link_NAG-ASN : angle 2.72055 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.8551 (tpp) cc_final: 0.8272 (mmm) REVERT: H 47 TRP cc_start: 0.8011 (OUTLIER) cc_final: 0.7609 (t60) REVERT: A 270 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7890 (pp) REVERT: B 124 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8016 (mmt) REVERT: B 149 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8238 (pt) REVERT: B 253 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8450 (mtmm) REVERT: B 390 LYS cc_start: 0.6577 (tmtt) cc_final: 0.6113 (mttm) REVERT: B 400 GLU cc_start: 0.7786 (tt0) cc_final: 0.7436 (mm-30) outliers start: 33 outliers final: 22 residues processed: 143 average time/residue: 0.0852 time to fit residues: 17.3478 Evaluate side-chains 151 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 423 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 94 optimal weight: 0.0170 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 99 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.137135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.109944 restraints weight = 11404.573| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.26 r_work: 0.3218 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8473 Z= 0.168 Angle : 0.678 12.527 11532 Z= 0.328 Chirality : 0.047 0.257 1292 Planarity : 0.004 0.044 1485 Dihedral : 8.460 100.185 1351 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 3.15 % Allowed : 19.78 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % 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: -3.02 (0.25), residues: 1044 helix: -2.49 (0.43), residues: 91 sheet: -2.34 (0.26), residues: 346 loop : -1.68 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 41 TYR 0.019 0.002 TYR A 288 PHE 0.017 0.002 PHE B 100 TRP 0.015 0.001 TRP H 47 HIS 0.006 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8455) covalent geometry : angle 0.64784 (11486) SS BOND : bond 0.00315 ( 8) SS BOND : angle 0.74484 ( 16) hydrogen bonds : bond 0.03008 ( 178) hydrogen bonds : angle 6.93102 ( 432) link_ALPHA1-3 : bond 0.02577 ( 1) link_ALPHA1-3 : angle 3.86719 ( 3) link_ALPHA1-4 : bond 0.02734 ( 2) link_ALPHA1-4 : angle 4.41741 ( 6) link_BETA1-4 : bond 0.00616 ( 3) link_BETA1-4 : angle 0.66006 ( 9) link_NAG-ASN : bond 0.00574 ( 4) link_NAG-ASN : angle 5.04518 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: H 10 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8034 (mm-30) REVERT: H 34 MET cc_start: 0.8573 (tpp) cc_final: 0.8286 (mmm) REVERT: H 47 TRP cc_start: 0.8021 (OUTLIER) cc_final: 0.7601 (t60) REVERT: H 60 TYR cc_start: 0.8146 (m-80) cc_final: 0.7927 (m-80) REVERT: A 270 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7843 (pp) REVERT: B 102 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6571 (pt) REVERT: B 124 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7979 (mmt) REVERT: B 149 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8199 (pt) REVERT: B 390 LYS cc_start: 0.6555 (tmtt) cc_final: 0.6088 (mttm) outliers start: 28 outliers final: 21 residues processed: 147 average time/residue: 0.0910 time to fit residues: 18.5536 Evaluate side-chains 149 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 423 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 4 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 89 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.137071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109972 restraints weight = 11398.087| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.27 r_work: 0.3227 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8473 Z= 0.156 Angle : 0.664 8.382 11532 Z= 0.323 Chirality : 0.046 0.245 1292 Planarity : 0.004 0.047 1485 Dihedral : 9.881 115.608 1351 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 3.26 % Allowed : 19.89 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.00 (0.25), residues: 1044 helix: -2.41 (0.43), residues: 91 sheet: -2.33 (0.26), residues: 346 loop : -1.68 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 41 TYR 0.017 0.001 TYR A 288 PHE 0.011 0.001 PHE A 171 TRP 0.014 0.001 TRP H 47 HIS 0.006 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8455) covalent geometry : angle 0.64660 (11486) SS BOND : bond 0.00289 ( 8) SS BOND : angle 0.77152 ( 16) hydrogen bonds : bond 0.02937 ( 178) hydrogen bonds : angle 6.92565 ( 432) link_ALPHA1-3 : bond 0.02507 ( 1) link_ALPHA1-3 : angle 3.90737 ( 3) link_ALPHA1-4 : bond 0.02729 ( 2) link_ALPHA1-4 : angle 4.50197 ( 6) link_BETA1-4 : bond 0.00628 ( 3) link_BETA1-4 : angle 1.31548 ( 9) link_NAG-ASN : bond 0.00258 ( 4) link_NAG-ASN : angle 2.73919 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2147.70 seconds wall clock time: 37 minutes 29.79 seconds (2249.79 seconds total)